Starting phenix.real_space_refine
on Thu Jul 31 06:20:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kle_0709/07_2025/6kle_0709.cif"
  }
  resolution = 4.5
  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=   0.000 sd=   0.005
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: 7
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     Zn      1      6.06       5
     P       7      5.49       5
     S      84      5.16       5
     C    8114      2.51       5
     N    2148      2.21       5
     O    2414      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12769
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1592, 12618
          Classifications: {'peptide': 1592}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 47, 'TRANS': 1544}
          Chain breaks: 16
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 125
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 105
    Chain: "B"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 149
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 4, 'rna3p': 2}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2171  SG  CYS A 284      38.187  73.702  27.629  1.00 99.80           S
  ATOM   2195  SG  CYS A 287      41.806  72.573  27.328  1.00103.32           S
  ATOM   3474  SG  CYS A 470      40.392  74.466  24.347  1.00121.98           S

  Time building chain proxies: 7.75, per 1000 atoms: 0.61
  Number of scatterers: 12769
  At special positions: 0
  Unit cell: (112.88, 115.6, 121.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Mn      1     24.99
     S      84     16.00
     P       7     15.00
     O    2414      8.00
     N    2148      7.00
     C    8114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1691 " - pdb=" SG  CYS A1776 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 3.07
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" ND1 HIS A 472 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 284 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 287 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A 470 "
      Number of angles added : 3


  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3034

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 9 sheets defined
      54.2% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 12
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.808A  pdb=" N   GLY A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 56
      removed outlier: 4.236A  pdb=" N   THR A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 59
      No H-bonds generated for 'chain 'A' and resid 57 through 59'
    Processing helix  chain 'A' and resid 68 through 76
      removed outlier: 3.582A  pdb=" N   ILE A  72 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ASN A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 125
      removed outlier: 3.897A  pdb=" N   ASN A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 3.725A  pdb=" N   SER A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.630A  pdb=" N   LEU A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 248
      removed outlier: 3.925A  pdb=" N   VAL A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASP A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 275
    Processing helix  chain 'A' and resid 284 through 288
      removed outlier: 3.708A  pdb=" N   CYS A 287 " --> pdb=" O   CYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 303
    Processing helix  chain 'A' and resid 322 through 339
      removed outlier: 3.971A  pdb=" N   GLY A 339 " --> pdb=" O   ASN A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
    Processing helix  chain 'A' and resid 389 through 391
      No H-bonds generated for 'chain 'A' and resid 389 through 391'
    Processing helix  chain 'A' and resid 396 through 404
    Processing helix  chain 'A' and resid 411 through 420
      removed outlier: 4.410A  pdb=" N   LYS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
    Processing helix  chain 'A' and resid 474 through 478
    Processing helix  chain 'A' and resid 481 through 503
      removed outlier: 3.639A  pdb=" N   ARG A 485 " --> pdb=" O   PHE A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 583
      removed outlier: 3.985A  pdb=" N   PHE A 579 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   LEU A 580 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
    Processing helix  chain 'A' and resid 586 through 598
    Processing helix  chain 'A' and resid 609 through 623
    Processing helix  chain 'A' and resid 625 through 644
      removed outlier: 3.768A  pdb=" N   GLN A 629 " --> pdb=" O   SER A 625 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASN A 644 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
    Processing helix  chain 'A' and resid 663 through 680
      removed outlier: 3.947A  pdb=" N   VAL A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 702
      removed outlier: 3.988A  pdb=" N   ARG A 692 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 706
    Processing helix  chain 'A' and resid 713 through 732
      Proline residue:  A 727  - end of helix
    Processing helix  chain 'A' and resid 745 through 760
    Processing helix  chain 'A' and resid 776 through 789
      removed outlier: 3.637A  pdb=" N   LEU A 780 " --> pdb=" O   CYS A 776 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 789 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 852
    Processing helix  chain 'A' and resid 864 through 874
      removed outlier: 3.917A  pdb=" N   LEU A 868 " --> pdb=" O   SER A 864 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A 869 " --> pdb=" O   THR A 865 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 873 " --> pdb=" O   ILE A 869 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR A 874 " --> pdb=" O   LEU A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 921
      removed outlier: 3.803A  pdb=" N   ASP A 921 " --> pdb=" O   ALA A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 968
      removed outlier: 3.786A  pdb=" N   VAL A 967 " --> pdb=" O   SER A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 971 through 975
