[phenixbb] problem refining Fe-S cluster

Edward A. Berry BerryE at upstate.edu
Fri Jul 5 13:32:06 PDT 2013


Pavel Afonine wrote:
> Hi Ed,
>
> it looks like occupancies and B-factors need to be refined and refined
> until convergence. Also, if you apply any distance restraints for
> clusters (restrain Fe-S distances) make sure these restraints are
> correct. I've seen many cases like this and typically refining
> occupancy/b-factors and making sure restraints are correct solves the
> problem. I've never seen fixing specific parameters help and I can't
> understand logic for doing this.
>

OK. I'm not giving any restraints for the cluster, it must be
in the monomers library. I can get SF4.cif from CCP4
and set the weights for bonds/angles very low to let the density rule.
But now I see the problem wasn't there a few rounds back, and the difference
seems to be that I was using 3 macro_cyles instead of 1.
Now I repeat exactly the same refinement both ways, seems to be it.

So maybe an artifact of not refining to convergence.
Odd though, because it was OK in the starting model, and I'm
not asking for the B's to be reset initially to 20 or something.

Problem seems to be solved by using the default 3 cycles, but
in case anyone is interested,
B-factors for Fe are pretty much unchanged after refining 3 cycles
B-factors for the Fe's but not the S's, decrease by about 5.0
on refining 1 cycle.
Overall and protein B-ave increase on refining 1 cycle
Looking at the step by step changes, the first cycle out of 3
is not like the single cycle.
This is dev-1420 version of phenix.

R-factors
refining 3 cycles
REMARK  R-factors, x-ray target values and norm of gradient of x-ray target
REMARK  stage     r-work r-free  xray_target_w  xray_target_t
REMARK    0    :  0.3205 0.3532   3.857969e+00   3.920754e+00
REMARK    1_bss:  0.2433 0.2823   3.683390e+00   3.779722e+00
REMARK 1_weight:  0.2433 0.2823   3.683390e+00   3.779722e+00
REMARK 1_xyzrec:  0.2457 0.2825   3.689060e+00   3.780966e+00
REMARK    1_adp:  0.2463 0.2823   3.690454e+00   3.780932e+00
REMARK    1_occ:  0.2463 0.2823   3.690455e+00   3.780936e+00
REMARK    2_bss:  0.2463 0.2823   3.690087e+00   3.780536e+00
REMARK 2_weight:  0.2463 0.2823   3.690087e+00   3.780536e+00
REMARK 2_xyzrec:  0.2439 0.2821   3.684528e+00   3.778960e+00
REMARK    2_adp:  0.2434 0.2823   3.683429e+00   3.779315e+00
REMARK    2_occ:  0.2434 0.2823   3.683429e+00   3.779316e+00
REMARK    3_bss:  0.2433 0.2825   3.683615e+00   3.779760e+00
REMARK 3_weight:  0.2433 0.2825   3.683615e+00   3.779760e+00
REMARK 3_xyzrec:  0.2455 0.2825   3.688717e+00   3.780899e+00
REMARK    3_adp:  0.2461 0.2824   3.689934e+00   3.780715e+00
REMARK    3_occ:  0.2461 0.2824   3.689934e+00   3.780714e+00
REMARK      end:  0.2457 0.2825   3.689963e+00   3.781089e+00
refining 1 cycle
REMARK  stage     r-work r-free  xray_target_w  xray_target_t
REMARK    0    :  0.3205 0.3532   3.857969e+00   3.920754e+00
REMARK    1_bss:  0.2222 0.2930   3.668217e+00   3.804573e+00
REMARK 1_weight:  0.2222 0.2930   3.668217e+00   3.804573e+00
REMARK 1_xyzrec:  0.2284 0.2941   3.681902e+00   3.808504e+00
REMARK    1_adp:  0.2594 0.3133   3.748285e+00   3.841014e+00
REMARK    1_occ:  0.2594 0.3133   3.748284e+00   3.841012e+00
REMARK      end:  0.2692 0.2912   3.759155e+00   3.806820e+00
REMARK ------------------------------------------------------------------------
R
B-factors
refining 3 cycles
REMARK            |-----overall-----|---macromolecule----|------solvent-------|
REMARK   stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
REMARK    0    :  90.34  16.23  43.10  90.34  16.23  42.91  80.33  27.29  46.57
REMARK    1_bss:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK 1_weight:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK 1_xyzrec:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK    1_adp:  89.27  16.38  42.96  89.27  16.38  42.79  80.39  26.98  46.24
REMARK    1_occ:  89.27  16.38  42.96  89.27  16.38  42.79  80.39  26.98  46.24
REMARK    2_bss:  89.37  16.47  43.06  89.37  16.47  42.88  80.49  27.08  46.34
REMARK 2_weight:  89.37  16.47  43.06  89.37  16.47  42.88  80.49  27.08  46.34
REMARK 2_xyzrec:  89.37  16.47  43.06  89.37  16.47  42.88  80.49  27.08  46.34
REMARK    2_adp:  89.46  16.19  42.92  89.46  16.19  42.74  80.48  26.86  46.22
REMARK    2_occ:  89.46  16.19  42.92  89.46  16.19  42.74  80.48  26.86  46.22
REMARK    3_bss:  89.63  16.36  43.09  89.63  16.36  42.92  80.66  27.03  46.39
REMARK 3_weight:  89.63  16.36  43.09  89.63  16.36  42.92  80.66  27.03  46.39
REMARK 3_xyzrec:  89.63  16.36  43.09  89.63  16.36  42.92  80.66  27.03  46.39
REMARK    3_adp:  89.22  16.53  42.92  89.22  16.53  42.75  80.45  26.77  46.08
REMARK    3_occ:  89.22  16.53  42.92  89.22  16.53  42.75  80.45  26.77  46.08
REMARK      end:  89.22  16.53  42.92  89.22  16.53  42.75  80.45  26.77  46.08
refining 1 cycle:
REMARK            |-----overall-----|---macromolecule----|------solvent-------|
REMARK   stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
REMARK    0    :  90.34  16.23  43.10  90.34  16.23  42.91  80.33  27.29  46.57
REMARK    1_bss:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK 1_weight:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK 1_xyzrec:  90.40  16.29  43.15  90.40  16.29  42.97  80.39  27.35  46.63
REMARK    1_adp:  85.40  23.38  49.20  85.40  23.38  49.17  81.25  33.88  49.84
REMARK    1_occ:  85.40  23.38  49.20  85.40  23.38  49.17  81.25  33.88  49.84
REMARK      end:  85.40  23.38  49.20  85.40  23.38  49.17  81.25  33.88  49.84
REMARK ------------------------------------------------------------------------
R
starting model
oswego 236% grep SF4 sqr1402e_002.pdb
ATOM   8568 FE4  SF4 B1003      15.699  21.265 101.440  1.00 31.53          Fe
ATOM   8569 FE1  SF4 B1003      15.302  20.444 104.268  1.00 28.32          Fe
ATOM   8570 FE3  SF4 B1003      15.072  18.385 101.975  1.00 30.57          Fe
ATOM   8571 FE2  SF4 B1003      17.702  19.420 102.964  1.00 32.57          Fe
ATOM   8572  S2  SF4 B1003      14.066  20.264 102.463  1.00 39.50           S
ATOM   8573  S3  SF4 B1003      16.963  21.440 103.248  1.00 28.46           S
ATOM   8574  S1  SF4 B1003      16.723  19.393 100.994  1.00 31.08           S
ATOM   8575  S4  SF4 B1003      16.026  18.425 103.963  1.00 29.56           S

