Starting phenix.real_space_refine
on Tue May 13 09:04:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p2s_17373/05_2025/8p2s_17373.cif"
  }
  resolution = 2.4
  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=   0.016
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
     Zn      1      6.06       5
     P       9      5.49       5
     Mg      2      5.21       5
     S      60      5.16       5
     C    6082      2.51       5
     N    1687      2.21       5
     O    1853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9694
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4417
          Classifications: {'peptide': 550}
          Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 529}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 651, 5184
          Classifications: {'peptide': 651}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 629}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {' MG': 1, 'TTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 63
          Unusual residues: {' MG': 1, ' ZN': 1, 'GTP': 1, 'TTP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9173  SG  CYS B 680      14.461  51.845  61.872  1.00 63.96           S
  ATOM   9195  SG  CYS B 683      13.936  55.137  59.924  1.00 64.44           S
  ATOM   9286  SG  CYS B 695      12.496  54.640  63.508  1.00 71.47           S
  ATOM   9308  SG  CYS B 698      11.067  52.943  60.445  1.00 72.94           S

  Time building chain proxies: 6.63, per 1000 atoms: 0.68
  Number of scatterers: 9694
  At special positions: 0
  Unit cell: (77.456, 105.472, 115.36, 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
     S      60     16.00
     P       9     15.00
     Mg      2     11.99
     O    1853      8.00
     N    1687      7.00
     C    6082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 2.63
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 804 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 698 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 683 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 695 "
        pdb="ZN    ZN B 804 " - pdb=" SG  CYS B 680 "
      Number of angles added : 6


  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2242

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 7 sheets defined
      51.7% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 139
      Proline residue:  A 136  - end of helix
    Processing helix  chain 'A' and resid 144 through 153
    Processing helix  chain 'A' and resid 175 through 183
      removed outlier: 4.095A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 213
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 229 through 248
    Processing helix  chain 'A' and resid 251 through 255
      removed outlier: 3.646A  pdb=" N   TYR A 255 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 302
    Processing helix  chain 'A' and resid 322 through 339
    Processing helix  chain 'A' and resid 367 through 381
    Processing helix  chain 'A' and resid 391 through 395
      removed outlier: 3.671A  pdb=" N   GLN A 395 " --> pdb=" O   THR A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 451
    Processing helix  chain 'A' and resid 455 through 486
    Processing helix  chain 'A' and resid 487 through 488
      No H-bonds generated for 'chain 'A' and resid 487 through 488'
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 503 through 507
      removed outlier: 3.546A  pdb=" N   LEU A 507 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 518
      removed outlier: 4.336A  pdb=" N   ASN A 518 " --> pdb=" O   GLU A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 534
    Processing helix  chain 'A' and resid 544 through 570
    Processing helix  chain 'A' and resid 585 through 596
      removed outlier: 3.889A  pdb=" N   LYS A 590 " --> pdb=" O   LYS A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 635
      Proline residue:  A 630  - end of helix
      removed outlier: 4.234A  pdb=" N   ASP A 633 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU A 634 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 666
    Processing helix  chain 'B' and resid 86 through 105
      removed outlier: 3.596A  pdb=" N   VAL B 103 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 141
      Proline residue:  B 136  - end of helix
    Processing helix  chain 'B' and resid 144 through 153
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 175 through 183
      removed outlier: 4.094A  pdb=" N   ILE B 179 " --> pdb=" O   PRO B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 213
    Processing helix  chain 'B' and resid 223 through 248
      Proline residue:  B 230  - end of helix
      removed outlier: 3.599A  pdb=" N   ARG B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 255
    Processing helix  chain 'B' and resid 272 through 302
      removed outlier: 3.739A  pdb=" N   ASN B 286 " --> pdb=" O   ASN B 282 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 339
    Processing helix  chain 'B' and resid 367 through 382
      removed outlier: 3.655A  pdb=" N   ARG B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 395
      removed outlier: 3.858A  pdb=" N   GLN B 395 " --> pdb=" O   THR B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 3.797A  pdb=" N   CYS B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 487
      removed outlier: 4.094A  pdb=" N   THR B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 493
      removed outlier: 3.512A  pdb=" N   PHE B 493 " --> pdb=" O   ALA B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 500
    Processing helix  chain 'B' and resid 513 through 518
