Starting phenix.real_space_refine
on Mon Jul 28 03:08:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wcz_21618/07_2025/6wcz_21618.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      56      5.16       5
     C    6251      2.51       5
     N    1776      2.21       5
     O    1809      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9894
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2829
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 333}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 7063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 881, 7063
          Classifications: {'peptide': 881}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 32, 'TRANS': 848}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6330  SG  CYS B 448      58.566  50.765  29.088  1.00170.38           S
  ATOM   6352  SG  CYS B 451      56.478  53.324  30.558  1.00177.22           S
  ATOM   9587  SG  CYS B 849      21.281  71.420  51.638  1.00143.74           S

  Time building chain proxies: 6.28, per 1000 atoms: 0.63
  Number of scatterers: 9894
  At special positions: 0
  Unit cell: (82.39, 105.93, 157.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      56     16.00
     O    1809      8.00
     N    1776      7.00
     C    6251      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: 2.69
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1001 "
        pdb="ZN    ZN B1001 " - pdb=" NE2 HIS B 443 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 451 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 448 "
      pdb="  ZN B1002 "
        pdb="ZN    ZN B1002 " - pdb=" NE2 HIS B 714 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 849 "


  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      47.4% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 140 through 182
      removed outlier: 3.669A  pdb=" N   GLU A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   ASP A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 243
      removed outlier: 3.802A  pdb=" N   ARG A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
    Processing helix  chain 'A' and resid 256 through 277
    Processing helix  chain 'A' and resid 294 through 314
    Processing helix  chain 'A' and resid 387 through 392
      removed outlier: 3.819A  pdb=" N   GLY A 391 " --> pdb=" O   THR A 387 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 387 through 392'
    Processing helix  chain 'A' and resid 423 through 427
      removed outlier: 3.771A  pdb=" N   GLU A 426 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU A 427 " --> pdb=" O   VAL A 424 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 423 through 427'
    Processing helix  chain 'A' and resid 460 through 474
      removed outlier: 4.109A  pdb=" N   ILE A 464 " --> pdb=" O   ASN A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 508
    Processing helix  chain 'B' and resid 8 through 10
      No H-bonds generated for 'chain 'B' and resid 8 through 10'
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 4.316A  pdb=" N   ASN B  17 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 29
      removed outlier: 3.792A  pdb=" N   PHE B  24 " --> pdb=" O   SER B  20 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 47
      removed outlier: 4.536A  pdb=" N   LYS B  45 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 85 through 93
      removed outlier: 3.931A  pdb=" N   THR B  93 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.826A  pdb=" N   HIS B 134 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   MET B 135 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 131 through 135'
    Processing helix  chain 'B' and resid 153 through 172
      removed outlier: 4.123A  pdb=" N   GLU B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG B 160 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 201
      removed outlier: 4.251A  pdb=" N   ARG B 197 " --> pdb=" O   GLU B 193 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   LEU B 198 " --> pdb=" O   THR B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 237
    Processing helix  chain 'B' and resid 238 through 243
    Processing helix  chain 'B' and resid 274 through 277
    Processing helix  chain 'B' and resid 278 through 287
      removed outlier: 3.810A  pdb=" N   ILE B 282 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 328
      removed outlier: 3.663A  pdb=" N   ARG B 327 " --> pdb=" O   ASN B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 360
    Processing helix  chain 'B' and resid 368 through 390
      removed outlier: 3.957A  pdb=" N   ARG B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 407
      removed outlier: 3.908A  pdb=" N   SER B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ASN B 407 " --> pdb=" O   LYS B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 427
    Processing helix  chain 'B' and resid 430 through 446
    Processing helix  chain 'B' and resid 479 through 491
    Processing helix  chain 'B' and resid 491 through 496
