Starting phenix.real_space_refine
on Sun Aug  4 05:09:28 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi5_37558/08_2024/8wi5_37558.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    6246      2.51       5
     N    1661      2.21       5
     O    1768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  360": "OE1" <-> "OE2"
    Residue "A GLU  677": "OE1" <-> "OE2"
    Residue "A ARG  697": "NH1" <-> "NH2"
    Residue "A GLU  950": "OE1" <-> "OE2"
    Residue "A GLU  981": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 9735
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1218, 9562
          Classifications: {'peptide': 1218}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 1180}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 173
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
  Time building chain proxies: 5.96, per 1000 atoms: 0.61
  Number of scatterers: 9735
  At special positions: 0
  Unit cell: (70.52, 111.52, 155.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1768      8.00
     N    1661      7.00
     C    6246      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.92
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2338

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 7 sheets defined
      66.9% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 112
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 158
    Processing helix  chain 'A' and resid 166 through 175
      removed outlier: 3.737A  pdb=" N   VAL A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 210
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 216 through 263
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 3.593A  pdb=" N   CYS A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
    Processing helix  chain 'A' and resid 300 through 316
      removed outlier: 3.551A  pdb=" N   ILE A 305 " --> pdb=" O   PRO A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 364
      removed outlier: 4.355A  pdb=" N   SER A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      Proline residue:  A 331  - end of helix
      removed outlier: 3.536A  pdb=" N   LYS A 346 " --> pdb=" O   TYR A 342 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 373 through 400
      removed outlier: 3.765A  pdb=" N   PHE A 377 " --> pdb=" O   TRP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 403
      No H-bonds generated for 'chain 'A' and resid 401 through 403'
    Processing helix  chain 'A' and resid 405 through 424
    Processing helix  chain 'A' and resid 429 through 472
      Proline residue:  A 451  - end of helix
      removed outlier: 3.606A  pdb=" N   LEU A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 610
    Processing helix  chain 'A' and resid 638 through 645
      removed outlier: 3.527A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 663 through 670
    Processing helix  chain 'A' and resid 672 through 676
      removed outlier: 3.605A  pdb=" N   THR A 676 " --> pdb=" O   SER A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 716 through 728
    Processing helix  chain 'A' and resid 743 through 748
      removed outlier: 4.076A  pdb=" N   TYR A 746 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL A 748 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 743 through 748'
    Processing helix  chain 'A' and resid 766 through 774
      removed outlier: 3.597A  pdb=" N   ASN A 774 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 786
      removed outlier: 3.687A  pdb=" N   LEU A 786 " --> pdb=" O   ASN A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 853
      removed outlier: 4.108A  pdb=" N   TYR A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 887
      removed outlier: 3.788A  pdb=" N   PHE A 859 " --> pdb=" O   GLY A 855 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY A 887 " --> pdb=" O   TRP A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 908
    Processing helix  chain 'A' and resid 910 through 958
    Processing helix  chain 'A' and resid 960 through 966
    Processing helix  chain 'A' and resid 967 through 1011
      removed outlier: 3.913A  pdb=" N   ILE A 971 " --> pdb=" O   PRO A 967 " (cutoff:3.500A)
      Proline residue:  A 987  - end of helix
    Processing helix  chain 'A' and resid 1014 through 1046
      Proline residue:  A1020  - end of helix
      removed outlier: 4.037A  pdb=" N   VAL A1034 " --> pdb=" O   ILE A1030 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A1035 " --> pdb=" O   VAL A1031 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG A1037 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG A1041 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A1046 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1060
    Processing helix  chain 'A' and resid 1060 through 1068
    Processing helix  chain 'A' and resid 1071 through 1120
      Proline residue:  A1087  - end of helix
      removed outlier: 3.786A  pdb=" N   MET A1120 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1139
      removed outlier: 3.594A  pdb=" N   ALA A1129 " --> pdb=" O   PRO A1125 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A1139 " --> pdb=" O   TYR A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1168
      removed outlier: 3.875A  pdb=" N   SER A1151 " --> pdb=" O   VAL A1147 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU A1152 " --> pdb=" O   ARG A1148 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A1153 " --> pdb=" O   LEU A1149 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   GLU A1154 " --> pdb=" O   ALA A1150 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A1155 " --> pdb=" O   SER A1151 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG A1156 " --> pdb=" O   GLU A1152 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   SER A1159 " --> pdb=" O   ALA A1155 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   TYR A1166 " --> pdb=" O   ARG A1162 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A1167 " --> pdb=" O   ILE A1163 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A1168 " --> pdb=" O   ASN A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1241