      removed outlier: 4.369A  pdb=" N   ASN B 518 " --> pdb=" O   GLU B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 570
    Processing helix  chain 'B' and resid 586 through 595
      removed outlier: 3.811A  pdb=" N   LYS B 590 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 635
      Proline residue:  B 630  - end of helix
      removed outlier: 4.258A  pdb=" N   ASP B 633 " --> pdb=" O   ALA B 629 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU B 634 " --> pdb=" O   PRO B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 652
      removed outlier: 4.000A  pdb=" N   HIS B 651 " --> pdb=" O   GLY B 647 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   ASN B 652 " --> pdb=" O   ASP B 648 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 647 through 652'
    Processing helix  chain 'B' and resid 653 through 666
      removed outlier: 3.526A  pdb=" N   GLU B 657 " --> pdb=" O   PRO B 653 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 720
      removed outlier: 3.579A  pdb=" N   TRP B 720 " --> pdb=" O   THR B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 730
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158
      removed outlier: 4.843A  pdb=" N   ASN A 435 " --> pdb=" O   THR A 521 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLY A 523 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER A 437 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   GLY A 525 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   SER A 439 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   ILE A 527 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ILE A 441 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173
      removed outlier: 6.604A  pdb=" N   VAL A 172 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   GLN A 219 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   ASN A 316 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE A 221 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   SER A 313 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ILE A 352 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE A 315 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   TYR A 317 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   PHE A 641 " --> pdb=" O   SER A 672 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   ASN A 674 " --> pdb=" O   PHE A 641 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL A 643 " --> pdb=" O   ASN A 674 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186
    Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158
      removed outlier: 7.660A  pdb=" N   GLY B 523 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   PHE B 438 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   GLY B 525 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   THR B 440 " --> pdb=" O   GLY B 525 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   ILE B 527 " --> pdb=" O   THR B 440 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ASN B 442 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   LEU B 522 " --> pdb=" O   SER B 574 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 576 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ILE B 524 " --> pdb=" O   LEU B 576 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173
      removed outlier: 6.230A  pdb=" N   VAL B 172 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLN B 219 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   ASN B 316 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ILE B 221 " --> pdb=" O   ASN B 316 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   SER B 313 " --> pdb=" O   ILE B 350 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ILE B 352 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE B 315 " --> pdb=" O   ILE B 352 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   LYS B 354 " --> pdb=" O   ILE B 315 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   TYR B 317 " --> pdb=" O   LYS B 354 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   PHE B 641 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ASN B 674 " --> pdb=" O   PHE B 641 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   VAL B 643 " --> pdb=" O   ASN B 674 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 184 through 186
    Processing sheet with id=AA7, first strand: chain 'B' and resid 686 through 687
      removed outlier: 3.807A  pdb=" N   GLN B 707 " --> pdb=" O   VAL B 714 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1269 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: 2.91

  Time building geometry restraints manager: 3.02 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: 3230
        1.34 -     1.46: 2040
        1.46 -     1.58: 4522
        1.58 -     1.69: 15
        1.69 -     1.81: 98
  Bond restraints: 9905
  Sorted by residual:
  bond pdb=" CA  ILE B 453 "
       pdb=" CB  ILE B 453 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.009 1.05e-02 9.07e+03 7.51e-01
  bond pdb=" CA  GLY B 538 "
       pdb=" C   GLY B 538 "
    ideal  model  delta    sigma   weight residual
    1.514  1.526 -0.012 1.41e-02 5.03e+03 6.85e-01
  bond pdb=" N   GLY A 523 "
       pdb=" CA  GLY A 523 "
    ideal  model  delta    sigma   weight residual
    1.452  1.442  0.010 1.40e-02 5.10e+03 5.17e-01
  bond pdb=" C   VAL B 516 "
       pdb=" O   VAL B 516 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.008 1.19e-02 7.06e+03 5.02e-01
  bond pdb=" CG1 ILE A 197 "
       pdb=" CD1 ILE A 197 "
    ideal  model  delta    sigma   weight residual