    Processing helix  chain 'B' and resid 500 through 505
    Processing helix  chain 'B' and resid 515 through 522
      removed outlier: 3.564A  pdb=" N   ILE B 519 " --> pdb=" O   ARG B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 543
      removed outlier: 3.870A  pdb=" N   ILE B 543 " --> pdb=" O   ASP B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 549
      removed outlier: 3.793A  pdb=" N   LEU B 548 " --> pdb=" O   SER B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 558
      removed outlier: 3.660A  pdb=" N   LEU B 553 " --> pdb=" O   ASN B 550 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 554 " --> pdb=" O   GLU B 551 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   MET B 558 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 574
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 607 through 628
      removed outlier: 3.617A  pdb=" N   LEU B 611 " --> pdb=" O   VAL B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 658
      removed outlier: 4.152A  pdb=" N   VAL B 645 " --> pdb=" O   LYS B 641 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   TRP B 654 " --> pdb=" O   GLN B 650 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   ASP B 655 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 674 through 679
      removed outlier: 3.748A  pdb=" N   ALA B 677 " --> pdb=" O   ASP B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 687
    Processing helix  chain 'B' and resid 733 through 738
    Processing helix  chain 'B' and resid 750 through 767
    Processing helix  chain 'B' and resid 772 through 785
      removed outlier: 3.584A  pdb=" N   LEU B 776 " --> pdb=" O   ARG B 772 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 807
      removed outlier: 3.901A  pdb=" N   MET B 806 " --> pdb=" O   GLY B 803 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR B 807 " --> pdb=" O   GLU B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 803 through 807'
    Processing helix  chain 'B' and resid 810 through 820
      removed outlier: 3.706A  pdb=" N   VAL B 814 " --> pdb=" O   ASP B 810 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 849
    Processing helix  chain 'B' and resid 855 through 862
    Processing helix  chain 'B' and resid 865 through 876
      removed outlier: 3.831A  pdb=" N   VAL B 872 " --> pdb=" O   THR B 868 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320
      removed outlier: 5.874A  pdb=" N   VAL A 318 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ARG A 345 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG A 343 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386
      removed outlier: 6.198A  pdb=" N   THR A 358 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LYS A 436 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378
    Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127
      removed outlier: 8.596A  pdb=" N   ARG B 125 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL B 100 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LYS B 127 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLY B 102 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   GLY B  75 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   VAL B 100 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B  77 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   GLY B 102 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP B  79 " --> pdb=" O   GLY B 102 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU B 143 " --> pdb=" O   CYS B 180 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LYS B 182 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   CYS B 145 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B 207 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 310
      removed outlier: 3.514A  pdb=" N   HIS B 307 " --> pdb=" O   ILE B 594 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ILE B 594 " --> pdb=" O   HIS B 307 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   SER B 309 " --> pdb=" O   MET B 592 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   MET B 592 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457
    Processing sheet with id=AA8, first strand: chain 'B' and resid 660 through 661
    Processing sheet with id=AA9, first strand: chain 'B' and resid 714 through 718

    404 hydrogen bonds defined for protein.
    1155 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: 2.92

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2401
        1.33 -     1.45: 2089
        1.45 -     1.57: 5527
        1.57 -     1.69: 1
        1.69 -     1.81: 91
  Bond restraints: 10109
  Sorted by residual:
  bond pdb=" N   ARG B  42 "
       pdb=" CA  ARG B  42 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.31e-02 5.83e+03 6.36e+00
  bond pdb=" N   GLY B 107 "
       pdb=" CA  GLY B 107 "
    ideal  model  delta    sigma   weight residual
    1.443  1.477 -0.034 1.37e-02 5.33e+03 6.21e+00
  bond pdb=" N   GLN A 141 "
