Starting phenix.real_space_refine
on Fri Mar 14 05:06:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5j_44214/03_2025/9b5j_44214.cif"
  }
  resolution = 2.86
  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=   0.074
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
     P       1      5.49       5
     S      42      5.16       5
     C    6078      2.51       5
     N    1575      2.21       5
     O    1829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9525
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Classifications: {'peptide': 1}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.56, per 1000 atoms: 0.69
  Number of scatterers: 9525
  At special positions: 0
  Unit cell: (82.992, 97.888, 120.232, 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)
     S      42     16.00
     P       1     15.00
     O    1829      8.00
     N    1575      7.00
     C    6078      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.93

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 9 sheets defined
      46.4% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.759A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
      removed outlier: 3.787A  pdb=" N   MET A  32 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 73 through 79
      removed outlier: 3.596A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.892A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.369A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
      removed outlier: 3.527A  pdb=" N   LYS A 121 " --> pdb=" O   GLU A 118 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN A 122 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE A 123 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 146
      removed outlier: 3.697A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 224
      removed outlier: 4.032A  pdb=" N   GLY A 224 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.286A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.625A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 3.978A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.577A  pdb=" N   SER A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.678A  pdb=" N   VAL A 483 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 4.001A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.888A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.628A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.518A  pdb=" N   SER A 581 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 582'
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.556A  pdb=" N   THR A 636 " --> pdb=" O   ASN A 632 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
      removed outlier: 3.817A  pdb=" N   VAL A 647 " --> pdb=" O   ASN A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 679
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.557A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 752
      removed outlier: 3.846A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 3.622A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 850
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.678A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.837A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 146
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.739A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.290A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.367A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.402A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ASP A 996 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   VAL A 942 " --> pdb=" O   ASP A 996 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.402A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 16
      removed outlier: 3.839A  pdb=" N   ARG B  42 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26
      removed outlier: 3.635A  pdb=" N   GLY C  24 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.20

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1619
        1.27 -     1.40: 2291
        1.40 -     1.54: 5697
        1.54 -     1.67: 66
        1.67 -     1.81: 64
  Bond restraints: 9737
  Sorted by residual:
  bond pdb=" C04 A1AIV D 201 "
       pdb=" C05 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.61e+00
  bond pdb=" C4  AMP B 101 "
       pdb=" C5  AMP B 101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.463  0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C   VAL A 949 "
       pdb=" O   VAL A 949 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.24e+00
  bond pdb=" C05 A1AIV D 201 "
       pdb=" N06 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 9.32e-01
  ... (remaining 9732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 13024
        1.45 -     2.89: 90
        2.89 -     4.34: 67
        4.34 -     5.79: 4