      removed outlier: 4.101A  pdb=" N   MET A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1261
      No H-bonds generated for 'chain 'A' and resid 1259 through 1261'
    Processing helix  chain 'A' and resid 1262 through 1267
    Processing helix  chain 'A' and resid 1295 through 1306
      removed outlier: 3.591A  pdb=" N   THR A1306 " --> pdb=" O   ALA A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1308 through 1314
    Processing helix  chain 'A' and resid 1324 through 1328
      removed outlier: 3.818A  pdb=" N   ASP A1328 " --> pdb=" O   GLU A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1346
      removed outlier: 3.604A  pdb=" N   LEU A1345 " --> pdb=" O   ALA A1341 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ARG A1346 " --> pdb=" O   ARG A1342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1361 through 1376
    Processing helix  chain 'A' and resid 1410 through 1415
    Processing helix  chain 'A' and resid 1420 through 1435
    Processing helix  chain 'B' and resid 48 through 56
      removed outlier: 4.773A  pdb=" N   ALA B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 575 through 586
      removed outlier: 3.519A  pdb=" N   THR A 577 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LEU A 497 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   HIS A 579 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ALA A 495 " --> pdb=" O   HIS A 579 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   ILE A 581 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS A 493 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLU A 491 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   ILE A 585 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER A 618 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ALA A 495 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   GLU A 616 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LEU A 614 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 628
      removed outlier: 5.868A  pdb=" N   ALA A 626 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ASP A 709 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL A 628 " --> pdb=" O   ASP A 709 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL A 740 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LEU A 708 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 590 " --> pdb=" O   GLU A 752 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE A 754 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   GLY A 592 " --> pdb=" O   ILE A 754 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   MET A 756 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   CYS A 594 " --> pdb=" O   MET A 756 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 755 " --> pdb=" O   GLU A 763 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   GLU A 763 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LYS A 757 " --> pdb=" O   ILE A 761 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   ILE A 761 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 894
      removed outlier: 3.608A  pdb=" N   VAL A 893 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1210 through 1213
      removed outlier: 5.835A  pdb=" N   LYS A1211 " --> pdb=" O   MET A1200 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   MET A1200 " --> pdb=" O   LYS A1211 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A1213 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL A1193 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A1217 " --> pdb=" O   VAL A1193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1210 through 1213
      removed outlier: 5.835A  pdb=" N   LYS A1211 " --> pdb=" O   MET A1200 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   MET A1200 " --> pdb=" O   LYS A1211 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A1213 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   ALA A1198 " --> pdb=" O   GLY A1248 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   GLY A1248 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1270 through 1273
      removed outlier: 4.126A  pdb=" N   ASP A1354 " --> pdb=" O   ILE A1273 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU A1351 " --> pdb=" O   LEU A1382 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ILE A1384 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU A1353 " --> pdb=" O   ILE A1384 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE A1223 " --> pdb=" O   THR A1383 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LYS A1222 " --> pdb=" O   ARG A1396 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   MET A1398 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   GLY A1224 " --> pdb=" O   MET A1398 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   LEU A1400 " --> pdb=" O   GLY A1224 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   VAL A1226 " --> pdb=" O   LEU A1400 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A1397 " --> pdb=" O   ASP A1409 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ASP A1409 " --> pdb=" O   ILE A1397 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL A1399 " --> pdb=" O   GLU A1407 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   GLU A1407 " --> pdb=" O   VAL A1399 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1282 through 1283

    608 hydrogen bonds defined for protein.