      removed outlier: 3.777A  pdb=" N   VAL A 974 " --> pdb=" O   ASP A 971 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 975 " --> pdb=" O   PRO A 972 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 971 through 975'
    Processing helix  chain 'A' and resid 981 through 990
      removed outlier: 3.518A  pdb=" N   LYS A 989 " --> pdb=" O   ASP A 985 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   SER A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1021
    Processing helix  chain 'A' and resid 1024 through 1035
    Processing helix  chain 'A' and resid 1135 through 1156
    Processing helix  chain 'A' and resid 1163 through 1181
    Processing helix  chain 'A' and resid 1191 through 1196
      removed outlier: 3.593A  pdb=" N   THR A1195 " --> pdb=" O   LYS A1191 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET A1196 " --> pdb=" O   TRP A1192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1191 through 1196'
    Processing helix  chain 'A' and resid 1197 through 1208
      removed outlier: 4.078A  pdb=" N   PHE A1201 " --> pdb=" O   SER A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1233
    Processing helix  chain 'A' and resid 1239 through 1249
    Processing helix  chain 'A' and resid 1264 through 1273
    Processing helix  chain 'A' and resid 1295 through 1319
    Processing helix  chain 'A' and resid 1351 through 1365
      removed outlier: 3.674A  pdb=" N   ILE A1355 " --> pdb=" O   TRP A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1395 through 1405
      removed outlier: 3.558A  pdb=" N   PHE A1399 " --> pdb=" O   LEU A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1429
      removed outlier: 3.711A  pdb=" N   ASN A1429 " --> pdb=" O   GLN A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1433 through 1450
      removed outlier: 3.778A  pdb=" N   THR A1437 " --> pdb=" O   THR A1433 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A1438 " --> pdb=" O   LYS A1434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1485
      removed outlier: 3.580A  pdb=" N   PHE A1485 " --> pdb=" O   ILE A1481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1489 through 1507
      removed outlier: 3.502A  pdb=" N   PHE A1493 " --> pdb=" O   LYS A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1514 through 1520
      removed outlier: 3.693A  pdb=" N   LEU A1518 " --> pdb=" O   ASN A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1535
      removed outlier: 3.521A  pdb=" N   LEU A1527 " --> pdb=" O   GLY A1523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1537 through 1545
      removed outlier: 3.510A  pdb=" N   LEU A1545 " --> pdb=" O   VAL A1541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1579 through 1590
      removed outlier: 3.579A  pdb=" N   LYS A1583 " --> pdb=" O   PRO A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1613 through 1626
      removed outlier: 3.668A  pdb=" N   GLY A1626 " --> pdb=" O   CYS A1622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1640 through 1646
    Processing helix  chain 'A' and resid 1664 through 1669
      removed outlier: 3.766A  pdb=" N   ASN A1669 " --> pdb=" O   ASN A1666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1678 through 1694
      removed outlier: 3.718A  pdb=" N   GLY A1694 " --> pdb=" O   ALA A1690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1699
      removed outlier: 3.681A  pdb=" N   SER A1699 " --> pdb=" O   TRP A1696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1744
      removed outlier: 4.006A  pdb=" N   GLN A1738 " --> pdb=" O   ASN A1734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1744 through 1750
      removed outlier: 3.718A  pdb=" N   GLU A1750 " --> pdb=" O   VAL A1746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1758 through 1764
      removed outlier: 4.393A  pdb=" N   SER A1762 " --> pdb=" O   ASP A1758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1777 through 1783
    Processing helix  chain 'A' and resid 1787 through 1793
    Processing helix  chain 'A' and resid 1805 through 1810
      removed outlier: 4.132A  pdb=" N   LEU A1810 " --> pdb=" O   SER A1806 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.901A  pdb=" N   LEU A  98 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ILE A 140 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LEU A 100 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ASP A 142 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLU A 102 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ARG A 144 " --> pdb=" O   GLU A 102 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE A 104 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387
    Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534
      removed outlier: 6.208A  pdb=" N   LEU A 559 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   GLU A 567 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1134
      removed outlier: 6.771A  pdb=" N   PHE A1117 " --> pdb=" O   GLU A1237 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1183 through 1188
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1630 through 1631
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1716 through 1719

    590 hydrogen bonds defined for protein.
    1704 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: 4.50

  Time building geometry restraints manager: 3.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4073
        1.34 -     1.46: 2279
        1.46 -     1.58: 6518
        1.58 -     1.70: 13
        1.70 -     1.82: 120
  Bond restraints: 13003
  Sorted by residual:
  bond pdb=" CA  LEU A1545 "
       pdb=" C   LEU A1545 "
    ideal  model  delta    sigma   weight residual
    1.522  1.503  0.019 1.72e-02 3.38e+03 1.18e+00
  bond pdb=" CG  LEU A  52 "
       pdb=" CD1 LEU A  52 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.15e+00
  bond pdb=" CB  LYS A 336 "
       pdb=" CG  LYS A 336 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.03e+00
  bond pdb=" CA  ARG A1521 "