       pdb=" CA  GLN A 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.55e+00
  bond pdb=" CB  TRP B 498 "
       pdb=" CG  TRP B 498 "
    ideal  model  delta    sigma   weight residual
    1.498  1.426  0.072 3.10e-02 1.04e+03 5.47e+00
  bond pdb=" CB  THR B 263 "
       pdb=" CG2 THR B 263 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.31e+00
  ... (remaining 10104 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 12370
        1.90 -     3.79: 1071
        3.79 -     5.69: 160
        5.69 -     7.59: 37
        7.59 -     9.48: 24
  Bond angle restraints: 13662
  Sorted by residual:
  angle pdb=" N   VAL B 132 "
        pdb=" CA  VAL B 132 "
        pdb=" CB  VAL B 132 "
      ideal   model   delta    sigma   weight residual
     112.39  105.29    7.10 1.17e+00 7.31e-01 3.68e+01
  angle pdb=" C   LEU A 307 "
        pdb=" N   LEU A 308 "
        pdb=" CA  LEU A 308 "
      ideal   model   delta    sigma   weight residual
     121.14  113.38    7.76 1.75e+00 3.27e-01 1.97e+01
  angle pdb=" CG  ARG A 300 "
        pdb=" CD  ARG A 300 "
        pdb=" NE  ARG A 300 "
      ideal   model   delta    sigma   weight residual
     112.00  121.48   -9.48 2.20e+00 2.07e-01 1.86e+01
  angle pdb=" C   ARG B 681 "
        pdb=" N   PHE B 682 "
        pdb=" CA  PHE B 682 "
      ideal   model   delta    sigma   weight residual
     121.54  129.66   -8.12 1.91e+00 2.74e-01 1.81e+01
  angle pdb=" N   LEU A 232 "
        pdb=" CA  LEU A 232 "
        pdb=" C   LEU A 232 "
      ideal   model   delta    sigma   weight residual
     109.81  118.81   -9.00 2.21e+00 2.05e-01 1.66e+01
  ... (remaining 13657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 5545
       16.81 -    33.63: 432
       33.63 -    50.44: 87
       50.44 -    67.26: 8
       67.26 -    84.07: 4
  Dihedral angle restraints: 6076
    sinusoidal: 2539
      harmonic: 3537
  Sorted by residual:
  dihedral pdb=" CA  ASN B 407 "
           pdb=" C   ASN B 407 "
           pdb=" N   ALA B 408 "
           pdb=" CA  ALA B 408 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.58  -44.42     0      5.00e+00 4.00e-02 7.89e+01
  dihedral pdb=" CA  LYS A 375 "
           pdb=" C   LYS A 375 "
           pdb=" N   PHE A 376 "
           pdb=" CA  PHE A 376 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.33   35.67     0      5.00e+00 4.00e-02 5.09e+01
  dihedral pdb=" CA  ILE B 278 "
           pdb=" C   ILE B 278 "
           pdb=" N   GLY B 279 "
           pdb=" CA  GLY B 279 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.72  -34.28     0      5.00e+00 4.00e-02 4.70e+01
  ... (remaining 6073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 875
       0.050 -    0.100: 427
       0.100 -    0.150: 135
       0.150 -    0.199: 30
       0.199 -    0.249: 7
  Chirality restraints: 1474
  Sorted by residual:
  chirality pdb=" CG  LEU B 435 "
            pdb=" CB  LEU B 435 "
            pdb=" CD1 LEU B 435 "
            pdb=" CD2 LEU B 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  ILE A 431 "
            pdb=" CA  ILE A 431 "
            pdb=" CG1 ILE A 431 "
            pdb=" CG2 ILE A 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  ILE A 363 "
            pdb=" CA  ILE A 363 "
            pdb=" CG1 ILE A 363 "
            pdb=" CG2 ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1471 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 107 "    0.065 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO B 108 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO B 108 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 108 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  42 "   -0.239 9.50e-02 1.11e+02   1.07e-01 7.01e+00
        pdb=" NE  ARG B  42 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  42 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  42 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  42 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 497 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.42e+00
        pdb=" N   PRO A 498 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 498 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 498 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 255
        2.65 -     3.21: 9063
        3.21 -     3.77: 16102
        3.77 -     4.34: 20515
        4.34 -     4.90: 31925
  Nonbonded interactions: 77860
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 439 "
            pdb="ZN    ZN B1001 "
     model   vdw
     2.085 2.230
  nonbonded pdb=" O   ARG B  41 "
            pdb=" NE  ARG B  42 "
     model   vdw
     2.115 3.120
  nonbonded pdb=" O   LEU B 611 "
            pdb=" OG1 THR B 615 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   MET B 375 "
            pdb=" OG  SER B 379 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLU A 259 "
            pdb=" OG1 THR A 263 "
     model   vdw
     2.236 3.040
  ... (remaining 77855 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=0.87 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     27.940
  Find NCS groups from input model:        0.100