    1803 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 4.30 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 3151
        1.34 -     1.46: 2224
        1.46 -     1.58: 4443
        1.58 -     1.70: 0
        1.70 -     1.82: 101
  Bond restraints: 9919
  Sorted by residual:
  bond pdb=" N   ILE A 693 "
       pdb=" CA  ILE A 693 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.43e+00
  bond pdb=" N   ARG A 697 "
       pdb=" CA  ARG A 697 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.86e+00
  bond pdb=" N   LEU A 695 "
       pdb=" CA  LEU A 695 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.77e+00
  bond pdb=" N   TYR A 700 "
       pdb=" CA  TYR A 700 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.63e+00
  bond pdb=" N   SER A 701 "
       pdb=" CA  SER A 701 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.57e+00
  ... (remaining 9914 not shown)

  Histogram of bond angle deviations from ideal:
      100.12 -   106.89: 224
      106.89 -   113.66: 5584
      113.66 -   120.42: 3638
      120.42 -   127.19: 3886
      127.19 -   133.96: 93
  Bond angle restraints: 13425
  Sorted by residual:
  angle pdb=" N   ILE A1340 "
        pdb=" CA  ILE A1340 "
        pdb=" CB  ILE A1340 "
      ideal   model   delta    sigma   weight residual
     110.77  115.79   -5.02 1.81e+00 3.05e-01 7.68e+00
  angle pdb=" CB  MET A1360 "
        pdb=" CG  MET A1360 "
        pdb=" SD  MET A1360 "
      ideal   model   delta    sigma   weight residual
     112.70  120.83   -8.13 3.00e+00 1.11e-01 7.35e+00
  angle pdb=" CA  LEU A 695 "
        pdb=" C   LEU A 695 "
        pdb=" O   LEU A 695 "
      ideal   model   delta    sigma   weight residual
     120.90  118.04    2.86 1.07e+00 8.73e-01 7.15e+00
  angle pdb=" C   LYS A1436 "
        pdb=" N   GLY A1437 "
        pdb=" CA  GLY A1437 "
      ideal   model   delta    sigma   weight residual
     121.70  126.40   -4.70 1.80e+00 3.09e-01 6.81e+00
  angle pdb=" CA  ILE A1340 "
        pdb=" CB  ILE A1340 "
        pdb=" CG1 ILE A1340 "
      ideal   model   delta    sigma   weight residual
     110.40  114.84   -4.44 1.70e+00 3.46e-01 6.81e+00
  ... (remaining 13420 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 5087
       17.94 -    35.89: 676
       35.89 -    53.83: 162
       53.83 -    71.77: 28
       71.77 -    89.72: 8
  Dihedral angle restraints: 5961
    sinusoidal: 2356
      harmonic: 3605
  Sorted by residual:
  dihedral pdb=" CD  ARG A 697 "
           pdb=" NE  ARG A 697 "
           pdb=" CZ  ARG A 697 "
           pdb=" NH1 ARG A 697 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.88   72.88     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" CA  ASP A1378 "
           pdb=" CB  ASP A1378 "
           pdb=" CG  ASP A1378 "
           pdb=" OD1 ASP A1378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.49   59.49     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  ASP A 702 "
           pdb=" CB  ASP A 702 "
           pdb=" CG  ASP A 702 "
           pdb=" OD1 ASP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.59   56.59     1      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 5958 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1145
       0.035 -    0.071: 335
       0.071 -    0.106: 60
       0.106 -    0.141: 31
       0.141 -    0.176: 3
  Chirality restraints: 1574
  Sorted by residual:
  chirality pdb=" CA  ILE A 693 "
            pdb=" N   ILE A 693 "
            pdb=" C   ILE A 693 "
            pdb=" CB  ILE A 693 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.78e-01
  chirality pdb=" CA  LEU A 699 "
            pdb=" N   LEU A 699 "
            pdb=" C   LEU A 699 "
            pdb=" CB  LEU A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  LEU A 695 "
            pdb=" N   LEU A 695 "
            pdb=" C   LEU A 695 "
            pdb=" CB  LEU A 695 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1571 not shown)

  Planarity restraints: 1684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 697 "    1.046 9.50e-02 1.11e+02   4.69e-01 1.33e+02
        pdb=" NE  ARG A 697 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 697 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 697 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 697 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1276 "    0.054 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO A1277 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A1277 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A1277 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 330 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 331 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1681 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 554
        2.74 -     3.28: 9521
        3.28 -     3.82: 16534
        3.82 -     4.36: 17153
        4.36 -     4.90: 31322
  Nonbonded interactions: 75084
  Sorted by model distance:
  nonbonded pdb=" O   HIS A1347 "
            pdb=" ND1 HIS A1347 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   SER A 419 "
            pdb=" OG1 THR A 423 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" ND2 ASN A 636 "
            pdb=" OG  SER A1052 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   HIS A1165 "
