Starting phenix.real_space_refine
on Sat Jul 26 01:23:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v0v_21003/07_2025/6v0v_21003.cif"
  }
  resolution = 3.61
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P      60      5.49       5
     S      51      5.16       5
     C    5002      2.51       5
     N    1428      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4286
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 516}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2673
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "F"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 617
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "I"
      Number of atoms: 613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 613
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2016  SG  CYS A 727      70.241  55.803  61.715  1.00 82.81           S
  ATOM   2037  SG  CYS A 730      72.316  58.531  60.217  1.00 86.87           S

  Time building chain proxies: 5.74, per 1000 atoms: 0.70
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (107.06, 95.4, 118.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      51     16.00
     P      60     15.00
     O    1648      8.00
     N    1428      7.00
     C    5002      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: 2.16
  Conformation dependent library (CDL) restraints added in 761.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1103 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 937 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 942 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 730 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 727 "
      Number of angles added : 2


  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1662

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      33.8% alpha, 25.0% beta
      28 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 3.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 463 through 474
      removed outlier: 3.849A  pdb=" N   CYS A 467 " --> pdb=" O   GLN A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 493
    Processing helix  chain 'A' and resid 499 through 511
      removed outlier: 3.670A  pdb=" N   ALA A 506 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A 508 " --> pdb=" O   ARG A 504 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   VAL A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 570
      removed outlier: 3.603A  pdb=" N   SER A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'A' and resid 664 through 682
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 708 through 716
      removed outlier: 3.579A  pdb=" N   GLU A 716 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 738
    Processing helix  chain 'A' and resid 750 through 763
    Processing helix  chain 'A' and resid 768 through 776
    Processing helix  chain 'A' and resid 793 through 814
      removed outlier: 3.964A  pdb=" N   GLY A 813 " --> pdb=" O   GLN A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 841
    Processing helix  chain 'A' and resid 850 through 858
      removed outlier: 4.005A  pdb=" N   MET A 858 " --> pdb=" O   ALA A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 870
      removed outlier: 3.548A  pdb=" N   VAL A 863 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 890
      removed outlier: 3.769A  pdb=" N   GLU A 877 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 895
    Processing helix  chain 'A' and resid 897 through 902
      removed outlier: 3.843A  pdb=" N   CYS A 902 " --> pdb=" O   PRO A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 924
      removed outlier: 5.330A  pdb=" N   SER A 910 " --> pdb=" O   LEU A 906 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   PHE A 911 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE A 916 " --> pdb=" O   ASN A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 942
      removed outlier: 3.904A  pdb=" N   HIS A 937 " --> pdb=" O   THR A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 950
      removed outlier: 3.787A  pdb=" N   GLU A 948 " --> pdb=" O   PRO A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 964
    Processing helix  chain 'A' and resid 964 through 975
      removed outlier: 3.567A  pdb=" N   PHE A 968 " --> pdb=" O   GLY A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.815A  pdb=" N   VAL A 987 " --> pdb=" O   GLU A 983 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU A 988 " --> pdb=" O   MET A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1001
    Processing helix  chain 'A' and resid 1002 through 1005
    Processing helix  chain 'B' and resid 11 through 15
      removed outlier: 4.008A  pdb=" N   LEU B  14 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   PHE A 624 " --> pdb=" O   PRO A 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ILE A 631 " --> pdb=" O   LYS A 639 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LYS A 639 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS A 633 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASN A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6
      removed outlier: 4.650A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24
      removed outlier: 4.147A  pdb=" N   VAL B  28 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP B  49 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62