refining 3 cycles
oswego 235% grep SF4 sqr1402e_006.pdb
ATOM   8568 FE4  SF4 B1003      15.708  21.268 101.432  1.00 31.37          Fe
ATOM   8569 FE1  SF4 B1003      15.283  20.449 104.291  1.00 28.14          Fe
ATOM   8570 FE3  SF4 B1003      15.062  18.373 101.986  1.00 30.15          Fe
ATOM   8571 FE2  SF4 B1003      17.720  19.419 102.961  1.00 32.34          Fe
ATOM   8572  S2  SF4 B1003      14.080  20.264 102.462  1.00 38.64           S
ATOM   8573  S3  SF4 B1003      16.943  21.422 103.257  1.00 28.96           S
ATOM   8574  S1  SF4 B1003      16.712  19.383 101.004  1.00 31.27           S
ATOM   8575  S4  SF4 B1003      16.036  18.446 103.959  1.00 29.32           S
refining 1 cycle
oswego 234% grep SF4 sqr1402e_005.pdb
ATOM   8568 FE4  SF4 B1003      15.763  21.282 101.383  1.00 26.59          Fe
ATOM   8569 FE1  SF4 B1003      15.274  20.434 104.305  1.00 23.38          Fe
ATOM   8570 FE3  SF4 B1003      15.026  18.351 102.006  1.00 25.63          Fe
ATOM   8571 FE2  SF4 B1003      17.779  19.437 102.902  1.00 27.63          Fe
ATOM   8572  S2  SF4 B1003      14.132  20.305 102.437  1.00 34.56           S
ATOM   8573  S3  SF4 B1003      16.929  21.408 103.255  1.00 28.42           S
ATOM   8574  S1  SF4 B1003      16.681  19.335 101.002  1.00 29.49           S
ATOM   8575  S4  SF4 B1003      16.105  18.462 103.923  1.00 28.25           S



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