       pdb=" C   ARG A1521 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.013 1.32e-02 5.74e+03 1.03e+00
  bond pdb=" CB  GLU A 797 "
       pdb=" CG  GLU A 797 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.74e-01
  ... (remaining 12998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 17247
        2.13 -     4.26: 279
        4.26 -     6.40: 39
        6.40 -     8.53: 5
        8.53 -    10.66: 2
  Bond angle restraints: 17572
  Sorted by residual:
  angle pdb=" N   GLY A1523 "
        pdb=" CA  GLY A1523 "
        pdb=" C   GLY A1523 "
      ideal   model   delta    sigma   weight residual
     113.18  123.84  -10.66 2.37e+00 1.78e-01 2.02e+01
  angle pdb=" N   VAL A 156 "
        pdb=" CA  VAL A 156 "
        pdb=" C   VAL A 156 "
      ideal   model   delta    sigma   weight residual
     112.96  108.98    3.98 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" N   ILE A1777 "
        pdb=" CA  ILE A1777 "
        pdb=" C   ILE A1777 "
      ideal   model   delta    sigma   weight residual
     112.96  109.26    3.70 1.00e+00 1.00e+00 1.37e+01
  angle pdb=" N   GLU A 268 "
        pdb=" CA  GLU A 268 "
        pdb=" CB  GLU A 268 "
      ideal   model   delta    sigma   weight residual
     110.12  115.25   -5.13 1.47e+00 4.63e-01 1.22e+01
  angle pdb=" N   ILE A1640 "
        pdb=" CA  ILE A1640 "
        pdb=" C   ILE A1640 "
      ideal   model   delta    sigma   weight residual
     112.96  109.61    3.35 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 17567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 7158
       17.72 -    35.45: 627
       35.45 -    53.17: 98
       53.17 -    70.89: 29
       70.89 -    88.62: 13
  Dihedral angle restraints: 7925
    sinusoidal: 3270
      harmonic: 4655
  Sorted by residual:
  dihedral pdb=" CB  CYS A1691 "
           pdb=" SG  CYS A1691 "
           pdb=" SG  CYS A1776 "
           pdb=" CB  CYS A1776 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.94   56.94     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CA  GLU A  21 "
           pdb=" C   GLU A  21 "
           pdb=" N   PHE A  22 "
           pdb=" CA  PHE A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.96   27.04     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  PHE A 300 "
           pdb=" C   PHE A 300 "
           pdb=" N   SER A 301 "
           pdb=" CA  SER A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.13   19.87     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 7922 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1437
       0.041 -    0.082: 445
       0.082 -    0.122: 125
       0.122 -    0.163: 17
       0.163 -    0.204: 7
  Chirality restraints: 2031
  Sorted by residual:
  chirality pdb=" CA  GLU A  21 "
            pdb=" N   GLU A  21 "
            pdb=" C   GLU A  21 "
            pdb=" CB  GLU A  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE A1375 "
            pdb=" CA  ILE A1375 "
            pdb=" CG1 ILE A1375 "
            pdb=" CG2 ILE A1375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.47e-01
  chirality pdb=" CA  THR A1753 "
            pdb=" N   THR A1753 "
            pdb=" C   THR A1753 "
            pdb=" CB  THR A1753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.91e-01
  ... (remaining 2028 not shown)

  Planarity restraints: 2196
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  22 "   -0.029 2.00e-02 2.50e+03   2.58e-02 1.16e+01
        pdb=" CG  PHE A  22 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  22 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  22 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  22 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  22 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  22 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1680 "   -0.016 2.00e-02 2.50e+03   1.46e-02 5.35e+00
        pdb=" CG  TRP A1680 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1680 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1680 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1680 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1680 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1680 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1680 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1680 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1680 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1528 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.90e+00
        pdb=" C   THR A1528 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR A1528 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A1529 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2193 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1141
        2.74 -     3.28: 14097
        3.28 -     3.82: 21012
        3.82 -     4.36: 24108
        4.36 -     4.90: 39520
  Nonbonded interactions: 99878
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A1150 "
            pdb=" ND2 ASN A1297 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   GLU A1525 "
            pdb=" OG1 THR A1528 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE A1447 "
            pdb=" OG  SER A1450 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ALA A 619 "
            pdb=" OG  SER A 623 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER A1537 "
            pdb=" OE1 GLU A1540 "
     model   vdw
     2.238 3.040
  ... (remaining 99873 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 group one per residue
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:             0.420
  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:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.330
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.070
  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:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
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      :  0.003   0.083  13009  Z= 0.137
  Angle     :  0.662  10.660  17579  Z= 0.340
  Chirality :  0.043   0.204   2031
  Planarity :  0.004   0.041   2196