    1.513  1.486  0.027 3.90e-02 6.57e+02 4.88e-01
  ... (remaining 9900 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 13269
        2.12 -     4.24: 115
        4.24 -     6.36: 19
        6.36 -     8.48: 1
        8.48 -    10.60: 1
  Bond angle restraints: 13405
  Sorted by residual:
  angle pdb=" C   ASN A 308 "
        pdb=" N   GLN A 309 "
        pdb=" CA  GLN A 309 "
      ideal   model   delta    sigma   weight residual
     121.54  127.95   -6.41 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" CA  LEU B 536 "
        pdb=" CB  LEU B 536 "
        pdb=" CG  LEU B 536 "
      ideal   model   delta    sigma   weight residual
     116.30  126.90  -10.60 3.50e+00 8.16e-02 9.17e+00
  angle pdb=" CA  VAL B 516 "
        pdb=" C   VAL B 516 "
        pdb=" N   ILE B 517 "
      ideal   model   delta    sigma   weight residual
     116.60  120.23   -3.63 1.45e+00 4.76e-01 6.28e+00
  angle pdb=" N   TYR A 407 "
        pdb=" CA  TYR A 407 "
        pdb=" C   TYR A 407 "
      ideal   model   delta    sigma   weight residual
     110.19  107.15    3.04 1.24e+00 6.50e-01 6.00e+00
  angle pdb=" CA  VAL A 516 "
        pdb=" C   VAL A 516 "
        pdb=" N   ILE A 517 "
      ideal   model   delta    sigma   weight residual
     116.60  119.95   -3.35 1.45e+00 4.76e-01 5.33e+00
  ... (remaining 13400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.43: 5845
       35.43 -    70.86: 71
       70.86 -   106.29: 8
      106.29 -   141.71: 2
      141.71 -   177.14: 2
  Dihedral angle restraints: 5928
    sinusoidal: 2432
      harmonic: 3496
  Sorted by residual:
  dihedral pdb=" C2  TTP A 801 "
           pdb=" C1' TTP A 801 "
           pdb=" N1  TTP A 801 "
           pdb=" O4' TTP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  124.54  177.14     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" C2  TTP B 802 "
           pdb=" C1' TTP B 802 "
           pdb=" N1  TTP B 802 "
           pdb=" O4' TTP B 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  125.82  175.87     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" C5' TTP A 801 "
           pdb=" O5' TTP A 801 "
           pdb=" PA  TTP A 801 "
           pdb=" O3A TTP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.97   42.01  137.96     1      2.00e+01 2.50e-03 4.18e+01
  ... (remaining 5925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 835
       0.030 -    0.059: 381
       0.059 -    0.089: 141
       0.089 -    0.119: 66
       0.119 -    0.148: 11
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" CG  LEU B 536 "
            pdb=" CB  LEU B 536 "
            pdb=" CD1 LEU B 536 "
            pdb=" CD2 LEU B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  VAL A 613 "
            pdb=" N   VAL A 613 "
            pdb=" C   VAL A 613 "
            pdb=" CB  VAL A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" CA  ILE B 703 "
            pdb=" N   ILE B 703 "
            pdb=" C   ILE B 703 "
            pdb=" CB  ILE B 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 1431 not shown)

  Planarity restraints: 1737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 295 "   -0.008 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   PHE B 295 "    0.026 2.00e-02 2.50e+03
        pdb=" O   PHE B 295 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 296 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 277 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C   GLU B 277 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLU B 277 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN B 278 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 231 "    0.014 2.00e-02 2.50e+03   8.84e-03 1.56e+00
        pdb=" CG  TYR B 231 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 231 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 231 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 231 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 231 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 231 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 231 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1734 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 165
        2.68 -     3.23: 9698
        3.23 -     3.79: 16295
        3.79 -     4.34: 23002
        4.34 -     4.90: 36997
  Nonbonded interactions: 86157
  Sorted by model distance:
  nonbonded pdb=" O3G TTP A 801 "
            pdb="MG    MG B 801 "
     model   vdw
     2.120 2.170
  nonbonded pdb=" OE1 GLN A 290 "
            pdb="MG    MG A 802 "
     model   vdw
     2.172 2.170
  nonbonded pdb=" OD1 ASN B 674 "
            pdb=" NH1 ARG B 708 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OD1 ASN B 652 "
            pdb=" OG  SER B 654 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OD1 ASP A 468 "
            pdb=" NH1 ARG A 561 "
     model   vdw
     2.236 3.120
  ... (remaining 86152 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.940
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.120
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:12.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
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   0.027   9909  Z= 0.123
  Angle     :  0.546  10.597  13411  Z= 0.293
  Chirality :  0.041   0.148   1434
  Planarity :  0.003   0.030   1737
  Dihedral  : 12.819 177.141   3686
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  :  5.83 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.29 (0.25), residues: 1195
  helix:  1.41 (0.22), residues: 563
  sheet:  0.24 (0.51), residues: 109
