Starting phenix.real_space_refine
on Sun Jun 15 11:03:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qxb_14197/06_2025/7qxb_14197.cif"
  }
  resolution = 3.9
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     277      5.49       5
     S      42      5.16       5
     C    9714      2.51       5
     N    3124      2.21       5
     O    3896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 117 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17053
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 951, 7626
          Classifications: {'peptide': 951}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 893}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 5431
          Classifications: {'RNA': 256}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 99, 'rna3p_pyr': 124}
          Link IDs: {'rna2p': 33, 'rna3p': 222}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 643
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "M"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "N"
      Number of atoms: 461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 461
          Classifications: {'DNA': 22}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 21}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 955
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1238
          Classifications: {'peptide': 251}
          Incomplete info: {'truncation_to_alanine': 226}
          Link IDs: {'PTRANS': 9, 'TRANS': 241}
          Chain breaks: 3
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 814
          Unresolved non-hydrogen angles: 1054
          Unresolved non-hydrogen dihedrals: 678
          Unresolved non-hydrogen chiralities: 88
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 13, 'GLU:plan': 7, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 420
  Time building chain proxies: 10.77, per 1000 atoms: 0.63
  Number of scatterers: 17053
  At special positions: 0
  Unit cell: (166.77, 128.62, 143.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P     277     15.00
     O    3896      8.00
     N    3124      7.00
     C    9714      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 982 " - pdb=" SG  CYS A1043 " distance=2.57

  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: 4.62
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2806

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 12 sheets defined
      50.9% alpha, 19.5% beta
      70 base pairs and 135 stacking pairs defined.
    Time for finding SS restraints: 7.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.742A  pdb=" N   ARG A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.559A  pdb=" N   LEU A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
    Processing helix  chain 'A' and resid 383 through 401
      removed outlier: 3.904A  pdb=" N   TRP A 387 " --> pdb=" O   PRO A 383 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG A 390 " --> pdb=" O   TYR A 386 " (cutoff:3.500A)
      Proline residue:  A 391  - end of helix
    Processing helix  chain 'A' and resid 404 through 413
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.554A  pdb=" N   GLN A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.666A  pdb=" N   VAL A 461 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.852A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.882A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 497 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
    Processing helix  chain 'A' and resid 530 through 551
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 3.786A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 3.792A  pdb=" N   ARG A 657 " --> pdb=" O   ARG A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
    Processing helix  chain 'A' and resid 682 through 688
      removed outlier: 3.742A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 699
    Processing helix  chain 'A' and resid 721 through 734
      removed outlier: 3.529A  pdb=" N   LEU A 725 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 835 through 854
      removed outlier: 3.719A  pdb=" N   THR A 839 " --> pdb=" O   SER A 835 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   LEU A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   LEU A 841 " --> pdb=" O   LEU A 837 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS A 852 " --> pdb=" O   ASP A 848 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 853 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 861
      removed outlier: 4.271A  pdb=" N   ASP A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 899 through 902
      removed outlier: 3.699A  pdb=" N   LYS A 902 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 899 through 902'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.521A  pdb=" N   ASN A 969 " --> pdb=" O   LYS A 965 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 980 " --> pdb=" O   GLY A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.704A  pdb=" N   LEU A 987 " --> pdb=" O   HIS A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1018
      removed outlier: 3.516A  pdb=" N   TYR A1010 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1028
      removed outlier: 3.504A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASN A1028 " --> pdb=" O   VAL A1025 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1024 through 1028'
    Processing helix  chain 'A' and resid 1029 through 1051
      removed outlier: 4.271A  pdb=" N   CYS A1043 " --> pdb=" O   THR A1039 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1085
      removed outlier: 3.758A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS A1081 " --> pdb=" O   ALA A1077 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ARG A1084 " --> pdb=" O   LEU A1080 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   HIS A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.618A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.150A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