  Dihedral  : 14.122  88.617   4885
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.21 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.87 (0.21), residues: 1558
  helix:  0.73 (0.19), residues: 780
  sheet: -0.09 (0.53), residues: 84
  loop : -2.27 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1680 
 HIS   0.008   0.001   HIS A 472 
 PHE   0.058   0.001   PHE A  22 
 TYR   0.018   0.001   TYR A 296 
 ARG   0.007   0.001   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12647 (  590)
  hydrogen bonds       : angle       5.38216 ( 1704)
  metal coordination   : bond        0.06855 (    4)
  metal coordination   : angle       5.95700 (    3)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       1.08416 (    4)
  covalent geometry    : bond        0.00268 (13003)
  covalent geometry    : angle       0.65744 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9421 (m-80) cc_final: 0.8962 (m-80)
REVERT: A   51 GLU cc_start: 0.7855 (pp20) cc_final: 0.7312 (tm-30)
REVERT: A  120 MET cc_start: 0.5225 (ptp) cc_final: 0.4961 (ptp)
REVERT: A  635 LEU cc_start: 0.9399 (mm) cc_final: 0.9101 (mm)
REVERT: A  702 LEU cc_start: 0.9510 (mt) cc_final: 0.9173 (mt)
REVERT: A  919 MET cc_start: 0.9237 (ppp) cc_final: 0.9017 (ppp)
REVERT: A 1136 LEU cc_start: 0.9278 (mt) cc_final: 0.8826 (tp)
REVERT: A 1141 MET cc_start: 0.8710 (mtm) cc_final: 0.8389 (mtt)
REVERT: A 1147 ASP cc_start: 0.8941 (m-30) cc_final: 0.8723 (m-30)
REVERT: A 1187 TYR cc_start: 0.8240 (m-10) cc_final: 0.7363 (m-10)
REVERT: A 1678 ILE cc_start: 0.8815 (tp) cc_final: 0.8385 (tp)
REVERT: A 1680 TRP cc_start: 0.7920 (t-100) cc_final: 0.7657 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2374
  time to fit residues: 70.2670
Evaluate side-chains
  152 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9990
   chunk 124 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0270
   chunk 75 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 144 optimal weight:    2.9990
   overall best weight:    0.4640

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
A1405 HIS
A1665 ASN
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.092548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.069130 restraints weight = 55772.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.070791 restraints weight = 40585.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.072103 restraints weight = 31886.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13009  Z= 0.110
  Angle     :  0.595   8.633  17579  Z= 0.299
  Chirality :  0.042   0.168   2031
  Planarity :  0.003   0.039   2196
  Dihedral  :  8.025  86.698   1806
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.69 %
    Favored  : 93.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.77 (0.21), residues: 1558
  helix:  0.77 (0.19), residues: 798
  sheet:  0.56 (0.56), residues: 74
  loop : -2.28 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1680 
 HIS   0.006   0.001   HIS A 472 
 PHE   0.041   0.001   PHE A  22 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.005   0.000   ARG A 851 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  590)
  hydrogen bonds       : angle       4.17077 ( 1704)
  metal coordination   : bond        0.01638 (    4)
  metal coordination   : angle       3.60731 (    3)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       0.79120 (    4)
  covalent geometry    : bond        0.00226 (13003)
  covalent geometry    : angle       0.59265 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9475 (m-80) cc_final: 0.9102 (m-80)
REVERT: A   51 GLU cc_start: 0.7822 (pp20) cc_final: 0.7267 (tm-30)
REVERT: A  394 LEU cc_start: 0.9070 (tp) cc_final: 0.8746 (tt)
REVERT: A  557 VAL cc_start: 0.9320 (t) cc_final: 0.9035 (p)
REVERT: A  565 MET cc_start: 0.7911 (tpt) cc_final: 0.7580 (tpp)
REVERT: A  620 ILE cc_start: 0.9388 (mt) cc_final: 0.9169 (mt)
REVERT: A  702 LEU cc_start: 0.9364 (mt) cc_final: 0.9013 (mt)
REVERT: A  708 LYS cc_start: 0.8771 (pttp) cc_final: 0.8143 (ptmm)
REVERT: A  836 ASP cc_start: 0.8393 (t0) cc_final: 0.8165 (t0)
REVERT: A  848 MET cc_start: 0.8568 (mmp) cc_final: 0.8333 (mmp)
REVERT: A  916 LEU cc_start: 0.9659 (mm) cc_final: 0.9450 (mt)
REVERT: A 1027 CYS cc_start: 0.7955 (t) cc_final: 0.7654 (t)
REVERT: A 1116 LYS cc_start: 0.7960 (tppt) cc_final: 0.7721 (tptt)
REVERT: A 1136 LEU cc_start: 0.9341 (mt) cc_final: 0.8896 (tp)
REVERT: A 1141 MET cc_start: 0.9009 (mtm) cc_final: 0.8661 (mtt)
REVERT: A 1147 ASP cc_start: 0.9179 (m-30) cc_final: 0.8978 (m-30)
REVERT: A 1210 LEU cc_start: 0.8438 (mm) cc_final: 0.8221 (mm)
REVERT: A 1678 ILE cc_start: 0.8857 (tp) cc_final: 0.8538 (tp)
REVERT: A 1773 LEU cc_start: 0.8788 (tt) cc_final: 0.8504 (tt)
  outliers start: 2
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2380
  time to fit residues: 71.5125
Evaluate side-chains
  150 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 113 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 128 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 127 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
A 189 HIS
A 430 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 GLN
A 800 ASN
A1231 HIS
** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1713 GLN
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.085243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062566 restraints weight = 61617.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.064094 restraints weight = 44279.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.064981 restraints weight = 34787.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  13009  Z= 0.265
  Angle     :  0.750  10.121  17579  Z= 0.386
  Chirality :  0.045   0.209   2031
  Planarity :  0.005   0.061   2196
  Dihedral  :  8.430  88.730   1806
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  7.11 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -1.15 (0.21), residues: 1558
  helix:  0.38 (0.18), residues: 798
  sheet: -0.00 (0.52), residues: 81
  loop : -2.32 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 116 