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
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      :  0.012   0.608  10114  Z= 0.484
  Angle     :  1.216   9.485  13662  Z= 0.659
  Chirality :  0.064   0.249   1474
  Planarity :  0.009   0.107   1749
  Dihedral  : 12.526  84.069   3798
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.94 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  8.40 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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: -4.79 (0.18), residues: 1221
  helix: -3.20 (0.15), residues: 510
  sheet: -2.21 (0.47), residues: 93
  loop : -3.34 (0.21), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.005   TRP A 238 
 HIS   0.011   0.003   HIS A 271 
 PHE   0.025   0.005   PHE B 432 
 TYR   0.031   0.004   TYR B 882 
 ARG   0.015   0.002   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17164 (  404)
  hydrogen bonds       : angle      11.71766 ( 1155)
  metal coordination   : bond        0.32845 (    5)
  covalent geometry    : bond        0.00917 (10109)
  covalent geometry    : angle       1.21645 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 GLU cc_start: 0.8598 (pt0) cc_final: 0.8300 (pm20)
REVERT: A  459 MET cc_start: 0.8583 (mmm) cc_final: 0.8344 (mmp)
REVERT: A  502 TRP cc_start: 0.6829 (m-10) cc_final: 0.6444 (m-10)
REVERT: B   17 ASN cc_start: 0.8891 (t160) cc_final: 0.8652 (m-40)
REVERT: B   45 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6685 (tptt)
REVERT: B  101 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7603 (mtm180)
REVERT: B  127 LYS cc_start: 0.8884 (tttt) cc_final: 0.8608 (ttmm)
REVERT: B  167 MET cc_start: 0.8698 (tpp) cc_final: 0.8265 (tpp)
REVERT: B  219 MET cc_start: 0.7572 (mtp) cc_final: 0.7096 (ttm)
REVERT: B  403 LYS cc_start: 0.9098 (tttt) cc_final: 0.8763 (tptp)
REVERT: B  531 MET cc_start: 0.8435 (mmp) cc_final: 0.7851 (mmm)
REVERT: B  581 VAL cc_start: 0.9169 (m) cc_final: 0.8967 (m)
REVERT: B  643 GLU cc_start: 0.9301 (tt0) cc_final: 0.9033 (tp30)
REVERT: B  647 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8658 (tpt90)
REVERT: B  735 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8422 (mp0)
  outliers start: 27
  outliers final: 12
  residues processed: 194
  average time/residue: 0.3179
  time to fit residues: 80.1128
Evaluate side-chains
  116 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  739 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0970
   chunk 62 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0020
   chunk 71 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 271 HIS
A 313 HIS
A 461 GLN
A 473 ASN
A 480 GLN
B  17 ASN
B 228 ASN
B 402 ASN
B 449 HIS
B 550 ASN
B 576 ASN
B 762 GLN
B 855 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.081709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.066485 restraints weight = 41322.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.068856 restraints weight = 23604.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.070431 restraints weight = 15466.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10114  Z= 0.141
  Angle     :  0.717   7.594  13662  Z= 0.374
  Chirality :  0.043   0.170   1474
  Planarity :  0.006   0.063   1749
  Dihedral  :  7.684  56.955   1379
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 11.80 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.09 (0.22), residues: 1221
  helix: -1.24 (0.21), residues: 506
  sheet: -1.76 (0.49), residues: 93
  loop : -2.86 (0.22), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 476 
 HIS   0.013   0.001   HIS A 313 
 PHE   0.028   0.002   PHE A 504 
 TYR   0.025   0.002   TYR A 402 
 ARG   0.006   0.001   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04689 (  404)
  hydrogen bonds       : angle       6.70349 ( 1155)
  metal coordination   : bond        0.00544 (    5)
  covalent geometry    : bond        0.00294 (10109)
  covalent geometry    : angle       0.71706 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 136
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ILE cc_start: 0.8785 (pt) cc_final: 0.8435 (tp)
REVERT: A  232 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7502 (tp)
REVERT: A  389 GLU cc_start: 0.8707 (pt0) cc_final: 0.8331 (pm20)
REVERT: A  459 MET cc_start: 0.9113 (mmm) cc_final: 0.8866 (mmp)
REVERT: A  507 TYR cc_start: 0.7465 (m-10) cc_final: 0.7258 (m-10)
REVERT: B   70 TYR cc_start: 0.7733 (m-10) cc_final: 0.7446 (m-10)
REVERT: B   80 LEU cc_start: 0.8761 (tp) cc_final: 0.8512 (tt)
REVERT: B  127 LYS cc_start: 0.8682 (tttt) cc_final: 0.8456 (ttmm)
REVERT: B  344 MET cc_start: 0.5684 (mtt) cc_final: 0.5161 (ppp)
REVERT: B  455 MET cc_start: 0.8483 (pmm) cc_final: 0.8090 (pmm)
REVERT: B  531 MET cc_start: 0.8425 (mmp) cc_final: 0.7902 (mmt)
REVERT: B  643 GLU cc_start: 0.9323 (tt0) cc_final: 0.8930 (tp30)
  outliers start: 36
  outliers final: 19
  residues processed: 165
  average time/residue: 0.2649
  time to fit residues: 60.3356
Evaluate side-chains