      removed outlier: 7.102A  pdb=" N   ILE B  61 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   CYS B 124 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LYS B 119 " --> pdb=" O   LYS B 115 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LYS B 115 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   THR B 121 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131
      removed outlier: 6.722A  pdb=" N   VAL B 130 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   SER B 194 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212
      removed outlier: 4.540A  pdb=" N   LEU B 233 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267
      removed outlier: 3.809A  pdb=" N   ILE B 262 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 266 " --> pdb=" O   GLU B 270 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLU B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 2.55 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: 2196
        1.33 -     1.45: 2147
        1.45 -     1.58: 3960
        1.58 -     1.70: 117
        1.70 -     1.82: 78
  Bond restraints: 8498
  Sorted by residual:
  bond pdb=" O3'  DT F  29 "
       pdb=" P    DG F  30 "
    ideal  model  delta    sigma   weight residual
    1.607  1.562  0.045 1.50e-02 4.44e+03 9.15e+00
  bond pdb=" CA  LEU A 735 "
       pdb=" C   LEU A 735 "
    ideal  model  delta    sigma   weight residual
    1.522  1.484  0.038 1.37e-02 5.33e+03 7.83e+00
  bond pdb=" N   MET A 847 "
       pdb=" CA  MET A 847 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.24e-02 6.50e+03 6.22e+00
  bond pdb=" C   PRO A 654 "
       pdb=" N   LEU A 655 "
    ideal  model  delta    sigma   weight residual
    1.331  1.299  0.033 1.40e-02 5.10e+03 5.47e+00
  bond pdb=" C3'  DG I   6 "
       pdb=" O3'  DG I   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.491 -0.069 3.00e-02 1.11e+03 5.34e+00
  ... (remaining 8493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 11497
        2.76 -     5.53: 234
        5.53 -     8.29: 22
        8.29 -    11.06: 4
       11.06 -    13.82: 1
  Bond angle restraints: 11758
  Sorted by residual:
  angle pdb=" C4'  DT F  29 "
        pdb=" C3'  DT F  29 "
        pdb=" O3'  DT F  29 "
      ideal   model   delta    sigma   weight residual
     110.00   96.18   13.82 1.50e+00 4.44e-01 8.49e+01
  angle pdb=" C2'  DC F  26 "
        pdb=" C1'  DC F  26 "
        pdb=" N1   DC F  26 "
      ideal   model   delta    sigma   weight residual
     113.50  120.36   -6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" C   ARG B 212 "
        pdb=" N   ASN B 213 "
        pdb=" CA  ASN B 213 "
      ideal   model   delta    sigma   weight residual
     121.54  130.19   -8.65 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" C4'  DT F  27 "
        pdb=" C3'  DT F  27 "
        pdb=" O3'  DT F  27 "
      ideal   model   delta    sigma   weight residual
     110.00  103.31    6.69 1.50e+00 4.44e-01 1.99e+01
  angle pdb=" C3'  DG I   6 "
        pdb=" O3'  DG I   6 "
        pdb=" P    DG I   7 "
      ideal   model   delta    sigma   weight residual
     120.20  125.96   -5.76 1.50e+00 4.44e-01 1.47e+01
  ... (remaining 11753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 4578
       35.36 -    70.72: 347
       70.72 -   106.09: 9
      106.09 -   141.45: 1
      141.45 -   176.81: 2
  Dihedral angle restraints: 4937
    sinusoidal: 2358
      harmonic: 2579
  Sorted by residual:
  dihedral pdb=" CA  ARG B 212 "
           pdb=" C   ARG B 212 "
           pdb=" N   ASN B 213 "
           pdb=" CA  ASN B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  CYS B  41 "
           pdb=" C   CYS B  41 "
           pdb=" N   PRO B  42 "
           pdb=" CA  PRO B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.91  -22.09     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  PRO A 871 "
           pdb=" C   PRO A 871 "
           pdb=" N   SER A 872 "
           pdb=" CA  SER A 872 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.23  -21.77     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 4934 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1013
       0.065 -    0.129: 244
       0.129 -    0.194: 33
       0.194 -    0.259: 6
       0.259 -    0.323: 2
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" C1'  DC F  26 "
            pdb=" O4'  DC F  26 "
            pdb=" C2'  DC F  26 "
            pdb=" N1   DC F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.15    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CB  VAL A 943 "
            pdb=" CA  VAL A 943 "
            pdb=" CG1 VAL A 943 "
            pdb=" CG2 VAL A 943 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL B   8 "
            pdb=" CA  VAL B   8 "
            pdb=" CG1 VAL B   8 "
            pdb=" CG2 VAL B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1295 not shown)

  Planarity restraints: 1303
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  26 "    0.095 2.00e-02 2.50e+03   4.30e-02 4.17e+01
        pdb=" N1   DC F  26 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2   DC F  26 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2   DC F  26 "   -0.030 2.00e-02 2.50e+03
        pdb=" N3   DC F  26 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DC F  26 "    0.009 2.00e-02 2.50e+03
        pdb=" N4   DC F  26 "    0.044 2.00e-02 2.50e+03
        pdb=" C5   DC F  26 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6   DC F  26 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 212 "    0.015 2.00e-02 2.50e+03   3.09e-02 9.57e+00