        5.79 -     7.23: 2
  Bond angle restraints: 13187
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.22   -6.52 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" C5' AMP B 101 "
        pdb=" O5' AMP B 101 "
        pdb=" P   AMP B 101 "
      ideal   model   delta    sigma   weight residual
     120.90  116.66    4.24 1.50e+00 4.44e-01 7.98e+00
  angle pdb=" O1P AMP B 101 "
        pdb=" P   AMP B 101 "
        pdb=" O2P AMP B 101 "
      ideal   model   delta    sigma   weight residual
     119.60  112.37    7.23 3.00e+00 1.11e-01 5.82e+00
  angle pdb=" C4' AMP B 101 "
        pdb=" C5' AMP B 101 "
        pdb=" O5' AMP B 101 "
      ideal   model   delta    sigma   weight residual
     111.70  108.35    3.35 1.50e+00 4.44e-01 4.99e+00
  angle pdb=" N   ASP A 813 "
        pdb=" CA  ASP A 813 "
        pdb=" CB  ASP A 813 "
      ideal   model   delta    sigma   weight residual
     113.65  111.05    2.60 1.47e+00 4.63e-01 3.13e+00
  ... (remaining 13182 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5671
       17.81 -    35.63: 185
       35.63 -    53.44: 38
       53.44 -    71.26: 8
       71.26 -    89.07: 3
  Dihedral angle restraints: 5905
    sinusoidal: 2399
      harmonic: 3506
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.30   50.30     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.58   18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" N   LEU A 115 "
           pdb=" CA  LEU A 115 "
           pdb=" CB  LEU A 115 "
           pdb=" CG  LEU A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.59   59.59     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 908
       0.030 -    0.060: 410
       0.060 -    0.091: 66
       0.091 -    0.121: 72
       0.121 -    0.151: 15
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" CA  ILE B  13 "
            pdb=" N   ILE B  13 "
            pdb=" C   ILE B  13 "
            pdb=" CB  ILE B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE B  36 "
            pdb=" N   ILE B  36 "
            pdb=" C   ILE B  36 "
            pdb=" CB  ILE B  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  VAL A 852 "
            pdb=" N   VAL A 852 "
            pdb=" C   VAL A 852 "
            pdb=" CB  VAL A 852 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1468 not shown)

  Planarity restraints: 1709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO C  95 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 120 "    0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO C 121 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO C 121 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 121 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  90 "    0.017 5.00e-02 4.00e+02   2.56e-02 1.05e+00
        pdb=" N   PRO A  91 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1706 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 250
        2.71 -     3.26: 9335
        3.26 -     3.80: 14628
        3.80 -     4.35: 19624
        4.35 -     4.90: 33842
  Nonbonded interactions: 77679
  Sorted by model distance:
  nonbonded pdb=" O   PRO C  18 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" ND2 ASN A 534 "
            pdb=" OE2 GLU A 558 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OE1 GLU A 658 "
            pdb=" OH  TYR A 732 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OD1 ASP A 463 "
            pdb=" O2' AMP B 101 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLU A 809 "
            pdb=" NE2 HIS A 819 "
     model   vdw
     2.269 3.120
  ... (remaining 77674 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.270
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.320
  Find NCS groups from input model:        0.110
  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:13.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
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      :  0.004   0.073   9737  Z= 0.234
  Angle     :  0.461   7.234  13187  Z= 0.232
  Chirality :  0.040   0.151   1471
  Planarity :  0.003   0.034   1709
  Dihedral  :  9.887  89.073   3638
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  2.83 %
    Favored  : 96.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.00 (0.25), residues: 1200
  helix:  1.59 (0.25), residues: 496
  sheet:  0.29 (0.37), residues: 189
  loop : -0.02 (0.28), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C  75 
 PHE   0.009   0.001   PHE A 237 
 TYR   0.009   0.001   TYR A 544 
 ARG   0.002   0.000   ARG A 409 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLN cc_start: 0.8001 (pt0) cc_final: 0.7762 (mp10)
REVERT: A  196 MET cc_start: 0.8737 (mmp) cc_final: 0.8453 (mmm)
REVERT: A  540 GLU cc_start: 0.7472 (tt0) cc_final: 0.7266 (mp0)
REVERT: A  583 GLN cc_start: 0.8129 (mt0) cc_final: 0.7261 (mm-40)