  125 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  366 ASN
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  550 ASN
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 114 optimal weight:    0.0870
   chunk 56 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    2.2164

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 598 GLN
** B 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.079846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.064962 restraints weight = 42449.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.067184 restraints weight = 25122.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.068676 restraints weight = 16629.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10114  Z= 0.165
  Angle     :  0.693   8.010  13662  Z= 0.360
  Chirality :  0.043   0.155   1474
  Planarity :  0.005   0.060   1749
  Dihedral  :  6.758  57.736   1361
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 14.07 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.22), residues: 1221
  helix: -0.71 (0.22), residues: 515
  sheet: -1.49 (0.53), residues: 91
  loop : -2.77 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 848 
 HIS   0.009   0.001   HIS A 313 
 PHE   0.025   0.002   PHE A 504 
 TYR   0.022   0.002   TYR A 288 
 ARG   0.004   0.000   ARG B 874 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04290 (  404)
  hydrogen bonds       : angle       6.22039 ( 1155)
  metal coordination   : bond        0.00205 (    5)
  covalent geometry    : bond        0.00355 (10109)
  covalent geometry    : angle       0.69268 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  389 GLU cc_start: 0.8632 (pt0) cc_final: 0.8249 (pm20)
REVERT: A  459 MET cc_start: 0.9080 (mmm) cc_final: 0.8835 (mmp)
REVERT: A  507 TYR cc_start: 0.7412 (m-10) cc_final: 0.7201 (m-10)
REVERT: B   19 MET cc_start: 0.6027 (mmt) cc_final: 0.5697 (ptp)
REVERT: B  344 MET cc_start: 0.5805 (mtt) cc_final: 0.5320 (ppp)
REVERT: B  531 MET cc_start: 0.8320 (mmp) cc_final: 0.7978 (mmm)
REVERT: B  558 MET cc_start: 0.7136 (ptt) cc_final: 0.6886 (ptt)
REVERT: B  623 ARG cc_start: 0.8972 (ttt180) cc_final: 0.8429 (ttt180)
REVERT: B  643 GLU cc_start: 0.9276 (tt0) cc_final: 0.8967 (tp30)
  outliers start: 42
  outliers final: 24
  residues processed: 142
  average time/residue: 0.2055
  time to fit residues: 42.2801
Evaluate side-chains
  126 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 109 optimal weight:    6.9990
   chunk 117 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.079673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.064858 restraints weight = 41940.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.067011 restraints weight = 24860.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.068496 restraints weight = 16614.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10114  Z= 0.157
  Angle     :  0.675   8.579  13662  Z= 0.347
  Chirality :  0.043   0.154   1474
  Planarity :  0.005   0.062   1749
  Dihedral  :  6.532  59.947   1361
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.49 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.23), residues: 1221
  helix: -0.43 (0.22), residues: 523
  sheet: -1.56 (0.52), residues: 97
  loop : -2.65 (0.23), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 539 
 HIS   0.009   0.001   HIS A 313 
 PHE   0.025   0.002   PHE A 504 
 TYR   0.017   0.002   TYR B 187 
 ARG   0.003   0.000   ARG B 601 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04028 (  404)
  hydrogen bonds       : angle       5.85147 ( 1155)
  metal coordination   : bond        0.00205 (    5)
  covalent geometry    : bond        0.00340 (10109)
  covalent geometry    : angle       0.67454 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 114
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  238 TRP cc_start: 0.8253 (t-100) cc_final: 0.8002 (t-100)
REVERT: A  288 TYR cc_start: 0.7857 (t80) cc_final: 0.7606 (t80)
REVERT: A  389 GLU cc_start: 0.8559 (pt0) cc_final: 0.8177 (pm20)
REVERT: A  459 MET cc_start: 0.9043 (mmm) cc_final: 0.8788 (mmp)
REVERT: B  344 MET cc_start: 0.5909 (mtt) cc_final: 0.5443 (ppp)
REVERT: B  465 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6557 (mt-10)
REVERT: B  531 MET cc_start: 0.8378 (mmp) cc_final: 0.8044 (mmm)
REVERT: B  643 GLU cc_start: 0.9245 (tt0) cc_final: 0.8980 (tp30)
REVERT: B  777 MET cc_start: 0.8010 (tpt) cc_final: 0.7726 (tpt)
  outliers start: 46
  outliers final: 32
  residues processed: 151
  average time/residue: 0.2119
  time to fit residues: 46.2248
Evaluate side-chains
  135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 115 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.081048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.066219 restraints weight = 41846.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.068465 restraints weight = 24031.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.069996 restraints weight = 15939.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10114  Z= 0.123