            pdb=" OG1 THR A1169 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER A 142 "
            pdb=" OD1 ASP A1082 "
     model   vdw
     2.290 3.040
  ... (remaining 75079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.100
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   9919  Z= 0.135
  Angle     :  0.465   8.131  13425  Z= 0.267
  Chirality :  0.037   0.176   1574
  Planarity :  0.012   0.469   1684
  Dihedral  : 16.841  89.716   3623
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 23.92 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.24), residues: 1232
  helix:  2.64 (0.19), residues: 770
  sheet:  3.34 (0.80), residues: 40
  loop : -0.16 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP A 633 
 HIS   0.007   0.000   HIS A1165 
 PHE   0.006   0.001   PHE A 724 
 TYR   0.019   0.001   TYR A 918 
 ARG   0.002   0.000   ARG A 147 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A  925 MET cc_start: 0.6760 (tmm) cc_final: 0.6250 (ptt)
  outliers start: 5
  outliers final: 3
  residues processed: 93
  average time/residue: 0.1953
  time to fit residues: 27.2503
Evaluate side-chains
  91 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  700 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 37 optimal weight:    0.4980
   chunk 58 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1044 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9919  Z= 0.181
  Angle     :  0.474   5.221  13425  Z= 0.250
  Chirality :  0.039   0.144   1574
  Planarity :  0.004   0.086   1684
  Dihedral  :  4.120  54.477   1343
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 21.29 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1232
  helix:  2.36 (0.18), residues: 778
  sheet:  3.33 (0.79), residues: 40
  loop : -0.30 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 114 
 HIS   0.006   0.001   HIS A 948 
 PHE   0.022   0.002   PHE A 434 
 TYR   0.021   0.001   TYR A 918 
 ARG   0.003   0.000   ARG A1037 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.935 
Fit side-chains
REVERT: B   65 MET cc_start: 0.1963 (OUTLIER) cc_final: 0.1149 (mmt)
REVERT: B   69 LEU cc_start: 0.1244 (OUTLIER) cc_final: 0.1010 (pp)
  outliers start: 19
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1875
  time to fit residues: 28.8184
Evaluate side-chains
  91 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  700 TYR
Chi-restraints excluded: chain A residue  704 SER
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue   69 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0870
   chunk 111 optimal weight:    1.9990
   chunk 120 optimal weight:   20.0000
   chunk 99 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.6160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 487 HIS
A 742 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   9919  Z= 0.153
  Angle     :  0.424   7.877  13425  Z= 0.224
  Chirality :  0.037   0.131   1574
  Planarity :  0.004   0.049   1684
  Dihedral  :  3.261  43.324   1338
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.23 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.24), residues: 1232
  helix:  2.42 (0.18), residues: 786
  sheet:  3.42 (0.79), residues: 40
  loop : -0.33 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1165 
 PHE   0.014   0.001   PHE A 434 
 TYR   0.014   0.001   TYR A 918 
 ARG   0.003   0.000   ARG A1346 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 1.097 
Fit side-chains
REVERT: A 1398 MET cc_start: 0.4378 (tpp) cc_final: 0.4105 (mmp)
REVERT: B   65 MET cc_start: 0.1888 (OUTLIER) cc_final: 0.1265 (mmt)
REVERT: B   69 LEU cc_start: 0.1224 (OUTLIER) cc_final: 0.0874 (pp)
  outliers start: 23
  outliers final: 10
  residues processed: 105
  average time/residue: 0.2026
  time to fit residues: 32.0046
Evaluate side-chains
  96 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  492 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain A residue 1324 MET
Chi-restraints excluded: chain A residue 1405 VAL
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue   69 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 112 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 209 GLN
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9919  Z= 0.263
  Angle     :  0.511   7.504  13425  Z= 0.275
  Chirality :  0.040   0.164   1574
  Planarity :  0.004   0.046   1684
  Dihedral  :  3.330  18.832   1336
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.70 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.24), residues: 1232
  helix:  1.93 (0.18), residues: 784
  sheet:  3.41 (0.79), residues: 40
  loop : -0.27 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 879 
 HIS   0.004   0.001   HIS A1347 
 PHE   0.028   0.002   PHE A 434 
 TYR   0.016   0.002   TYR A 918 
 ARG   0.003   0.000   ARG A1346 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A 1135 TYR cc_start: 0.8470 (m-80) cc_final: 0.8105 (m-80)
REVERT: B   65 MET cc_start: 0.2032 (mmt) cc_final: 0.1362 (mmt)
  outliers start: 24
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1880
  time to fit residues: 30.8576
Evaluate side-chains
  93 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  492 MET
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1111 THR