 HIS   0.011   0.002   HIS A 472 
 PHE   0.026   0.002   PHE A  22 
 TYR   0.017   0.002   TYR A1449 
 ARG   0.012   0.001   ARG A1521 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  590)
  hydrogen bonds       : angle       4.54844 ( 1704)
  metal coordination   : bond        0.01281 (    4)
  metal coordination   : angle       6.47910 (    3)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       1.10329 (    4)
  covalent geometry    : bond        0.00548 (13003)
  covalent geometry    : angle       0.74532 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 1.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9541 (m-80) cc_final: 0.9187 (m-80)
REVERT: A  387 MET cc_start: 0.8418 (pmm) cc_final: 0.8182 (pmm)
REVERT: A  394 LEU cc_start: 0.9215 (tp) cc_final: 0.8902 (tp)
REVERT: A  478 MET cc_start: 0.7777 (mtt) cc_final: 0.7379 (mtt)
REVERT: A  565 MET cc_start: 0.8814 (tpt) cc_final: 0.8523 (tmm)
REVERT: A  595 MET cc_start: 0.8786 (tpt) cc_final: 0.8570 (mmm)
REVERT: A  695 TYR cc_start: 0.9443 (t80) cc_final: 0.8843 (t80)
REVERT: A  708 LYS cc_start: 0.9088 (pttp) cc_final: 0.8351 (ptmm)
REVERT: A  836 ASP cc_start: 0.8254 (t0) cc_final: 0.8043 (t0)
REVERT: A  848 MET cc_start: 0.8630 (mmp) cc_final: 0.8321 (mmp)
REVERT: A 1027 CYS cc_start: 0.7948 (t) cc_final: 0.7645 (t)
REVERT: A 1097 TYR cc_start: 0.7692 (t80) cc_final: 0.7401 (t80)
REVERT: A 1141 MET cc_start: 0.9090 (mtm) cc_final: 0.8810 (mtt)
REVERT: A 1147 ASP cc_start: 0.9260 (m-30) cc_final: 0.9041 (m-30)
REVERT: A 1210 LEU cc_start: 0.8532 (mm) cc_final: 0.8283 (mm)
REVERT: A 1375 ILE cc_start: 0.9211 (mm) cc_final: 0.8963 (mm)
REVERT: A 1680 TRP cc_start: 0.8912 (t-100) cc_final: 0.8106 (t-100)
REVERT: A 1773 LEU cc_start: 0.8873 (tt) cc_final: 0.8496 (tt)
  outliers start: 3
  outliers final: 0
  residues processed: 169
  average time/residue: 0.3628
  time to fit residues: 91.9991
Evaluate side-chains
  127 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 2.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 116 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 70 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 158 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 145 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0370
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
A 189 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
A1405 HIS
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.088769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.065559 restraints weight = 58574.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.067203 restraints weight = 41695.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.068429 restraints weight = 32359.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  13009  Z= 0.115
  Angle     :  0.622   8.903  17579  Z= 0.311
  Chirality :  0.042   0.180   2031
  Planarity :  0.003   0.039   2196
  Dihedral  :  8.141  85.954   1806
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.04 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.89 (0.21), residues: 1558
  helix:  0.69 (0.18), residues: 793
  sheet:  0.03 (0.56), residues: 76
  loop : -2.28 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 116 
 HIS   0.005   0.001   HIS A1231 
 PHE   0.042   0.001   PHE A  22 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.008   0.001   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  590)
  hydrogen bonds       : angle       4.16093 ( 1704)
  metal coordination   : bond        0.02727 (    4)
  metal coordination   : angle       4.29760 (    3)
  SS BOND              : bond        0.00312 (    2)
  SS BOND              : angle       1.19730 (    4)
  covalent geometry    : bond        0.00242 (13003)
  covalent geometry    : angle       0.61926 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 2.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9519 (m-80) cc_final: 0.9150 (m-80)
REVERT: A   51 GLU cc_start: 0.7900 (pp20) cc_final: 0.7286 (tm-30)
REVERT: A  394 LEU cc_start: 0.9146 (tp) cc_final: 0.8552 (tt)
REVERT: A  629 GLN cc_start: 0.9211 (pt0) cc_final: 0.8889 (pt0)
REVERT: A  695 TYR cc_start: 0.9361 (t80) cc_final: 0.8956 (t80)
REVERT: A  702 LEU cc_start: 0.9430 (mt) cc_final: 0.9016 (mt)
REVERT: A  708 LYS cc_start: 0.9011 (pttp) cc_final: 0.8427 (ptmm)
REVERT: A 1027 CYS cc_start: 0.7900 (t) cc_final: 0.7592 (t)
REVERT: A 1136 LEU cc_start: 0.9362 (mt) cc_final: 0.8971 (tp)
REVERT: A 1141 MET cc_start: 0.9011 (mtm) cc_final: 0.8733 (mtt)
REVERT: A 1147 ASP cc_start: 0.9364 (m-30) cc_final: 0.8934 (m-30)
REVERT: A 1210 LEU cc_start: 0.8343 (mm) cc_final: 0.8107 (mm)
REVERT: A 1274 MET cc_start: 0.8587 (ttt) cc_final: 0.8238 (tpp)
REVERT: A 1375 ILE cc_start: 0.9013 (mm) cc_final: 0.8759 (mm)
REVERT: A 1680 TRP cc_start: 0.8894 (t-100) cc_final: 0.8253 (t-100)
REVERT: A 1773 LEU cc_start: 0.8808 (tt) cc_final: 0.8445 (tt)
REVERT: A 1782 MET cc_start: 0.8944 (mtp) cc_final: 0.8680 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 189
  average time/residue: 0.4290
  time to fit residues: 122.9544
Evaluate side-chains
  139 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 3.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 132 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 143 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   chunk 150 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
A1665 ASN
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.086155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.063449 restraints weight = 59385.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.065067 restraints weight = 43297.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.066148 restraints weight = 33826.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13009  Z= 0.177
  Angle     :  0.652   9.176  17579  Z= 0.332
  Chirality :  0.043   0.167   2031
  Planarity :  0.004   0.041   2196
  Dihedral  :  8.194  85.748   1806
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.49 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.94 (0.21), residues: 1558