  Angle     :  0.654   9.544  13662  Z= 0.330
  Chirality :  0.043   0.187   1474
  Planarity :  0.004   0.062   1749
  Dihedral  :  6.171  56.685   1361
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.13 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.23), residues: 1221
  helix: -0.07 (0.23), residues: 521
  sheet: -1.45 (0.52), residues: 99
  loop : -2.54 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP B 539 
 HIS   0.007   0.001   HIS A 313 
 PHE   0.022   0.002   PHE A 504 
 TYR   0.015   0.001   TYR B 187 
 ARG   0.007   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  404)
  hydrogen bonds       : angle       5.51508 ( 1155)
  metal coordination   : bond        0.00104 (    5)
  covalent geometry    : bond        0.00269 (10109)
  covalent geometry    : angle       0.65414 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  288 TYR cc_start: 0.7921 (t80) cc_final: 0.7496 (t80)
REVERT: A  365 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7606 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8575 (pt0) cc_final: 0.8187 (pm20)
REVERT: A  459 MET cc_start: 0.9037 (mmm) cc_final: 0.8767 (mmp)
REVERT: B  218 GLU cc_start: 0.8767 (pt0) cc_final: 0.8254 (pm20)
REVERT: B  344 MET cc_start: 0.6057 (mtt) cc_final: 0.5651 (ppp)
REVERT: B  531 MET cc_start: 0.8438 (mmp) cc_final: 0.8151 (mmt)
REVERT: B  614 PHE cc_start: 0.8300 (t80) cc_final: 0.8020 (t80)
REVERT: B  734 ASP cc_start: 0.8003 (t0) cc_final: 0.7758 (t0)
REVERT: B  777 MET cc_start: 0.7962 (tpt) cc_final: 0.7607 (tpt)
  outliers start: 41
  outliers final: 30
  residues processed: 144
  average time/residue: 0.1966
  time to fit residues: 41.9843
Evaluate side-chains
  131 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  708 VAL
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 35 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    0.1980
   chunk 87 optimal weight:   10.0000
   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 242 GLN
A 313 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.082728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.067879 restraints weight = 42066.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.070182 restraints weight = 23959.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.071754 restraints weight = 15810.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10114  Z= 0.115
  Angle     :  0.659   9.008  13662  Z= 0.325
  Chirality :  0.043   0.159   1474
  Planarity :  0.004   0.062   1749
  Dihedral  :  5.911  53.561   1361
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.47 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.23), residues: 1221
  helix:  0.03 (0.23), residues: 528
  sheet: -1.29 (0.53), residues: 99
  loop : -2.48 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 539 
 HIS   0.005   0.001   HIS A 313 
 PHE   0.027   0.002   PHE A 504 
 TYR   0.015   0.001   TYR B 187 
 ARG   0.007   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  404)
  hydrogen bonds       : angle       5.37391 ( 1155)
  metal coordination   : bond        0.00060 (    5)
  covalent geometry    : bond        0.00256 (10109)
  covalent geometry    : angle       0.65874 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 122
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  365 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7607 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8553 (pt0) cc_final: 0.8221 (pm20)
REVERT: A  459 MET cc_start: 0.8982 (mmm) cc_final: 0.8690 (mmp)
REVERT: B  218 GLU cc_start: 0.8739 (pt0) cc_final: 0.8030 (pm20)
REVERT: B  344 MET cc_start: 0.6057 (mtt) cc_final: 0.5705 (ppp)
REVERT: B  531 MET cc_start: 0.8376 (mmp) cc_final: 0.8112 (mmt)
REVERT: B  592 MET cc_start: 0.7999 (tmm) cc_final: 0.7702 (tpp)
REVERT: B  734 ASP cc_start: 0.7931 (t0) cc_final: 0.7672 (t0)
REVERT: B  777 MET cc_start: 0.7876 (tpt) cc_final: 0.7519 (tpt)
  outliers start: 47
  outliers final: 29
  residues processed: 156
  average time/residue: 0.2693
  time to fit residues: 59.3973
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  619 VAL
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 117 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0470
   chunk 45 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 113 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.8482

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
B 442 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.082625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.067781 restraints weight = 42276.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.070154 restraints weight = 23911.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.071729 restraints weight = 15580.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10114  Z= 0.117
  Angle     :  0.673  10.129  13662  Z= 0.330
  Chirality :  0.043   0.191   1474
  Planarity :  0.004   0.061   1749
  Dihedral  :  5.778  51.554   1361
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.55 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.24), residues: 1221