Chi-restraints excluded: chain A residue 1324 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 101 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1326 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9919  Z= 0.180
  Angle     :  0.462   6.715  13425  Z= 0.246
  Chirality :  0.038   0.139   1574
  Planarity :  0.004   0.046   1684
  Dihedral  :  3.320  15.968   1336
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 23.55 %
    Favored  : 74.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.24), residues: 1232
  helix:  2.09 (0.18), residues: 787
  sheet:  2.79 (0.74), residues: 46
  loop : -0.29 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1097 
 HIS   0.002   0.000   HIS A1065 
 PHE   0.013   0.001   PHE A 434 
 TYR   0.029   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A 147 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  360 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: A 1135 TYR cc_start: 0.8425 (m-80) cc_final: 0.8065 (m-80)
REVERT: B   65 MET cc_start: 0.1854 (mmt) cc_final: 0.1232 (mmt)
  outliers start: 23
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1799
  time to fit residues: 29.6774
Evaluate side-chains
  99 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  492 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  921 SER
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain A residue 1398 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 119 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 114 optimal weight:   30.0000
   overall best weight:    2.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 282 ASN
A 721 ASN
A1326 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9919  Z= 0.350
  Angle     :  0.599   9.678  13425  Z= 0.315
  Chirality :  0.042   0.171   1574
  Planarity :  0.004   0.048   1684
  Dihedral  :  3.641  18.732   1336
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.42 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1232
  helix:  1.57 (0.18), residues: 783
  sheet:  2.55 (0.71), residues: 47
  loop : -0.36 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1097 
 HIS   0.005   0.001   HIS A 203 
 PHE   0.029   0.002   PHE A 434 
 TYR   0.029   0.002   TYR A 364 
 ARG   0.004   0.000   ARG A1305 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.6957 (ttp-110) cc_final: 0.6565 (mtm-85)
REVERT: A  360 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7812 (tt0)
REVERT: A  424 LEU cc_start: 0.8175 (mp) cc_final: 0.7849 (mp)
REVERT: A  956 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8456 (mp)
REVERT: A  979 MET cc_start: 0.7600 (mmt) cc_final: 0.7397 (mmt)
REVERT: A 1135 TYR cc_start: 0.8595 (m-80) cc_final: 0.8225 (m-80)
REVERT: B   65 MET cc_start: 0.1889 (mmt) cc_final: 0.1235 (mmt)
  outliers start: 33
  outliers final: 22
  residues processed: 119
  average time/residue: 0.1972
  time to fit residues: 34.5716
Evaluate side-chains
  112 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TRP
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  921 SER
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  956 LEU
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1023 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1027 VAL
Chi-restraints excluded: chain A residue 1059 GLN
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain A residue 1272 ILE
Chi-restraints excluded: chain A residue 1324 MET
Chi-restraints excluded: chain A residue 1398 MET
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 948 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9919  Z= 0.186
  Angle     :  0.507  10.909  13425  Z= 0.264
  Chirality :  0.038   0.139   1574
  Planarity :  0.004   0.047   1684
  Dihedral  :  3.536  16.230   1336
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 23.92 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.24), residues: 1232
  helix:  1.84 (0.18), residues: 784
  sheet:  2.59 (0.72), residues: 46
  loop : -0.40 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1065 
 PHE   0.013   0.001   PHE A 434 
 TYR   0.031   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A1305 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 1.061 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.6902 (ttp-110) cc_final: 0.6541 (mtm-85)
REVERT: A  360 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7895 (tt0)
REVERT: A 1135 TYR cc_start: 0.8516 (m-80) cc_final: 0.8128 (m-80)
REVERT: B   65 MET cc_start: 0.1714 (mmt) cc_final: 0.1108 (mmt)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1756
  time to fit residues: 29.1933
Evaluate side-chains
  100 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  921 SER
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1209 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0270
   chunk 22 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 93 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0980
   overall best weight:    0.3838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9919  Z= 0.139
  Angle     :  0.479  12.594  13425  Z= 0.246
  Chirality :  0.038   0.132   1574
  Planarity :  0.003   0.046   1684
  Dihedral  :  3.405  16.935   1336
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.20 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.24), residues: 1232
  helix:  2.13 (0.18), residues: 787
  sheet:  2.72 (0.73), residues: 46
  loop : -0.35 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1097 