  loop : -1.20 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 720 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.010   0.001   PHE B 224 
 TYR   0.020   0.001   TYR B 231 
 ARG   0.003   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14117 (  443)
  hydrogen bonds       : angle       6.06829 ( 1269)
  metal coordination   : bond        0.00267 (    4)
  metal coordination   : angle       3.26291 (    6)
  covalent geometry    : bond        0.00254 ( 9905)
  covalent geometry    : angle       0.54149 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 278
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7355 (mm-30)
REVERT: B  292 MET cc_start: 0.8366 (mmp) cc_final: 0.7631 (mmp)
REVERT: B  546 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5868 (pptt)
  outliers start: 31
  outliers final: 4
  residues processed: 295
  average time/residue: 1.1287
  time to fit residues: 357.7936
Evaluate side-chains
  231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 226
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ASN
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  597 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.2980
   chunk 90 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 108 optimal weight:    0.0570
   overall best weight:    0.2136

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
A 455 ASN
A 492 GLN
** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
B 219 GLN
B 242 ASN
B 290 GLN
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 ASN
B 388 ASN
B 394 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.148695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.137671 restraints weight = 11963.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.37
r_work: 0.3819 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9909  Z= 0.120
  Angle     :  0.559  11.248  13411  Z= 0.283
  Chirality :  0.043   0.186   1434
  Planarity :  0.004   0.034   1737
  Dihedral  : 11.567 176.592   1365
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.19 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.80 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.54 (0.25), residues: 1195
  helix:  1.66 (0.22), residues: 576
  sheet: -0.13 (0.49), residues: 108
  loop : -1.06 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 720 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.012   0.001   PHE B 224 
 TYR   0.019   0.001   TYR B 231 
 ARG   0.007   0.000   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  443)
  hydrogen bonds       : angle       4.47637 ( 1269)
  metal coordination   : bond        0.00513 (    4)
  metal coordination   : angle       5.53094 (    6)
  covalent geometry    : bond        0.00259 ( 9905)
  covalent geometry    : angle       0.54692 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7570 (mmm) cc_final: 0.7298 (mmm)
REVERT: B  161 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7276 (mtmt)
  outliers start: 26
  outliers final: 7
  residues processed: 244
  average time/residue: 1.1817
  time to fit residues: 309.4240
Evaluate side-chains
  223 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 216
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  597 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 103 optimal weight:    0.9980
   chunk 94 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 360 ASN
A 388 ASN
A 483 GLN
A 492 GLN
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.145495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.134419 restraints weight = 12045.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.37
r_work: 0.3778 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9909  Z= 0.190
  Angle     :  0.605  10.293  13411  Z= 0.307
  Chirality :  0.045   0.161   1434
  Planarity :  0.004   0.038   1737
  Dihedral  : 11.766 177.100   1363
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.69 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.16 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.37 (0.25), residues: 1195
  helix:  1.47 (0.22), residues: 574
  sheet: -0.13 (0.49), residues: 108
  loop : -1.10 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 425 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.016   0.002   PHE A 482 
 TYR   0.024   0.002   TYR B 231 
 ARG   0.008   0.001   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  443)
  hydrogen bonds       : angle       4.57674 ( 1269)
  metal coordination   : bond        0.00510 (    4)
  metal coordination   : angle       5.35452 (    6)
  covalent geometry    : bond        0.00446 ( 9905)
  covalent geometry    : angle       0.59466 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 223
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8355 (mm)
REVERT: B  161 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7335 (ttpt)
REVERT: B  537 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5401 (mt)
  outliers start: 30
  outliers final: 11
  residues processed: 241
  average time/residue: 1.1979
  time to fit residues: 309.3772
Evaluate side-chains
  235 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 222
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  117 MET
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  597 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0270
   chunk 86 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 388 ASN
A 492 GLN
A 548 GLN
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
B 219 GLN
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 GLN
B 548 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.146141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.135051 restraints weight = 11889.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 1.36