  helix:  0.61 (0.18), residues: 799
  sheet:  0.04 (0.53), residues: 81
  loop : -2.31 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 116 
 HIS   0.006   0.001   HIS A 472 
 PHE   0.025   0.001   PHE A  22 
 TYR   0.016   0.001   TYR A 296 
 ARG   0.008   0.001   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  590)
  hydrogen bonds       : angle       4.27497 ( 1704)
  metal coordination   : bond        0.01550 (    4)
  metal coordination   : angle       5.26919 (    3)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       1.31901 (    4)
  covalent geometry    : bond        0.00375 (13003)
  covalent geometry    : angle       0.64814 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 4.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9514 (m-80) cc_final: 0.9144 (m-80)
REVERT: A  394 LEU cc_start: 0.9164 (tp) cc_final: 0.8577 (tt)
REVERT: A  695 TYR cc_start: 0.9394 (t80) cc_final: 0.8902 (t80)
REVERT: A  702 LEU cc_start: 0.9397 (mt) cc_final: 0.8995 (mt)
REVERT: A  708 LYS cc_start: 0.9097 (pttp) cc_final: 0.8462 (ptmm)
REVERT: A 1027 CYS cc_start: 0.7958 (t) cc_final: 0.7637 (t)
REVERT: A 1097 TYR cc_start: 0.7861 (t80) cc_final: 0.7633 (t80)
REVERT: A 1141 MET cc_start: 0.9009 (mtm) cc_final: 0.8783 (mtt)
REVERT: A 1143 ARG cc_start: 0.8808 (ptm160) cc_final: 0.8563 (ptm160)
REVERT: A 1147 ASP cc_start: 0.9239 (m-30) cc_final: 0.8951 (m-30)
REVERT: A 1210 LEU cc_start: 0.8421 (mm) cc_final: 0.8153 (mm)
REVERT: A 1274 MET cc_start: 0.8720 (ttt) cc_final: 0.8395 (tpp)
REVERT: A 1375 ILE cc_start: 0.9213 (mm) cc_final: 0.8926 (mm)
REVERT: A 1680 TRP cc_start: 0.8925 (t-100) cc_final: 0.8199 (t-100)
REVERT: A 1773 LEU cc_start: 0.8802 (tt) cc_final: 0.8545 (tt)
REVERT: A 1782 MET cc_start: 0.8963 (mtp) cc_final: 0.8706 (mtt)
  outliers start: 2
  outliers final: 2
  residues processed: 169
  average time/residue: 0.4419
  time to fit residues: 116.8257
Evaluate side-chains
  134 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 2.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 125 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 134 optimal weight:    7.9990
   chunk 119 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 155 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
A1405 HIS
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.087027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.064132 restraints weight = 59413.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.065773 restraints weight = 42934.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.066871 restraints weight = 33521.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13009  Z= 0.131
  Angle     :  0.632  10.491  17579  Z= 0.317
  Chirality :  0.042   0.172   2031
  Planarity :  0.003   0.040   2196
  Dihedral  :  8.127  85.708   1806
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.87 (0.21), residues: 1558
  helix:  0.67 (0.18), residues: 792
  sheet: -0.12 (0.50), residues: 91
  loop : -2.25 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 116 
 HIS   0.006   0.001   HIS A1405 
 PHE   0.023   0.001   PHE A  22 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  590)
  hydrogen bonds       : angle       4.19307 ( 1704)
  metal coordination   : bond        0.02071 (    4)
  metal coordination   : angle       4.83737 (    3)
  SS BOND              : bond        0.00267 (    2)
  SS BOND              : angle       1.15400 (    4)
  covalent geometry    : bond        0.00280 (13003)
  covalent geometry    : angle       0.62859 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9477 (m-80) cc_final: 0.9087 (m-80)
REVERT: A   51 GLU cc_start: 0.7931 (pp20) cc_final: 0.7301 (tm-30)
REVERT: A  478 MET cc_start: 0.7666 (mtt) cc_final: 0.7297 (mtt)
REVERT: A  695 TYR cc_start: 0.9254 (t80) cc_final: 0.8823 (t80)
REVERT: A  702 LEU cc_start: 0.9436 (mt) cc_final: 0.9069 (mt)
REVERT: A  708 LYS cc_start: 0.9052 (pttp) cc_final: 0.8567 (ptmm)
REVERT: A  851 ARG cc_start: 0.8924 (ptt180) cc_final: 0.8610 (ptt180)
REVERT: A  916 LEU cc_start: 0.9672 (mm) cc_final: 0.9433 (mt)
REVERT: A 1027 CYS cc_start: 0.7959 (t) cc_final: 0.7651 (t)
REVERT: A 1136 LEU cc_start: 0.9414 (mt) cc_final: 0.9050 (tp)
REVERT: A 1141 MET cc_start: 0.8947 (mtm) cc_final: 0.8692 (mtt)
REVERT: A 1147 ASP cc_start: 0.9196 (m-30) cc_final: 0.8956 (m-30)
REVERT: A 1210 LEU cc_start: 0.8277 (mm) cc_final: 0.8047 (mm)
REVERT: A 1375 ILE cc_start: 0.9113 (mm) cc_final: 0.8763 (mm)
REVERT: A 1515 LEU cc_start: 0.8844 (mm) cc_final: 0.8628 (mm)
REVERT: A 1680 TRP cc_start: 0.8991 (t-100) cc_final: 0.8394 (t-100)
REVERT: A 1773 LEU cc_start: 0.8752 (tt) cc_final: 0.8465 (tt)
REVERT: A 1782 MET cc_start: 0.8886 (mtp) cc_final: 0.8533 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2475
  time to fit residues: 64.4975
Evaluate side-chains
  138 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 146 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 134 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 ASN
A1231 HIS
** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.086811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.064092 restraints weight = 59126.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.065716 restraints weight = 42784.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.066788 restraints weight = 33462.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13009  Z= 0.145
  Angle     :  0.650  10.318  17579  Z= 0.326
  Chirality :  0.043   0.184   2031
  Planarity :  0.004   0.045   2196
  Dihedral  :  8.136  86.014   1806
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.58 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.93 (0.21), residues: 1558
  helix:  0.62 (0.18), residues: 795
  sheet: -0.29 (0.50), residues: 89
  loop : -2.25 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 116 
 HIS   0.005   0.001   HIS A 472 
 PHE   0.020   0.001   PHE A  22 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.009   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  590)