REVERT: A  614 GLU cc_start: 0.7511 (tp30) cc_final: 0.6492 (tm-30)
REVERT: A  619 GLN cc_start: 0.7466 (tp40) cc_final: 0.6890 (tm-30)
REVERT: A  811 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5524 (tp30)
REVERT: A  840 ASP cc_start: 0.7768 (p0) cc_final: 0.7459 (p0)
REVERT: A  879 LYS cc_start: 0.8373 (mttm) cc_final: 0.8092 (mttm)
REVERT: B   51 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: C   32 HIS cc_start: 0.7849 (t-170) cc_final: 0.7533 (t70)
REVERT: C   72 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8237 (mmm-85)
REVERT: C  140 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7303 (tm-30)
  outliers start: 11
  outliers final: 2
  residues processed: 142
  average time/residue: 1.6994
  time to fit residues: 255.0094
Evaluate side-chains
  98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 108 optimal weight:    0.4980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.093840 restraints weight = 11961.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.38
r_work: 0.2926 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9737  Z= 0.272
  Angle     :  0.529   5.732  13187  Z= 0.274
  Chirality :  0.043   0.159   1471
  Planarity :  0.004   0.043   1709
  Dihedral  :  5.776  78.903   1308
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.01 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1200
  helix:  1.42 (0.24), residues: 503
  sheet:  0.65 (0.37), residues: 186
  loop : -0.03 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.008   0.001   HIS A 819 
 PHE   0.013   0.001   PHE A1007 
 TYR   0.010   0.001   TYR A 834 
 ARG   0.005   0.001   ARG B  74 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLN cc_start: 0.8199 (pt0) cc_final: 0.7872 (mp10)
REVERT: A  196 MET cc_start: 0.8773 (mmp) cc_final: 0.8522 (mmm)
REVERT: A  469 LYS cc_start: 0.8312 (mppt) cc_final: 0.8088 (mmtm)
REVERT: A  540 GLU cc_start: 0.7839 (tt0) cc_final: 0.7394 (mp0)
REVERT: A  583 GLN cc_start: 0.8265 (mt0) cc_final: 0.7313 (mm-40)
REVERT: A  614 GLU cc_start: 0.7243 (tp30) cc_final: 0.6430 (tm-30)
REVERT: A  619 GLN cc_start: 0.7342 (tp40) cc_final: 0.6752 (tm-30)
REVERT: A  840 ASP cc_start: 0.7514 (p0) cc_final: 0.7237 (p0)
REVERT: A  913 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7050 (mp)
REVERT: B   51 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7953 (mt-10)
REVERT: B   60 ASN cc_start: 0.8512 (m-40) cc_final: 0.8179 (t0)
REVERT: C   32 HIS cc_start: 0.7483 (t-170) cc_final: 0.7183 (t70)
REVERT: C   72 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8159 (mmm-85)
REVERT: C  140 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7271 (tm-30)
  outliers start: 18
  outliers final: 7
  residues processed: 116
  average time/residue: 1.4681
  time to fit residues: 181.5680
Evaluate side-chains
  105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.093477 restraints weight = 12128.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.41
r_work: 0.2923 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9737  Z= 0.278
  Angle     :  0.504   5.948  13187  Z= 0.260
  Chirality :  0.043   0.152   1471
  Planarity :  0.004   0.047   1709
  Dihedral  :  5.299  66.523   1305
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  9.14 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1200
  helix:  1.36 (0.24), residues: 503
  sheet:  0.68 (0.38), residues: 185
  loop : -0.06 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 819 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.015   0.001   TYR A 250 
 ARG   0.005   0.001   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLN cc_start: 0.8204 (pt0) cc_final: 0.7865 (mp10)
REVERT: A  196 MET cc_start: 0.8770 (mmp) cc_final: 0.8560 (mmm)
REVERT: A  216 LYS cc_start: 0.7174 (pttm) cc_final: 0.6731 (pptt)
REVERT: A  540 GLU cc_start: 0.7836 (tt0) cc_final: 0.7399 (mp0)
REVERT: A  583 GLN cc_start: 0.8288 (mt0) cc_final: 0.7325 (mm-40)
REVERT: A  614 GLU cc_start: 0.7309 (tp30) cc_final: 0.6456 (tm-30)
REVERT: A  619 GLN cc_start: 0.7326 (tp40) cc_final: 0.6705 (tm-30)
REVERT: A  840 ASP cc_start: 0.7428 (p0) cc_final: 0.7144 (p0)
REVERT: A  913 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7055 (mp)
REVERT: B   51 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: B   60 ASN cc_start: 0.8505 (m-40) cc_final: 0.8200 (t0)
REVERT: C   32 HIS cc_start: 0.7526 (t-170) cc_final: 0.7206 (t70)
REVERT: C   72 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8174 (mmm-85)
REVERT: C  101 LYS cc_start: 0.8381 (mptp) cc_final: 0.8104 (mmtp)
REVERT: C  140 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7270 (tm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 115
  average time/residue: 1.9332
  time to fit residues: 238.7519
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 116 optimal weight:    2.9990
   chunk 112 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0570