        pdb=" C   ARG B 212 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B 212 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 213 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO B  99 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1300 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 83
        2.53 -     3.12: 5775
        3.12 -     3.71: 13865
        3.71 -     4.31: 18150
        4.31 -     4.90: 28488
  Nonbonded interactions: 66361
  Sorted by model distance:
  nonbonded pdb=" OP1  DC I  17 "
            pdb="CA    CA A1102 "
     model   vdw
     1.932 2.510
  nonbonded pdb=" OE1 GLU A 962 "
            pdb="CA    CA A1102 "
     model   vdw
     2.026 2.510
  nonbonded pdb=" OD1 ASP A 600 "
            pdb="CA    CA A1101 "
     model   vdw
     2.193 2.510
  nonbonded pdb=" OE2 GLU A 803 "
            pdb=" OH  TYR A 928 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   SER A 958 "
            pdb=" OG  SER A 958 "
     model   vdw
     2.266 3.040
  ... (remaining 66356 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     28.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.008   0.156   8502  Z= 0.373
  Angle     :  1.101  46.250  11760  Z= 0.584
  Chirality :  0.057   0.323   1298
  Planarity :  0.007   0.075   1303
  Dihedral  : 21.033 176.809   3275
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.28 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.88 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -3.85 (0.23), residues: 879
  helix: -2.89 (0.22), residues: 271
  sheet: -1.77 (0.40), residues: 158
  loop : -2.63 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 893 
 HIS   0.008   0.002   HIS B  47 
 PHE   0.035   0.003   PHE A 804 
 TYR   0.016   0.002   TYR A 805 
 ARG   0.006   0.001   ARG A 696 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14331 (  359)
  hydrogen bonds       : angle       7.42489 (  977)
  metal coordination   : bond        0.10255 (    4)
  metal coordination   : angle      34.40681 (    2)
  covalent geometry    : bond        0.00772 ( 8498)
  covalent geometry    : angle       1.00539 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: A  753 ASN cc_start: 0.8184 (t0) cc_final: 0.6963 (t0)
REVERT: A  857 LEU cc_start: 0.9194 (mt) cc_final: 0.8898 (tt)
REVERT: B   24 PHE cc_start: 0.6579 (m-10) cc_final: 0.6234 (m-80)
REVERT: B   80 TYR cc_start: 0.7482 (t80) cc_final: 0.6994 (t80)
REVERT: B   90 GLN cc_start: 0.8212 (pt0) cc_final: 0.7827 (pt0)
REVERT: B  269 ASP cc_start: 0.6285 (t0) cc_final: 0.6067 (t0)
REVERT: B  281 ASN cc_start: 0.7903 (p0) cc_final: 0.7451 (p0)
REVERT: B  313 HIS cc_start: 0.8340 (t70) cc_final: 0.7986 (t-90)
  outliers start: 3
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2086
  time to fit residues: 39.1671
Evaluate side-chains
  80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0010
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS
A 800 ASN
A 820 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 267 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.087579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.066308 restraints weight = 24792.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.068125 restraints weight = 13663.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.069306 restraints weight = 9493.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8502  Z= 0.144
  Angle     :  0.645   9.919  11760  Z= 0.349
  Chirality :  0.042   0.164   1298
  Planarity :  0.005   0.058   1303
  Dihedral  : 23.607 176.020   1618
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.62 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -2.32 (0.26), residues: 879
  helix: -1.12 (0.29), residues: 272
  sheet: -0.77 (0.41), residues: 164
  loop : -2.12 (0.25), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 937 
 PHE   0.032   0.002   PHE A 804 
 TYR   0.012   0.001   TYR A 757 
 ARG   0.006   0.001   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  359)
  hydrogen bonds       : angle       5.08595 (  977)
  metal coordination   : bond        0.00927 (    4)
  metal coordination   : angle       7.01897 (    2)
  covalent geometry    : bond        0.00318 ( 8498)
  covalent geometry    : angle       0.63857 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: A  841 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7943 (mmp)
REVERT: A  919 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8193 (tt)
REVERT: B   80 TYR cc_start: 0.7645 (t80) cc_final: 0.7368 (t80)
REVERT: B   90 GLN cc_start: 0.8161 (pt0) cc_final: 0.7783 (pt0)
REVERT: B  313 HIS cc_start: 0.8480 (t70) cc_final: 0.8180 (t-90)
  outliers start: 14
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1902
  time to fit residues: 31.2057
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 GLU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue  272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 83 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A 842 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.087149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.065408 restraints weight = 24749.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.067236 restraints weight = 13681.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068428 restraints weight = 9517.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8502  Z= 0.134
  Angle     :  0.616   9.539  11760  Z= 0.329