r_work: 0.3784 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9909  Z= 0.159
  Angle     :  0.587  10.181  13411  Z= 0.295
  Chirality :  0.044   0.143   1434
  Planarity :  0.004   0.045   1737
  Dihedral  : 11.711 177.076   1363
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.77 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.65 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.42 (0.25), residues: 1195
  helix:  1.54 (0.22), residues: 568
  sheet:  0.00 (0.49), residues: 113
  loop : -1.11 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 425 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.014   0.002   PHE A 482 
 TYR   0.022   0.001   TYR B 231 
 ARG   0.010   0.001   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  443)
  hydrogen bonds       : angle       4.50780 ( 1269)
  metal coordination   : bond        0.00513 (    4)
  metal coordination   : angle       5.30022 (    6)
  covalent geometry    : bond        0.00367 ( 9905)
  covalent geometry    : angle       0.57675 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8327 (mm)
REVERT: A  548 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7050 (tm130)
REVERT: B  537 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5340 (mt)
  outliers start: 34
  outliers final: 13
  residues processed: 241
  average time/residue: 1.0947
  time to fit residues: 283.7170
Evaluate side-chains
  234 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  602 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 57 optimal weight:    0.1980
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 360 ASN
A 388 ASN
A 492 GLN
A 548 GLN
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 540 HIS
B 548 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.143889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.133039 restraints weight = 12011.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 1.35
r_work: 0.3767 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   9909  Z= 0.200
  Angle     :  0.617  10.163  13411  Z= 0.311
  Chirality :  0.045   0.138   1434
  Planarity :  0.004   0.040   1737
  Dihedral  : 11.859 177.694   1363
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.03 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.72 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.29 (0.25), residues: 1195
  helix:  1.45 (0.22), residues: 562
  sheet: -0.03 (0.50), residues: 108
  loop : -1.17 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 425 
 HIS   0.007   0.001   HIS B 540 
 PHE   0.017   0.002   PHE B 129 
 TYR   0.024   0.002   TYR B 231 
 ARG   0.007   0.001   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  443)
  hydrogen bonds       : angle       4.59759 ( 1269)
  metal coordination   : bond        0.00503 (    4)
  metal coordination   : angle       5.45418 (    6)
  covalent geometry    : bond        0.00470 ( 9905)
  covalent geometry    : angle       0.60625 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 217
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8328 (mm)
REVERT: A  548 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7169 (tm130)
REVERT: A  644 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7294 (mm-30)
  outliers start: 32
  outliers final: 14
  residues processed: 237
  average time/residue: 1.1333
  time to fit residues: 288.8450
Evaluate side-chains
  227 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 211
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  602 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 73 optimal weight:    0.2980
   chunk 59 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 388 ASN
A 492 GLN
A 548 GLN
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
B 394 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.143409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.132550 restraints weight = 12023.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 1.35
r_work: 0.3757 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9909  Z= 0.225
  Angle     :  0.647  10.184  13411  Z= 0.326
  Chirality :  0.046   0.152   1434
  Planarity :  0.004   0.043   1737
  Dihedral  : 11.924 177.132   1363
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.19 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.52 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.15 (0.25), residues: 1195
  helix:  1.35 (0.22), residues: 560
  sheet: -0.06 (0.50), residues: 108
  loop : -1.25 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 425 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.019   0.002   PHE B 129 
 TYR   0.026   0.002   TYR B 231 
 ARG   0.004   0.001   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04473 (  443)
  hydrogen bonds       : angle       4.65815 ( 1269)
  metal coordination   : bond        0.00495 (    4)
  metal coordination   : angle       5.55287 (    6)
  covalent geometry    : bond        0.00533 ( 9905)
  covalent geometry    : angle       0.63660 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 226
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.8386 (mtp) cc_final: 0.8103 (mtp)
REVERT: A  336 THR cc_start: 0.8149 (m) cc_final: 0.7495 (p)
REVERT: A  431 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8335 (mm)
REVERT: A  644 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7260 (mm-30)
REVERT: B  161 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7508 (ttpt)
REVERT: B  706 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7370 (tt)
  outliers start: 35
  outliers final: 14
  residues processed: 248