   chunk 53 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.4298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.095389 restraints weight = 11943.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.40
r_work: 0.2950 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9737  Z= 0.170
  Angle     :  0.465   6.588  13187  Z= 0.240
  Chirality :  0.041   0.142   1471
  Planarity :  0.004   0.047   1709
  Dihedral  :  5.200  67.785   1305
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  9.71 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.08 (0.25), residues: 1200
  helix:  1.49 (0.24), residues: 503
  sheet:  0.81 (0.38), residues: 183
  loop : -0.01 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.018   0.001   TYR C 127 
 ARG   0.006   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8180 (pt0) cc_final: 0.7835 (mp-120)
REVERT: A  540 GLU cc_start: 0.7774 (tt0) cc_final: 0.7349 (mp0)
REVERT: A  583 GLN cc_start: 0.8298 (mt0) cc_final: 0.7335 (mm-40)
REVERT: A  614 GLU cc_start: 0.7287 (tp30) cc_final: 0.6458 (tm-30)
REVERT: A  619 GLN cc_start: 0.7210 (tp40) cc_final: 0.6648 (tm-30)
REVERT: A  840 ASP cc_start: 0.7420 (p0) cc_final: 0.7128 (p0)
REVERT: A  913 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7047 (mp)
REVERT: B   51 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: B   60 ASN cc_start: 0.8425 (m-40) cc_final: 0.8122 (t0)
REVERT: C   32 HIS cc_start: 0.7504 (t-170) cc_final: 0.7191 (t70)
REVERT: C   72 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8144 (mmm-85)
REVERT: C  101 LYS cc_start: 0.8385 (mptp) cc_final: 0.8122 (mmtp)
  outliers start: 19
  outliers final: 7
  residues processed: 114
  average time/residue: 1.4630
  time to fit residues: 178.0317
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0040
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    0.6192

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.092826 restraints weight = 12015.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 2.46
r_work: 0.2932 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9737  Z= 0.221
  Angle     :  0.504  12.654  13187  Z= 0.255
  Chirality :  0.042   0.191   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.081  70.128   1304
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.40 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.07 (0.25), residues: 1200
  helix:  1.51 (0.24), residues: 502
  sheet:  0.72 (0.38), residues: 187
  loop :  0.00 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.019   0.001   TYR C 127 
 ARG   0.006   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8168 (pt0) cc_final: 0.7827 (mp-120)
REVERT: A  221 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7769 (tp)
REVERT: A  540 GLU cc_start: 0.7777 (tt0) cc_final: 0.7339 (mp0)
REVERT: A  583 GLN cc_start: 0.8312 (mt0) cc_final: 0.7336 (mm-40)
REVERT: A  614 GLU cc_start: 0.7280 (tp30) cc_final: 0.6507 (tm-30)
REVERT: A  619 GLN cc_start: 0.7209 (tp40) cc_final: 0.6599 (tm-30)
REVERT: A  840 ASP cc_start: 0.7396 (p0) cc_final: 0.7114 (p0)
REVERT: A  913 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7043 (mp)
REVERT: B   51 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7916 (mt-10)
REVERT: B   60 ASN cc_start: 0.8381 (m-40) cc_final: 0.8073 (t0)
REVERT: C   32 HIS cc_start: 0.7498 (t-170) cc_final: 0.7186 (t70)
REVERT: C   72 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8149 (mmm-85)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 1.4281
  time to fit residues: 167.9958
Evaluate side-chains
  108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.133387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.092797 restraints weight = 12087.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.46
r_work: 0.2930 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9737  Z= 0.223
  Angle     :  0.497  11.271  13187  Z= 0.253
  Chirality :  0.042   0.212   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.071  68.633   1304
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.88 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.12 (0.25), residues: 1200
  helix:  1.60 (0.24), residues: 497
  sheet:  0.73 (0.38), residues: 187
  loop : -0.00 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.021   0.001   TYR C 127 
 ARG   0.007   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8197 (pt0) cc_final: 0.7846 (mp-120)
REVERT: A  221 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7810 (tp)
REVERT: A  540 GLU cc_start: 0.7829 (tt0) cc_final: 0.7387 (mp0)
REVERT: A  583 GLN cc_start: 0.8337 (mt0) cc_final: 0.7359 (mm-40)
REVERT: A  614 GLU cc_start: 0.7304 (tp30) cc_final: 0.6535 (tm-30)
REVERT: A  619 GLN cc_start: 0.7235 (tp40) cc_final: 0.6611 (tm-30)
REVERT: A  811 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5742 (tp30)