  Chirality :  0.041   0.162   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.333 175.363   1618
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.87 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.58 (0.27), residues: 879
  helix: -0.32 (0.31), residues: 273
  sheet: -0.47 (0.41), residues: 173
  loop : -1.76 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 317 
 HIS   0.002   0.001   HIS A 937 
 PHE   0.036   0.002   PHE A 804 
 TYR   0.012   0.001   TYR A 757 
 ARG   0.006   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  359)
  hydrogen bonds       : angle       4.64656 (  977)
  metal coordination   : bond        0.00513 (    4)
  metal coordination   : angle       3.89757 (    2)
  covalent geometry    : bond        0.00301 ( 8498)
  covalent geometry    : angle       0.61400 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8043 (ttm) cc_final: 0.7636 (ttm)
REVERT: A  576 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: A  657 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8522 (pp)
REVERT: A  760 TRP cc_start: 0.8832 (OUTLIER) cc_final: 0.8438 (t-100)
REVERT: A  887 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9079 (mp)
REVERT: A  919 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8155 (tt)
REVERT: A  961 ASN cc_start: 0.6879 (t0) cc_final: 0.6597 (t0)
REVERT: A  965 ASN cc_start: 0.8024 (m-40) cc_final: 0.7709 (m110)
REVERT: B   80 TYR cc_start: 0.7725 (t80) cc_final: 0.7426 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1916
  time to fit residues: 26.3584
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0980
   chunk 83 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.087043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.065229 restraints weight = 24481.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.067066 restraints weight = 13515.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068248 restraints weight = 9384.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8502  Z= 0.131
  Angle     :  0.594   8.150  11760  Z= 0.321
  Chirality :  0.041   0.163   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.219 175.954   1618
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.33 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.04 (0.28), residues: 879
  helix:  0.20 (0.32), residues: 269
  sheet: -0.09 (0.41), residues: 173
  loop : -1.52 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 317 
 HIS   0.002   0.001   HIS A 937 
 PHE   0.038   0.001   PHE A 804 
 TYR   0.010   0.001   TYR A 757 
 ARG   0.005   0.000   ARG A 848 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  359)
  hydrogen bonds       : angle       4.45171 (  977)
  metal coordination   : bond        0.00393 (    4)
  metal coordination   : angle       3.36316 (    2)
  covalent geometry    : bond        0.00292 ( 8498)
  covalent geometry    : angle       0.59265 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8078 (ttm) cc_final: 0.7756 (ttm)
REVERT: A  576 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8081 (tm-30)
REVERT: A  760 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.8450 (t-100)
REVERT: A  849 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6552 (mtm)
REVERT: A  883 MET cc_start: 0.8233 (tpt) cc_final: 0.8023 (tpp)
REVERT: A  919 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8166 (tt)
REVERT: B   80 TYR cc_start: 0.7749 (t80) cc_final: 0.7491 (t80)
  outliers start: 24
  outliers final: 9
  residues processed: 96
  average time/residue: 0.2011
  time to fit residues: 30.0198
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 750 HIS
A 852 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN
B  33 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.083900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.061953 restraints weight = 24404.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.063666 restraints weight = 13861.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.064784 restraints weight = 9804.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8502  Z= 0.174
  Angle     :  0.655  10.586  11760  Z= 0.344
  Chirality :  0.042   0.193   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.255 175.975   1618
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.12 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.28), residues: 879
  helix:  0.29 (0.33), residues: 270
  sheet:  0.39 (0.43), residues: 152
  loop : -1.39 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 317 
 HIS   0.005   0.001   HIS A 515 
 PHE   0.043   0.002   PHE A 804 
 TYR   0.010   0.001   TYR A 757 
 ARG   0.005   0.001   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  359)
  hydrogen bonds       : angle       4.47641 (  977)
  metal coordination   : bond        0.00723 (    4)
  metal coordination   : angle       4.63751 (    2)
  covalent geometry    : bond        0.00396 ( 8498)
  covalent geometry    : angle       0.65269 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: A  760 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.8688 (t-100)
REVERT: A  844 LYS cc_start: 0.6641 (mmtt) cc_final: 0.5924 (tttp)
REVERT: A  919 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: B  170 GLU cc_start: 0.8079 (mp0) cc_final: 0.7874 (mp0)
REVERT: B  280 GLU cc_start: 0.7980 (pm20) cc_final: 0.7707 (pm20)
  outliers start: 21
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1837
  time to fit residues: 25.1876