    Processing helix  chain 'A' and resid 1124 through 1129
      removed outlier: 3.899A  pdb=" N   LYS A1128 " --> pdb=" O   PRO A1124 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   THR A1129 " --> pdb=" O   SER A1125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1124 through 1129'
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 38
      removed outlier: 3.826A  pdb=" N   ARG L  32 " --> pdb=" O   VAL L  28 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ARG L  33 " --> pdb=" O   GLY L  29 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG L  36 " --> pdb=" O   ARG L  32 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS L  37 " --> pdb=" O   ARG L  33 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 73
      removed outlier: 4.571A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL L  55 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LEU L  56 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR L  58 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU L  64 " --> pdb=" O   THR L  60 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA L  67 " --> pdb=" O   ILE L  63 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASP L  73 " --> pdb=" O   ASN L  69 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 90
      removed outlier: 3.816A  pdb=" N   LEU L  84 " --> pdb=" O   ILE L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 98
      removed outlier: 3.590A  pdb=" N   LEU L  97 " --> pdb=" O   GLU L  93 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 38 through 50
      removed outlier: 3.843A  pdb=" N   TYR M  43 " --> pdb=" O   SER M  39 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL M  45 " --> pdb=" O   TYR M  41 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 4.111A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL M  67 " --> pdb=" O   MET M  63 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE M  74 " --> pdb=" O   ILE M  70 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 4.149A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL M  99 " --> pdb=" O   ILE M  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU M 101 " --> pdb=" O   THR M  97 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 124
      removed outlier: 3.593A  pdb=" N   LYS M 109 " --> pdb=" O   GLY M 105 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS M 121 " --> pdb=" O   LYS M 117 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 98 through 104
    Processing helix  chain 'O' and resid 158 through 165
    Processing helix  chain 'O' and resid 169 through 173
    Processing helix  chain 'O' and resid 223 through 226
    Processing helix  chain 'O' and resid 227 through 238
    Processing helix  chain 'P' and resid 65 through 69
      removed outlier: 3.525A  pdb=" N   LEU P  69 " --> pdb=" O   TYR P  66 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 152 through 156
    Processing helix  chain 'P' and resid 206 through 214
      removed outlier: 3.529A  pdb=" N   GLN P 214 " --> pdb=" O   ILE P 210 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 215 through 217
      No H-bonds generated for 'chain 'P' and resid 215 through 217'
    Processing helix  chain 'P' and resid 225 through 232
      removed outlier: 4.198A  pdb=" N   VAL P 229 " --> pdb=" O   ASN P 225 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 269 through 273
    Processing helix  chain 'P' and resid 282 through 299
      removed outlier: 3.697A  pdb=" N   THR P 298 " --> pdb=" O   SER P 294 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 4.110A  pdb=" N   ALA A 167 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   GLU A 793 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 790 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   LEU A 798 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   TYR A 739 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 600
      removed outlier: 7.101A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE A 633 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 624 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY A 629 " --> pdb=" O   LYS A 626 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 865
    Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 44
      removed outlier: 7.850A  pdb=" N   ARG L  43 " --> pdb=" O   ILE M  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 122
      removed outlier: 6.832A  pdb=" N   LEU O 145 " --> pdb=" O   LEU O 118 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   VAL O 120 " --> pdb=" O   THR O 143 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   THR O 143 " --> pdb=" O   VAL O 120 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL O 206 " --> pdb=" O   CYS O 187 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   CYS O 187 " --> pdb=" O   VAL O 206 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ARG O 208 " --> pdb=" O   GLN O 185 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LEU O 181 " --> pdb=" O   LEU O 212 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG O 180 " --> pdb=" O   LEU O 117 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'P' and resid 21 through 37
      removed outlier: 6.728A  pdb=" N   THR P  48 " --> pdb=" O   LYS P  30 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE P  32 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL P  46 " --> pdb=" O   PHE P  32 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   CYS P  44 " --> pdb=" O   PRO P  34 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   THR P  93 " --> pdb=" O   LYS P  56 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   THR P  58 " --> pdb=" O   THR P  93 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   PHE P  62 " --> pdb=" O   THR P  97 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   SER P  99 " --> pdb=" O   PHE P  62 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ARG P  83 " --> pdb=" O   SER P  98 " (cutoff:3.500A)