  hydrogen bonds       : angle       4.29961 ( 1704)
  metal coordination   : bond        0.01896 (    4)
  metal coordination   : angle       5.02856 (    3)
  SS BOND              : bond        0.00678 (    2)
  SS BOND              : angle       1.86072 (    4)
  covalent geometry    : bond        0.00315 (13003)
  covalent geometry    : angle       0.64657 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9486 (m-80) cc_final: 0.9097 (m-80)
REVERT: A   51 GLU cc_start: 0.7860 (pp20) cc_final: 0.7247 (tm-30)
REVERT: A  478 MET cc_start: 0.7583 (mtt) cc_final: 0.7248 (mtt)
REVERT: A  595 MET cc_start: 0.8791 (tpt) cc_final: 0.8590 (mmm)
REVERT: A  695 TYR cc_start: 0.9223 (t80) cc_final: 0.8771 (t80)
REVERT: A  702 LEU cc_start: 0.9412 (mt) cc_final: 0.8969 (mt)
REVERT: A  708 LYS cc_start: 0.9082 (pttp) cc_final: 0.8555 (ptmm)
REVERT: A 1027 CYS cc_start: 0.8000 (t) cc_final: 0.7622 (t)
REVERT: A 1136 LEU cc_start: 0.9408 (mt) cc_final: 0.9058 (tp)
REVERT: A 1141 MET cc_start: 0.8930 (mtm) cc_final: 0.8687 (mtt)
REVERT: A 1210 LEU cc_start: 0.8258 (mm) cc_final: 0.8022 (mm)
REVERT: A 1279 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8937 (pp30)
REVERT: A 1375 ILE cc_start: 0.9083 (mm) cc_final: 0.8869 (mm)
REVERT: A 1680 TRP cc_start: 0.9044 (t-100) cc_final: 0.8400 (t-100)
REVERT: A 1773 LEU cc_start: 0.8785 (tt) cc_final: 0.8484 (tt)
REVERT: A 1782 MET cc_start: 0.8980 (mtp) cc_final: 0.8688 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2402
  time to fit residues: 61.3777
Evaluate side-chains
  135 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 ASN
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 ASN
A1231 HIS
A1405 HIS
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.087488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.064110 restraints weight = 59824.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065878 restraints weight = 41885.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.067130 restraints weight = 32088.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13009  Z= 0.123
  Angle     :  0.653  10.958  17579  Z= 0.325
  Chirality :  0.043   0.203   2031
  Planarity :  0.003   0.039   2196
  Dihedral  :  8.036  86.189   1806
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.94 (0.21), residues: 1558
  helix:  0.63 (0.19), residues: 794
  sheet: -0.29 (0.50), residues: 89
  loop : -2.27 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 116 
 HIS   0.009   0.001   HIS A1405 
 PHE   0.023   0.001   PHE A1357 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.007   0.000   ARG A 553 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03218 (  590)
  hydrogen bonds       : angle       4.23559 ( 1704)
  metal coordination   : bond        0.02300 (    4)
  metal coordination   : angle       4.71103 (    3)
  SS BOND              : bond        0.00393 (    2)
  SS BOND              : angle       1.25332 (    4)
  covalent geometry    : bond        0.00264 (13003)
  covalent geometry    : angle       0.65033 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9485 (m-80) cc_final: 0.9093 (m-80)
REVERT: A   51 GLU cc_start: 0.7928 (pp20) cc_final: 0.7339 (tm-30)
REVERT: A  478 MET cc_start: 0.7477 (mtt) cc_final: 0.7158 (mtt)
REVERT: A  595 MET cc_start: 0.8796 (tpt) cc_final: 0.8581 (mmm)
REVERT: A  695 TYR cc_start: 0.9192 (t80) cc_final: 0.8769 (t80)
REVERT: A  702 LEU cc_start: 0.9401 (mt) cc_final: 0.8935 (mt)
REVERT: A  707 THR cc_start: 0.8860 (m) cc_final: 0.8538 (p)
REVERT: A  708 LYS cc_start: 0.9073 (pttp) cc_final: 0.7981 (ptmm)
REVERT: A  722 GLU cc_start: 0.8910 (pt0) cc_final: 0.8243 (pt0)
REVERT: A  850 GLU cc_start: 0.9464 (tp30) cc_final: 0.8958 (pt0)
REVERT: A 1027 CYS cc_start: 0.8000 (t) cc_final: 0.7621 (t)
REVERT: A 1136 LEU cc_start: 0.9381 (mt) cc_final: 0.9026 (tp)
REVERT: A 1141 MET cc_start: 0.8972 (mtm) cc_final: 0.8720 (mtt)
REVERT: A 1210 LEU cc_start: 0.8240 (mm) cc_final: 0.7996 (mm)
REVERT: A 1279 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8923 (pp30)
REVERT: A 1375 ILE cc_start: 0.9103 (mm) cc_final: 0.8858 (mm)
REVERT: A 1515 LEU cc_start: 0.8811 (mm) cc_final: 0.8606 (mm)
REVERT: A 1680 TRP cc_start: 0.9074 (t-100) cc_final: 0.8388 (t-100)
REVERT: A 1773 LEU cc_start: 0.8826 (tt) cc_final: 0.8535 (tt)
REVERT: A 1782 MET cc_start: 0.9015 (mtp) cc_final: 0.8677 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2435
  time to fit residues: 65.4427
Evaluate side-chains
  140 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 155 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0570
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 148 optimal weight:    0.9990
   chunk 141 optimal weight:    0.8980
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
A1405 HIS
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.088691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.065878 restraints weight = 58107.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.067568 restraints weight = 41838.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.068730 restraints weight = 32486.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13009  Z= 0.116
  Angle     :  0.679  12.804  17579  Z= 0.332
  Chirality :  0.043   0.195   2031
  Planarity :  0.003   0.038   2196
  Dihedral  :  7.986  85.943   1806
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.94 (0.21), residues: 1558
  helix:  0.59 (0.18), residues: 793
  sheet: -0.23 (0.50), residues: 89
  loop : -2.21 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 116 
 HIS   0.007   0.001   HIS A1405 
 PHE   0.029   0.001   PHE A1755 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.006   0.000   ARG A 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 (  590)
  hydrogen bonds       : angle       4.20933 ( 1704)
  metal coordination   : bond        0.02631 (    4)
  metal coordination   : angle       4.28433 (    3)
  SS BOND              : bond        0.00370 (    2)
  SS BOND              : angle       1.15697 (    4)
  covalent geometry    : bond        0.00247 (13003)