  helix:  0.10 (0.23), residues: 531
  sheet: -1.68 (0.49), residues: 109
  loop : -2.32 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 238 
 HIS   0.013   0.001   HIS A 313 
 PHE   0.027   0.002   PHE A 504 
 TYR   0.022   0.001   TYR A 507 
 ARG   0.006   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  404)
  hydrogen bonds       : angle       5.30888 ( 1155)
  metal coordination   : bond        0.00078 (    5)
  covalent geometry    : bond        0.00262 (10109)
  covalent geometry    : angle       0.67264 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 113
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  298 ASP cc_start: 0.7220 (m-30) cc_final: 0.6978 (m-30)
REVERT: A  365 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7570 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8943 (pt0) cc_final: 0.8692 (pm20)
REVERT: A  459 MET cc_start: 0.8959 (mmm) cc_final: 0.8656 (mmp)
REVERT: B  135 MET cc_start: 0.8554 (mmm) cc_final: 0.8337 (mmm)
REVERT: B  218 GLU cc_start: 0.8579 (pt0) cc_final: 0.8231 (pm20)
REVERT: B  219 MET cc_start: 0.7934 (mmm) cc_final: 0.7158 (mmm)
REVERT: B  344 MET cc_start: 0.5975 (mtt) cc_final: 0.5661 (ppp)
REVERT: B  531 MET cc_start: 0.8331 (mmp) cc_final: 0.7921 (mmm)
REVERT: B  734 ASP cc_start: 0.7952 (t0) cc_final: 0.7692 (t0)
REVERT: B  777 MET cc_start: 0.7836 (tpt) cc_final: 0.7471 (tpt)
  outliers start: 42
  outliers final: 32
  residues processed: 142
  average time/residue: 0.1947
  time to fit residues: 40.6373
Evaluate side-chains
  138 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  471 TRP
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  609 TYR
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.081036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.066267 restraints weight = 42729.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.068467 restraints weight = 24379.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.069991 restraints weight = 16234.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10114  Z= 0.138
  Angle     :  0.681   9.856  13662  Z= 0.336
  Chirality :  0.043   0.157   1474
  Planarity :  0.004   0.060   1749
  Dihedral  :  5.519  47.785   1357
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.02 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.24), residues: 1221
  helix:  0.12 (0.23), residues: 539
  sheet: -1.86 (0.49), residues: 111
  loop : -2.26 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 238 
 HIS   0.014   0.001   HIS A 313 
 PHE   0.026   0.002   PHE A 504 
 TYR   0.018   0.001   TYR A 402 
 ARG   0.005   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  404)
  hydrogen bonds       : angle       5.35151 ( 1155)
  metal coordination   : bond        0.00179 (    5)
  covalent geometry    : bond        0.00306 (10109)
  covalent geometry    : angle       0.68059 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 103
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  365 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7634 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8920 (pt0) cc_final: 0.8629 (pm20)
REVERT: A  459 MET cc_start: 0.8991 (mmm) cc_final: 0.8709 (mmp)
REVERT: B  219 MET cc_start: 0.7874 (mmm) cc_final: 0.7211 (mmm)
REVERT: B  344 MET cc_start: 0.6108 (mtt) cc_final: 0.5716 (ppp)
REVERT: B  531 MET cc_start: 0.8382 (mmp) cc_final: 0.7949 (mmm)
REVERT: B  592 MET cc_start: 0.8026 (tmm) cc_final: 0.7504 (tpp)
REVERT: B  734 ASP cc_start: 0.8003 (t0) cc_final: 0.7722 (t0)
REVERT: B  777 MET cc_start: 0.7952 (tpt) cc_final: 0.7588 (tpt)
  outliers start: 39
  outliers final: 32
  residues processed: 130
  average time/residue: 0.2373
  time to fit residues: 45.7224
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  520 LEU
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 98 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 32 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 117 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 115 optimal weight:    0.6980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.081569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.066884 restraints weight = 42765.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.069079 restraints weight = 24324.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.070566 restraints weight = 16117.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10114  Z= 0.125
  Angle     :  0.682  12.534  13662  Z= 0.333
  Chirality :  0.043   0.155   1474
  Planarity :  0.004   0.060   1749
  Dihedral  :  5.294  40.033   1355
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.02 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.24), residues: 1221
  helix:  0.19 (0.23), residues: 532
  sheet: -1.78 (0.49), residues: 111
  loop : -2.22 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 238 
 HIS   0.010   0.001   HIS A 313 
 PHE   0.026   0.002   PHE A 504 
 TYR   0.018   0.001   TYR A 402 
 ARG   0.004   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  404)