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.084151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.062095 restraints weight = 24680.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063869 restraints weight = 13569.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.065024 restraints weight = 9431.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8502  Z= 0.156
  Angle     :  0.638  10.180  11760  Z= 0.331
  Chirality :  0.042   0.179   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.227 177.981   1618
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.84 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.28), residues: 879
  helix:  0.47 (0.33), residues: 269
  sheet:  0.59 (0.43), residues: 150
  loop : -1.23 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.040   0.002   PHE A 804 
 TYR   0.009   0.001   TYR A 805 
 ARG   0.004   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  359)
  hydrogen bonds       : angle       4.37853 (  977)
  metal coordination   : bond        0.00675 (    4)
  metal coordination   : angle       2.72371 (    2)
  covalent geometry    : bond        0.00355 ( 8498)
  covalent geometry    : angle       0.63666 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  485 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8348 (t80)
REVERT: A  568 MET cc_start: 0.8702 (ttm) cc_final: 0.8361 (ttm)
REVERT: A  576 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: A  760 TRP cc_start: 0.8978 (OUTLIER) cc_final: 0.8606 (t-100)
REVERT: A  843 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: A  844 LYS cc_start: 0.6507 (mmtt) cc_final: 0.6082 (tttp)
REVERT: A  919 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8199 (tt)
REVERT: B  280 GLU cc_start: 0.7937 (pm20) cc_final: 0.7653 (pm20)
REVERT: B  302 MET cc_start: 0.7871 (mmm) cc_final: 0.7667 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1690
  time to fit residues: 21.9425
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 71 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 836 HIS
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.083484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.061643 restraints weight = 24638.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.063342 restraints weight = 13767.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.064443 restraints weight = 9665.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8502  Z= 0.164
  Angle     :  0.642  12.090  11760  Z= 0.336
  Chirality :  0.042   0.180   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.242 177.927   1618
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.84 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.28), residues: 879
  helix:  0.57 (0.33), residues: 269
  sheet:  0.60 (0.43), residues: 156
  loop : -1.14 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.039   0.002   PHE A 804 
 TYR   0.010   0.001   TYR A 805 
 ARG   0.006   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  359)
  hydrogen bonds       : angle       4.32579 (  977)
  metal coordination   : bond        0.00654 (    4)
  metal coordination   : angle       3.13247 (    2)
  covalent geometry    : bond        0.00375 ( 8498)
  covalent geometry    : angle       0.64075 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: A  760 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8800 (t-100)
REVERT: A  844 LYS cc_start: 0.6587 (mmtt) cc_final: 0.6021 (tttp)
REVERT: A  919 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: B  199 GLU cc_start: 0.7384 (mp0) cc_final: 0.7148 (mp0)
REVERT: B  280 GLU cc_start: 0.7973 (pm20) cc_final: 0.7738 (pm20)
REVERT: B  302 MET cc_start: 0.8001 (mmm) cc_final: 0.7758 (mmm)
REVERT: B  322 MET cc_start: 0.8666 (mtm) cc_final: 0.8028 (mpp)
  outliers start: 22
  outliers final: 15
  residues processed: 83
  average time/residue: 0.1622
  time to fit residues: 20.1471
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 64 optimal weight:    0.3980
   chunk 71 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.084378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062196 restraints weight = 25011.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.063982 restraints weight = 13639.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.065152 restraints weight = 9462.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8502  Z= 0.146
  Angle     :  0.639  12.800  11760  Z= 0.331
  Chirality :  0.042   0.177   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.190 178.670   1618
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.50 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.29), residues: 879
  helix:  0.61 (0.34), residues: 269
  sheet:  0.59 (0.43), residues: 161
  loop : -1.15 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.037   0.002   PHE A 804 
 TYR   0.019   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  359)
  hydrogen bonds       : angle       4.32314 (  977)
  metal coordination   : bond        0.00436 (    4)
  metal coordination   : angle       2.31946 (    2)
  covalent geometry    : bond        0.00332 ( 8498)
  covalent geometry    : angle       0.63857 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: A  760 TRP cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (t-100)
REVERT: A  844 LYS cc_start: 0.6931 (mmtt) cc_final: 0.5837 (tttp)
REVERT: A  919 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8242 (tt)
REVERT: B  280 GLU cc_start: 0.7930 (pm20) cc_final: 0.7709 (pm20)
REVERT: B  302 MET cc_start: 0.8148 (mmm) cc_final: 0.7908 (mmm)