  covalent geometry    : angle       0.67662 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9480 (m-80) cc_final: 0.9103 (m-80)
REVERT: A   51 GLU cc_start: 0.7773 (pp20) cc_final: 0.7186 (tm-30)
REVERT: A  478 MET cc_start: 0.7727 (mtt) cc_final: 0.7279 (mtt)
REVERT: A  695 TYR cc_start: 0.9281 (t80) cc_final: 0.8855 (t80)
REVERT: A  702 LEU cc_start: 0.9406 (mt) cc_final: 0.8996 (mt)
REVERT: A  708 LYS cc_start: 0.8903 (pttp) cc_final: 0.7770 (ptmm)
REVERT: A 1026 MET cc_start: 0.7585 (mmp) cc_final: 0.6944 (mtm)
REVERT: A 1136 LEU cc_start: 0.9443 (mt) cc_final: 0.9004 (tp)
REVERT: A 1141 MET cc_start: 0.9000 (mtm) cc_final: 0.8760 (mtt)
REVERT: A 1174 MET cc_start: 0.8810 (ptp) cc_final: 0.8584 (ptt)
REVERT: A 1210 LEU cc_start: 0.8295 (mm) cc_final: 0.8052 (mm)
REVERT: A 1274 MET cc_start: 0.8383 (ttt) cc_final: 0.7903 (tpp)
REVERT: A 1279 GLN cc_start: 0.9252 (tp-100) cc_final: 0.8884 (pp30)
REVERT: A 1304 LEU cc_start: 0.9318 (tt) cc_final: 0.8939 (tt)
REVERT: A 1680 TRP cc_start: 0.9177 (t-100) cc_final: 0.8411 (t-100)
REVERT: A 1773 LEU cc_start: 0.8793 (tt) cc_final: 0.8464 (tt)
REVERT: A 1782 MET cc_start: 0.9087 (mtp) cc_final: 0.8801 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.2463
  time to fit residues: 66.9398
Evaluate side-chains
  136 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 13 optimal weight:   20.0000
   chunk 115 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 HIS
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.088502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065731 restraints weight = 58133.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067373 restraints weight = 41939.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.068538 restraints weight = 32808.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13009  Z= 0.120
  Angle     :  0.685  11.699  17579  Z= 0.339
  Chirality :  0.044   0.238   2031
  Planarity :  0.004   0.054   2196
  Dihedral  :  7.984  86.123   1806
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.99 (0.21), residues: 1558
  helix:  0.55 (0.18), residues: 790
  sheet: -0.18 (0.50), residues: 89
  loop : -2.25 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 116 
 HIS   0.006   0.001   HIS A1231 
 PHE   0.040   0.001   PHE A  22 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.012   0.001   ARG A 851 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03259 (  590)
  hydrogen bonds       : angle       4.21398 ( 1704)
  metal coordination   : bond        0.02393 (    4)
  metal coordination   : angle       4.34026 (    3)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       2.09477 (    4)
  covalent geometry    : bond        0.00258 (13003)
  covalent geometry    : angle       0.68178 (17572)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9460 (m-80) cc_final: 0.9078 (m-80)
REVERT: A  338 LYS cc_start: 0.9484 (pptt) cc_final: 0.9160 (pptt)
REVERT: A  478 MET cc_start: 0.7703 (mtt) cc_final: 0.7228 (mtt)
REVERT: A  595 MET cc_start: 0.8674 (tpt) cc_final: 0.8406 (mmm)
REVERT: A  635 LEU cc_start: 0.9488 (mm) cc_final: 0.9246 (mm)
REVERT: A  695 TYR cc_start: 0.9139 (t80) cc_final: 0.8868 (t80)
REVERT: A  702 LEU cc_start: 0.9417 (mt) cc_final: 0.9005 (mt)
REVERT: A  708 LYS cc_start: 0.8791 (pttp) cc_final: 0.7738 (ptmm)
REVERT: A  848 MET cc_start: 0.8613 (mmp) cc_final: 0.8074 (mmm)
REVERT: A  851 ARG cc_start: 0.9017 (ptt180) cc_final: 0.8312 (ptt-90)
REVERT: A 1026 MET cc_start: 0.7651 (mmp) cc_final: 0.7074 (mtt)
REVERT: A 1119 LEU cc_start: 0.8861 (tp) cc_final: 0.8645 (tp)
REVERT: A 1136 LEU cc_start: 0.9431 (mt) cc_final: 0.8904 (tp)
REVERT: A 1141 MET cc_start: 0.8917 (mtm) cc_final: 0.8665 (mtt)
REVERT: A 1210 LEU cc_start: 0.8182 (mm) cc_final: 0.7954 (mm)
REVERT: A 1279 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8916 (pp30)
REVERT: A 1680 TRP cc_start: 0.9058 (t-100) cc_final: 0.8352 (t-100)
REVERT: A 1773 LEU cc_start: 0.8764 (tt) cc_final: 0.8474 (tt)
REVERT: A 1782 MET cc_start: 0.8961 (mtp) cc_final: 0.8603 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2438
  time to fit residues: 65.4126
Evaluate side-chains
  133 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 83 optimal weight:    0.0470
   chunk 51 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 138 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 121 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   overall best weight:    2.7484

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

Flipped N/Q/H residues before XYZ refinement:
** A  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 ASN
A1231 HIS
A1405 HIS
** A1730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.085179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.062124 restraints weight = 62266.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.063819 restraints weight = 43543.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.065020 restraints weight = 33474.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  13009  Z= 0.200
  Angle     :  0.729  12.044  17579  Z= 0.369
  Chirality :  0.045   0.205   2031
  Planarity :  0.004   0.068   2196
  Dihedral  :  8.185  88.026   1806
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -1.10 (0.21), residues: 1558
  helix:  0.47 (0.18), residues: 793
  sheet: -0.46 (0.50), residues: 89
  loop : -2.29 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 116 
 HIS   0.011   0.001   HIS A1405 
 PHE   0.028   0.002   PHE A1755 
 TYR   0.016   0.002   TYR A1318 
 ARG   0.011   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  590)
  hydrogen bonds       : angle       4.44021 ( 1704)
  metal coordination   : bond        0.01354 (    4)
  metal coordination   : angle       5.61679 (    3)
  SS BOND              : bond        0.00484 (    2)
  SS BOND              : angle       2.19209 (    4)
  covalent geometry    : bond        0.00423 (13003)
  covalent geometry    : angle       0.72509 (17572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4105.84 seconds
wall clock time: 76 minutes 55.47 seconds (4615.47 seconds total)