  hydrogen bonds       : angle       5.26000 ( 1155)
  metal coordination   : bond        0.00139 (    5)
  covalent geometry    : bond        0.00281 (10109)
  covalent geometry    : angle       0.68187 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 105
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  298 ASP cc_start: 0.7104 (m-30) cc_final: 0.6847 (m-30)
REVERT: A  365 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7693 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8905 (pt0) cc_final: 0.8594 (pm20)
REVERT: A  459 MET cc_start: 0.8976 (mmm) cc_final: 0.8679 (mmp)
REVERT: B  104 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8324 (m)
REVERT: B  219 MET cc_start: 0.7990 (mmm) cc_final: 0.7359 (mmm)
REVERT: B  344 MET cc_start: 0.6093 (mtt) cc_final: 0.5716 (ppp)
REVERT: B  531 MET cc_start: 0.8342 (mmp) cc_final: 0.7930 (mmm)
REVERT: B  592 MET cc_start: 0.7820 (tmm) cc_final: 0.7324 (tpp)
REVERT: B  734 ASP cc_start: 0.7969 (t0) cc_final: 0.7702 (t0)
REVERT: B  777 MET cc_start: 0.7881 (tpt) cc_final: 0.7514 (tpt)
  outliers start: 40
  outliers final: 33
  residues processed: 134
  average time/residue: 0.2759
  time to fit residues: 54.8595
Evaluate side-chains
  139 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  471 TRP
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  618 VAL
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 105 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
B 557 GLN
** B 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.079675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.064881 restraints weight = 43249.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.067046 restraints weight = 24987.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.068509 restraints weight = 16761.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10114  Z= 0.170
  Angle     :  0.719   9.403  13662  Z= 0.360
  Chirality :  0.044   0.153   1474
  Planarity :  0.004   0.058   1749
  Dihedral  :  5.508  44.298   1355
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.87 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.24), residues: 1221
  helix:  0.14 (0.23), residues: 525
  sheet: -1.86 (0.49), residues: 111
  loop : -2.24 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 238 
 HIS   0.012   0.001   HIS A 313 
 PHE   0.028   0.002   PHE A 504 
 TYR   0.019   0.002   TYR A 402 
 ARG   0.003   0.000   ARG B 775 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  404)
  hydrogen bonds       : angle       5.43394 ( 1155)
  metal coordination   : bond        0.00205 (    5)
  covalent geometry    : bond        0.00375 (10109)
  covalent geometry    : angle       0.71903 (13662)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it.
REVERT: A  365 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (pmt-80)
REVERT: A  389 GLU cc_start: 0.8934 (pt0) cc_final: 0.8626 (pm20)
REVERT: A  459 MET cc_start: 0.9028 (mmm) cc_final: 0.8751 (mmp)
REVERT: B  531 MET cc_start: 0.8397 (mmp) cc_final: 0.7961 (mmm)
REVERT: B  592 MET cc_start: 0.7688 (tmm) cc_final: 0.7370 (tmm)
REVERT: B  734 ASP cc_start: 0.8054 (t0) cc_final: 0.7790 (t0)
REVERT: B  777 MET cc_start: 0.7960 (tpt) cc_final: 0.7600 (tpt)
  outliers start: 34
  outliers final: 32
  residues processed: 126
  average time/residue: 0.2579
  time to fit residues: 48.8205
Evaluate side-chains
  133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 LEU
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  456 MET
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  718 LEU
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  808 THR
Chi-restraints excluded: chain B residue  852 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.079877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.064913 restraints weight = 42956.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.067162 restraints weight = 24608.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.068664 restraints weight = 16201.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10114  Z= 0.155
  Angle     :  0.728  14.523  13662  Z= 0.360
  Chirality :  0.044   0.230   1474
  Planarity :  0.004   0.059   1749
  Dihedral  :  5.499  46.512   1355
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.68 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.24), residues: 1221
  helix:  0.09 (0.22), residues: 535
  sheet: -1.80 (0.50), residues: 111
  loop : -2.25 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 238 
 HIS   0.009   0.001   HIS A 313 
 PHE   0.026   0.002   PHE A 504 
 TYR   0.018   0.001   TYR A 402 
 ARG   0.003   0.000   ARG B 724 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  404)
  hydrogen bonds       : angle       5.46968 ( 1155)
  metal coordination   : bond        0.00181 (    5)
  covalent geometry    : bond        0.00345 (10109)
  covalent geometry    : angle       0.72837 (13662)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4013.36 seconds
wall clock time: 72 minutes 59.97 seconds (4379.97 seconds total)