 HIS   0.001   0.000   HIS A1053 
 PHE   0.008   0.001   PHE A1088 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.002   0.000   ARG A1342 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.6854 (ttp-110) cc_final: 0.6501 (mtm-85)
REVERT: A  358 MET cc_start: 0.8032 (mmt) cc_final: 0.7807 (mmm)
REVERT: A 1131 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7798 (tp)
REVERT: A 1135 TYR cc_start: 0.8440 (m-80) cc_final: 0.8089 (m-80)
REVERT: B   65 MET cc_start: 0.1643 (mmt) cc_final: 0.1135 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2004
  time to fit residues: 30.7271
Evaluate side-chains
  99 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  200 MET
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  492 MET
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1131 LEU
Chi-restraints excluded: chain A residue 1209 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 110 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0270
   chunk 99 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   overall best weight:    1.0044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9919  Z= 0.206
  Angle     :  0.521  14.218  13425  Z= 0.266
  Chirality :  0.039   0.143   1574
  Planarity :  0.004   0.046   1684
  Dihedral  :  3.429  17.203   1336
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 23.55 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1232
  helix:  2.05 (0.18), residues: 782
  sheet:  2.69 (0.73), residues: 46
  loop : -0.32 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1097 
 HIS   0.003   0.000   HIS A 203 
 PHE   0.020   0.001   PHE A 434 
 TYR   0.019   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A1305 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.6877 (ttp-110) cc_final: 0.6509 (mtm-85)
REVERT: A  424 LEU cc_start: 0.7993 (mp) cc_final: 0.7754 (mp)
REVERT: A 1131 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (tp)
REVERT: A 1135 TYR cc_start: 0.8494 (m-80) cc_final: 0.8138 (m-80)
REVERT: A 1360 MET cc_start: 0.4614 (tpp) cc_final: 0.4383 (tpp)
REVERT: B   65 MET cc_start: 0.1563 (mmt) cc_final: 0.1092 (mmt)
  outliers start: 20
  outliers final: 13
  residues processed: 103
  average time/residue: 0.1872
  time to fit residues: 29.1775
Evaluate side-chains
  99 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  921 SER
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1131 LEU
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain B residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 81 optimal weight:    0.4980
   chunk 122 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 103 optimal weight:    8.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 910 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9919  Z= 0.250
  Angle     :  0.555  14.682  13425  Z= 0.284
  Chirality :  0.040   0.149   1574
  Planarity :  0.004   0.046   1684
  Dihedral  :  3.561  16.908   1336
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 24.02 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.24), residues: 1232
  helix:  1.89 (0.18), residues: 780
  sheet:  2.39 (0.72), residues: 47
  loop : -0.35 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 203 
 PHE   0.021   0.002   PHE A 434 
 TYR   0.018   0.002   TYR A 364 
 ARG   0.004   0.000   ARG A1305 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.6911 (ttp-110) cc_final: 0.6535 (mtm-85)
REVERT: A  424 LEU cc_start: 0.8032 (mp) cc_final: 0.7759 (mp)
REVERT: A 1131 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: A 1135 TYR cc_start: 0.8539 (m-80) cc_final: 0.8205 (m-80)
REVERT: B   65 MET cc_start: 0.1583 (mmt) cc_final: 0.1114 (mmt)
  outliers start: 15
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1888
  time to fit residues: 28.7148
Evaluate side-chains
  99 residues out of total 1066 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  628 VAL
Chi-restraints excluded: chain A residue  893 VAL
Chi-restraints excluded: chain A residue  921 SER
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1131 LEU
Chi-restraints excluded: chain A residue 1209 VAL
Chi-restraints excluded: chain B residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.242573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.224137 restraints weight = 9344.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 0.61
r_work: 0.3912 rms_B_bonded: 0.94 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 1.81 restraints_weight: 0.2500
r_work: 0.3762 rms_B_bonded: 3.35 restraints_weight: 0.1250
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9919  Z= 0.191
  Angle     :  0.537  15.065  13425  Z= 0.272
  Chirality :  0.039   0.141   1574
  Planarity :  0.004   0.047   1684
  Dihedral  :  3.522  17.721   1336
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 24.39 %
    Favored  : 74.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.24), residues: 1232
  helix:  1.97 (0.18), residues: 780
  sheet:  2.34 (0.72), residues: 47
  loop : -0.35 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1097 
 HIS   0.003   0.000   HIS A 203 
 PHE   0.015   0.001   PHE A 434 
 TYR   0.018   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A1305 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2065.01 seconds
wall clock time: 37 minutes 42.08 seconds (2262.08 seconds total)