  average time/residue: 1.1185
  time to fit residues: 298.8043
Evaluate side-chains
  237 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 221
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  706 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 388 ASN
A 541 HIS
A 548 GLN
A 594 GLN
A 611 ASN
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.144120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.133100 restraints weight = 12108.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 1.36
r_work: 0.3760 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9909  Z= 0.222
  Angle     :  0.657  11.677  13411  Z= 0.331
  Chirality :  0.046   0.151   1434
  Planarity :  0.004   0.044   1737
  Dihedral  : 11.898 176.601   1362
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.11 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.49 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.07 (0.25), residues: 1195
  helix:  1.26 (0.22), residues: 562
  sheet: -0.07 (0.50), residues: 108
  loop : -1.28 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 425 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.019   0.002   PHE B 129 
 TYR   0.025   0.002   TYR B 231 
 ARG   0.004   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  443)
  hydrogen bonds       : angle       4.67946 ( 1269)
  metal coordination   : bond        0.00491 (    4)
  metal coordination   : angle       5.61797 (    6)
  covalent geometry    : bond        0.00525 ( 9905)
  covalent geometry    : angle       0.64613 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8351 (mm)
REVERT: A  548 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.6978 (tm130)
REVERT: A  644 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7240 (mm-30)
REVERT: B  662 MET cc_start: 0.7555 (ptp) cc_final: 0.7124 (mtm)
REVERT: B  706 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7375 (tt)
  outliers start: 23
  outliers final: 12
  residues processed: 237
  average time/residue: 1.1372
  time to fit residues: 289.4237
Evaluate side-chains
  234 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 219
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  706 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 9 optimal weight:    0.0070
   chunk 103 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
A 157 HIS
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 388 ASN
A 492 GLN
A 548 GLN
A 594 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.144126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.133139 restraints weight = 12247.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 1.37
r_work: 0.3758 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3632 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9909  Z= 0.229
  Angle     :  0.672  12.435  13411  Z= 0.339
  Chirality :  0.047   0.159   1434
  Planarity :  0.005   0.045   1737
  Dihedral  : 11.899 176.428   1360
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.19 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.46 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.03 (0.24), residues: 1195
  helix:  1.23 (0.22), residues: 560
  sheet: -0.10 (0.50), residues: 108
  loop : -1.31 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 425 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.021   0.002   PHE B 129 
 TYR   0.026   0.002   TYR B 231 
 ARG   0.004   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  443)
  hydrogen bonds       : angle       4.71284 ( 1269)
  metal coordination   : bond        0.00484 (    4)
  metal coordination   : angle       5.63874 (    6)
  covalent geometry    : bond        0.00544 ( 9905)
  covalent geometry    : angle       0.66162 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 215
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8351 (mm)
REVERT: A  644 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7259 (mm-30)
REVERT: B  546 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6482 (pttt)
REVERT: B  662 MET cc_start: 0.7547 (ptp) cc_final: 0.7078 (mtm)
REVERT: B  706 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7346 (tt)
  outliers start: 25
  outliers final: 12
  residues processed: 230
  average time/residue: 1.1888
  time to fit residues: 293.5082
Evaluate side-chains
  232 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 217
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  706 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:    0.2980
   chunk 113 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 117 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 388 ASN
A 541 HIS
A 548 GLN
A 594 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.144929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.133885 restraints weight = 12137.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 1.37
r_work: 0.3769 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9909  Z= 0.197
  Angle     :  0.641  10.087  13411  Z= 0.326
  Chirality :  0.046   0.151   1434
  Planarity :  0.004   0.045   1737
  Dihedral  : 11.819 176.480   1360
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.11 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.76 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.07 (0.25), residues: 1195
  helix:  1.27 (0.22), residues: 562
  sheet: -0.14 (0.50), residues: 108
  loop : -1.27 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 425 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.017   0.002   PHE B 129 
 TYR   0.024   0.002   TYR B 231 
 ARG   0.004   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  443)