REVERT: A  840 ASP cc_start: 0.7427 (p0) cc_final: 0.7140 (p0)
REVERT: A  913 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7073 (mp)
REVERT: B   51 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7943 (mt-10)
REVERT: B   60 ASN cc_start: 0.8424 (m-40) cc_final: 0.8132 (t0)
REVERT: C   32 HIS cc_start: 0.7510 (t-170) cc_final: 0.7197 (t70)
REVERT: C   72 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8180 (mmm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 109
  average time/residue: 1.3415
  time to fit residues: 156.5135
Evaluate side-chains
  108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.133622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.093009 restraints weight = 12064.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.46
r_work: 0.2941 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9737  Z= 0.220
  Angle     :  0.497   9.946  13187  Z= 0.253
  Chirality :  0.042   0.205   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.052  68.430   1304
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.78 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.14 (0.25), residues: 1200
  helix:  1.61 (0.24), residues: 497
  sheet:  0.72 (0.38), residues: 188
  loop :  0.01 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.021   0.001   TYR C 127 
 ARG   0.006   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8202 (pt0) cc_final: 0.7851 (mp-120)
REVERT: A  221 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7919 (tp)
REVERT: A  540 GLU cc_start: 0.7856 (tt0) cc_final: 0.7427 (mp0)
REVERT: A  583 GLN cc_start: 0.8342 (mt0) cc_final: 0.7364 (mm-40)
REVERT: A  614 GLU cc_start: 0.7325 (tp30) cc_final: 0.6554 (tm-30)
REVERT: A  619 GLN cc_start: 0.7323 (tp40) cc_final: 0.6673 (tm-30)
REVERT: A  811 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5776 (tp30)
REVERT: A  840 ASP cc_start: 0.7411 (p0) cc_final: 0.7132 (p0)
REVERT: A  913 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7023 (mp)
REVERT: B   51 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: B   60 ASN cc_start: 0.8412 (m-40) cc_final: 0.8124 (t0)
REVERT: C   32 HIS cc_start: 0.7539 (t-170) cc_final: 0.7222 (t70)
REVERT: C   72 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8180 (mmm-85)
  outliers start: 15
  outliers final: 9
  residues processed: 112
  average time/residue: 1.3210
  time to fit residues: 158.3854
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  136 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.133362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.092751 restraints weight = 12268.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.43
r_work: 0.2939 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9737  Z= 0.247
  Angle     :  0.508  10.663  13187  Z= 0.259
  Chirality :  0.043   0.201   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.053  64.866   1304
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.82 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.13 (0.25), residues: 1200
  helix:  1.60 (0.24), residues: 496
  sheet:  0.73 (0.38), residues: 188
  loop :  0.01 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.021   0.001   TYR C 127 
 ARG   0.006   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8195 (pt0) cc_final: 0.7843 (mp-120)
REVERT: A  221 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (tp)
REVERT: A  442 MET cc_start: 0.8057 (tpp) cc_final: 0.7758 (tpp)
REVERT: A  540 GLU cc_start: 0.7816 (tt0) cc_final: 0.7381 (mp0)
REVERT: A  583 GLN cc_start: 0.8334 (mt0) cc_final: 0.7350 (mm-40)
REVERT: A  614 GLU cc_start: 0.7309 (tp30) cc_final: 0.6526 (tm-30)
REVERT: A  619 GLN cc_start: 0.7485 (tp40) cc_final: 0.6797 (tm-30)
REVERT: A  811 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5772 (tp30)
REVERT: A  840 ASP cc_start: 0.7388 (p0) cc_final: 0.7114 (p0)
REVERT: A  913 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7079 (mp)
REVERT: B   51 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7896 (mt-10)
REVERT: B   60 ASN cc_start: 0.8398 (m-40) cc_final: 0.8115 (t0)
REVERT: C   32 HIS cc_start: 0.7520 (t-170) cc_final: 0.7206 (t70)
REVERT: C   72 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8173 (mmm-85)
  outliers start: 11
  outliers final: 7
  residues processed: 108
  average time/residue: 1.3312
  time to fit residues: 154.0659
Evaluate side-chains
  104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 111 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0370
   chunk 114 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.4656

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.134244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.093811 restraints weight = 12067.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.41
r_work: 0.2953 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9737  Z= 0.190