REVERT: B  322 MET cc_start: 0.8674 (mtm) cc_final: 0.8057 (mpp)
  outliers start: 19
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1806
  time to fit residues: 22.2544
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 57 optimal weight:    0.4980
   chunk 92 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.083497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.061508 restraints weight = 25176.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.063284 restraints weight = 13844.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.064394 restraints weight = 9601.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8502  Z= 0.159
  Angle     :  0.643  12.829  11760  Z= 0.335
  Chirality :  0.042   0.177   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.194 178.364   1618
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.24 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.29), residues: 879
  helix:  0.64 (0.33), residues: 267
  sheet:  0.47 (0.42), residues: 168
  loop : -1.12 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.036   0.002   PHE A 804 
 TYR   0.021   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  359)
  hydrogen bonds       : angle       4.34586 (  977)
  metal coordination   : bond        0.00596 (    4)
  metal coordination   : angle       3.01965 (    2)
  covalent geometry    : bond        0.00364 ( 8498)
  covalent geometry    : angle       0.64220 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: A  760 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8795 (t-100)
REVERT: A  844 LYS cc_start: 0.6989 (mmtt) cc_final: 0.5827 (tttp)
REVERT: A  919 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8221 (tt)
REVERT: B  280 GLU cc_start: 0.7942 (pm20) cc_final: 0.7711 (pm20)
REVERT: B  302 MET cc_start: 0.8183 (mmm) cc_final: 0.7845 (mmm)
REVERT: B  322 MET cc_start: 0.8707 (mtm) cc_final: 0.8059 (mpp)
  outliers start: 21
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1857
  time to fit residues: 22.3376
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0570
   chunk 11 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.3502

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.082437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.060548 restraints weight = 24858.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.062248 restraints weight = 13949.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.063353 restraints weight = 9810.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8502  Z= 0.188
  Angle     :  0.676  13.412  11760  Z= 0.350
  Chirality :  0.043   0.179   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.261 178.421   1618
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.50 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.28), residues: 879
  helix:  0.41 (0.32), residues: 277
  sheet:  0.66 (0.43), residues: 161
  loop : -1.30 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 795 
 PHE   0.035   0.002   PHE A 804 
 TYR   0.024   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  359)
  hydrogen bonds       : angle       4.44567 (  977)
  metal coordination   : bond        0.00837 (    4)
  metal coordination   : angle       3.43836 (    2)
  covalent geometry    : bond        0.00431 ( 8498)
  covalent geometry    : angle       0.67432 (11758)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A  844 LYS cc_start: 0.6895 (mmtt) cc_final: 0.5734 (tttp)
REVERT: A  919 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8309 (tt)
REVERT: B  280 GLU cc_start: 0.7951 (pm20) cc_final: 0.7700 (pm20)
REVERT: B  302 MET cc_start: 0.8208 (mmm) cc_final: 0.7947 (mmm)
REVERT: B  322 MET cc_start: 0.8718 (mtm) cc_final: 0.8061 (mpp)
  outliers start: 20
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1686
  time to fit residues: 20.8019
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 83 optimal weight:    7.9990
   chunk 84 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 92 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0370
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 501 HIS
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.084572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.062431 restraints weight = 24908.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.064261 restraints weight = 13479.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065432 restraints weight = 9287.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8502  Z= 0.134
  Angle     :  0.633  13.024  11760  Z= 0.331
  Chirality :  0.042   0.186   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.155 179.642   1618
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.56 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.29), residues: 879
  helix:  0.70 (0.33), residues: 267
  sheet:  0.54 (0.41), residues: 171
  loop : -1.08 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.036   0.002   PHE A 804 
 TYR   0.020   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 838 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03325 (  359)
  hydrogen bonds       : angle       4.36471 (  977)
  metal coordination   : bond        0.00328 (    4)
  metal coordination   : angle       1.38122 (    2)
  covalent geometry    : bond        0.00307 ( 8498)
  covalent geometry    : angle       0.63262 (11758)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2839.45 seconds
wall clock time: 51 minutes 24.97 seconds (3084.97 seconds total)