  hydrogen bonds       : angle       4.65069 ( 1269)
  metal coordination   : bond        0.00481 (    4)
  metal coordination   : angle       5.53025 (    6)
  covalent geometry    : bond        0.00466 ( 9905)
  covalent geometry    : angle       0.63021 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.7561 (mt) cc_final: 0.7297 (mt)
REVERT: A  431 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8349 (mm)
REVERT: A  453 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7428 (mm)
REVERT: A  548 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6877 (tm130)
REVERT: A  644 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7283 (mm-30)
REVERT: B  195 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7688 (mtpt)
REVERT: B  546 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6481 (pttt)
REVERT: B  662 MET cc_start: 0.7517 (ptp) cc_final: 0.7013 (mtm)
REVERT: B  706 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (tt)
  outliers start: 22
  outliers final: 11
  residues processed: 226
  average time/residue: 1.1739
  time to fit residues: 284.6881
Evaluate side-chains
  224 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain B residue  450 CYS
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  706 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    0.1980
   chunk 115 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 117 optimal weight:    0.8980
   chunk 45 optimal weight:    0.2980
   chunk 93 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
A 492 GLN
A 548 GLN
A 594 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
B 442 ASN
B 548 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.145387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.134408 restraints weight = 12226.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.37
r_work: 0.3776 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9909  Z= 0.175
  Angle     :  0.638  11.511  13411  Z= 0.323
  Chirality :  0.045   0.216   1434
  Planarity :  0.004   0.044   1737
  Dihedral  : 11.769 176.672   1360
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.28 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.14 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.14 (0.25), residues: 1195
  helix:  1.28 (0.22), residues: 568
  sheet: -0.01 (0.49), residues: 112
  loop : -1.26 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.017   0.002   PHE B 129 
 TYR   0.023   0.002   TYR B 231 
 ARG   0.005   0.000   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  443)
  hydrogen bonds       : angle       4.62771 ( 1269)
  metal coordination   : bond        0.00471 (    4)
  metal coordination   : angle       5.40259 (    6)
  covalent geometry    : bond        0.00411 ( 9905)
  covalent geometry    : angle       0.62752 (13405)

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

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

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2390 Ramachandran restraints generated.
    1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 213
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8330 (mm)
REVERT: A  548 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6774 (tm130)
REVERT: A  644 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7253 (mm-30)
REVERT: B  546 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6443 (pttt)
REVERT: B  706 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7327 (tt)
  outliers start: 18
  outliers final: 11
  residues processed: 224
  average time/residue: 1.1276
  time to fit residues: 273.3949
Evaluate side-chains
  230 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  548 GLN
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain B residue  450 CYS
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  546 LYS
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  706 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 102 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 117 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
A 360 ASN
A 548 GLN
** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 360 ASN
B 548 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.144660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.133662 restraints weight = 12080.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3848 rms_B_bonded: 1.36
r_work: 0.3765 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3640 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9909  Z= 0.215
  Angle     :  0.661   9.929  13411  Z= 0.336
  Chirality :  0.046   0.155   1434
  Planarity :  0.005   0.044   1737
  Dihedral  : 11.858 177.105   1360
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.36 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.76 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.76 %
    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:  0.04 (0.25), residues: 1195
  helix:  1.20 (0.22), residues: 562
  sheet: -0.05 (0.49), residues: 113
  loop : -1.27 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.007   0.001   HIS A 540 
 PHE   0.022   0.002   PHE B 129 
 TYR   0.025   0.002   TYR B 231 
 ARG   0.006   0.001   ARG B 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04424 (  443)
  hydrogen bonds       : angle       4.67876 ( 1269)
  metal coordination   : bond        0.00468 (    4)
  metal coordination   : angle       5.55815 (    6)
  covalent geometry    : bond        0.00509 ( 9905)
  covalent geometry    : angle       0.65098 (13405)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8144.25 seconds
wall clock time: 140 minutes 57.89 seconds (8457.89 seconds total)