  Angle     :  0.492  10.033  13187  Z= 0.250
  Chirality :  0.042   0.189   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  4.970  60.771   1304
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.82 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.16 (0.25), residues: 1200
  helix:  1.61 (0.24), residues: 498
  sheet:  0.76 (0.38), residues: 188
  loop :  0.04 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.021   0.001   TYR C 127 
 ARG   0.006   0.000   ARG C 139 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8211 (pt0) cc_final: 0.7854 (mp-120)
REVERT: A  221 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (tp)
REVERT: A  442 MET cc_start: 0.8089 (tpp) cc_final: 0.7789 (tpp)
REVERT: A  540 GLU cc_start: 0.7847 (tt0) cc_final: 0.7431 (mp0)
REVERT: A  583 GLN cc_start: 0.8347 (mt0) cc_final: 0.7370 (mm-40)
REVERT: A  614 GLU cc_start: 0.7269 (tp30) cc_final: 0.6499 (tm-30)
REVERT: A  619 GLN cc_start: 0.7487 (tp40) cc_final: 0.6797 (tm-30)
REVERT: A  811 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5776 (tp30)
REVERT: A  840 ASP cc_start: 0.7424 (p0) cc_final: 0.7152 (p0)
REVERT: A  913 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7019 (mp)
REVERT: B   51 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: B   60 ASN cc_start: 0.8407 (m-40) cc_final: 0.8124 (t0)
REVERT: C   32 HIS cc_start: 0.7553 (t-170) cc_final: 0.7239 (t70)
REVERT: C   72 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8206 (mmm-85)
  outliers start: 13
  outliers final: 9
  residues processed: 107
  average time/residue: 1.5665
  time to fit residues: 178.9118
Evaluate side-chains
  105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  286 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.132955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.092183 restraints weight = 12252.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.48
r_work: 0.2925 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9737  Z= 0.276
  Angle     :  0.521  10.580  13187  Z= 0.265
  Chirality :  0.043   0.199   1471
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.056  62.143   1304
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 13.20 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.25), residues: 1200
  helix:  1.55 (0.24), residues: 498
  sheet:  0.77 (0.38), residues: 187
  loop : -0.01 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 818 
 PHE   0.011   0.001   PHE A1007 
 TYR   0.022   0.001   TYR C 127 
 ARG   0.005   0.000   ARG A 841 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  105 GLN cc_start: 0.8200 (pt0) cc_final: 0.7849 (mp-120)
REVERT: A  221 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: A  442 MET cc_start: 0.8073 (tpp) cc_final: 0.7778 (tpp)
REVERT: A  540 GLU cc_start: 0.7847 (tt0) cc_final: 0.7401 (mp0)
REVERT: A  583 GLN cc_start: 0.8339 (mt0) cc_final: 0.7352 (mm-40)
REVERT: A  614 GLU cc_start: 0.7301 (tp30) cc_final: 0.6544 (tm-30)
REVERT: A  619 GLN cc_start: 0.7476 (tp40) cc_final: 0.6738 (tm-30)
REVERT: A  811 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5762 (tp30)
REVERT: A  840 ASP cc_start: 0.7385 (p0) cc_final: 0.7117 (p0)
REVERT: A  913 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7092 (mp)
REVERT: B   51 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: B   60 ASN cc_start: 0.8415 (m-40) cc_final: 0.8133 (t0)
REVERT: C   32 HIS cc_start: 0.7554 (t-170) cc_final: 0.7242 (t70)
REVERT: C   72 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8204 (mmm-85)
  outliers start: 10
  outliers final: 7
  residues processed: 103
  average time/residue: 1.4453
  time to fit residues: 159.4426
Evaluate side-chains
  103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0570
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 97 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0050
   overall best weight:    0.3512

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.134342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.093690 restraints weight = 12139.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.48
r_work: 0.2949 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9737  Z= 0.164
  Angle     :  0.491  10.116  13187  Z= 0.250
  Chirality :  0.041   0.190   1471
  Planarity :  0.004   0.047   1709
  Dihedral  :  4.952  58.675   1304
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.10 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.18 (0.25), residues: 1200
  helix:  1.63 (0.24), residues: 498
  sheet:  0.80 (0.38), residues: 187
  loop :  0.02 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 819 
 PHE   0.011   0.001   PHE A 842 
 TYR   0.022   0.001   TYR C 127 
 ARG   0.005   0.000   ARG A 841 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 7013.70 seconds
wall clock time: 122 minutes 27.08 seconds (7347.08 seconds total)