      removed outlier: 11.364A  pdb=" N   GLY P 100 " --> pdb=" O   PHE P  81 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   PHE P  81 " --> pdb=" O   GLY P 100 " (cutoff:3.500A)
      removed outlier: 11.031A  pdb=" N   ALA P 102 " --> pdb=" O   VAL P  79 " (cutoff:3.500A)
      removed outlier: 9.775A  pdb=" N   VAL P  79 " --> pdb=" O   ALA P 102 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ILE P  78 " --> pdb=" O   VAL P  29 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL P  29 " --> pdb=" O   ILE P  78 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ARG P  80 " --> pdb=" O   GLY P  27 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   GLY P  27 " --> pdb=" O   ARG P  80 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   HIS P  82 " --> pdb=" O   VAL P  25 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL P  25 " --> pdb=" O   HIS P  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'P' and resid 204 through 205
      removed outlier: 6.580A  pdb=" N   LYS P 182 " --> pdb=" O   LEU P 169 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   LYS P 171 " --> pdb=" O   LEU P 180 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LEU P 180 " --> pdb=" O   LYS P 171 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLU P 173 " --> pdb=" O   SER P 178 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   SER P 178 " --> pdb=" O   GLU P 173 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   PHE P 263 " --> pdb=" O   ASP P 219 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE P 238 " --> pdb=" O   LEU P 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'P' and resid 204 through 205
      removed outlier: 5.081A  pdb=" N   PHE P 162 " --> pdb=" O   SER P 243 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE P 238 " --> pdb=" O   LEU P 278 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1596 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      186 hydrogen bonds
      352 hydrogen bond angles
      0 basepair planarities
      70 basepair parallelities
      135 stacking parallelities
  Total time for adding SS restraints: 10.70

  Time building geometry restraints manager: 5.46 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3290
        1.33 -     1.46: 5953
        1.46 -     1.59: 8201
        1.59 -     1.73: 445
        1.73 -     1.86: 55
  Bond restraints: 17944
  Sorted by residual:
  bond pdb=" N   SER A 586 "
       pdb=" CA  SER A 586 "
    ideal  model  delta    sigma   weight residual
    1.459  1.529 -0.070 1.20e-02 6.94e+03 3.38e+01
  bond pdb=" CE1 TYR A 638 "
       pdb=" CZ  TYR A 638 "
    ideal  model  delta    sigma   weight residual
    1.378  1.501 -0.123 2.40e-02 1.74e+03 2.64e+01
  bond pdb=" N   PHE A 544 "
       pdb=" CA  PHE A 544 "
    ideal  model  delta    sigma   weight residual
    1.459  1.402  0.057 1.17e-02 7.31e+03 2.40e+01
  bond pdb=" CA  VAL A1087 "
       pdb=" CB  VAL A1087 "
    ideal  model  delta    sigma   weight residual
    1.540  1.606 -0.066 1.36e-02 5.41e+03 2.38e+01
  bond pdb=" N   LEU A1082 "
       pdb=" CA  LEU A1082 "
    ideal  model  delta    sigma   weight residual
    1.458  1.518 -0.060 1.30e-02 5.92e+03 2.13e+01
  ... (remaining 17939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 24346
        2.98 -     5.97: 1204
        5.97 -     8.95: 98
        8.95 -    11.93: 8
       11.93 -    14.91: 3
  Bond angle restraints: 25659
  Sorted by residual:
  angle pdb=" O3'   C B 142 "
        pdb=" C3'   C B 142 "
        pdb=" C2'   C B 142 "
      ideal   model   delta    sigma   weight residual
     113.70  128.61  -14.91 1.50e+00 4.44e-01 9.88e+01
  angle pdb=" C4'   G B 300 "
        pdb=" C3'   G B 300 "
        pdb=" O3'   G B 300 "
      ideal   model   delta    sigma   weight residual
     109.40  122.48  -13.08 1.50e+00 4.44e-01 7.60e+01
  angle pdb=" N   ARG A1084 "
        pdb=" CA  ARG A1084 "
        pdb=" C   ARG A1084 "
      ideal   model   delta    sigma   weight residual
     111.14  119.63   -8.49 1.08e+00 8.57e-01 6.17e+01
  angle pdb=" C4'   C B 321 "
        pdb=" C3'   C B 321 "
        pdb=" O3'   C B 321 "
      ideal   model   delta    sigma   weight residual
     113.00  124.45  -11.45 1.50e+00 4.44e-01 5.83e+01
  angle pdb=" N   ASP A 516 "
        pdb=" CA  ASP A 516 "
        pdb=" C   ASP A 516 "
      ideal   model   delta    sigma   weight residual
     111.82  120.52   -8.70 1.16e+00 7.43e-01 5.62e+01
  ... (remaining 25654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.39: 10302
       34.39 -    68.78: 745
       68.78 -   103.17: 119
      103.17 -   137.56: 9
      137.56 -   171.95: 14
  Dihedral angle restraints: 11189
    sinusoidal: 6865
      harmonic: 4324
  Sorted by residual:
  dihedral pdb=" C5'   A B 176 "
           pdb=" C4'   A B 176 "
           pdb=" C3'   A B 176 "
           pdb=" O3'   A B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   71.59   75.41     1      8.00e+00 1.56e-02 1.12e+02
  dihedral pdb=" O4'   U B 194 "
           pdb=" C1'   U B 194 "
           pdb=" N1    U B 194 "
           pdb=" C2    U B 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   28.05  171.95     1      1.50e+01 4.44e-03 8.49e+01
  dihedral pdb=" O4'   U B 316 "
           pdb=" C1'   U B 316 "
           pdb=" N1    U B 316 "
           pdb=" C2    U B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.96  159.04     1      1.50e+01 4.44e-03 8.25e+01
  ... (remaining 11186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 2533
       0.118 -    0.236: 552
       0.236 -    0.354: 53
       0.354 -    0.472: 10
       0.472 -    0.590: 5
  Chirality restraints: 3153
  Sorted by residual:
  chirality pdb=" C3'   A B 176 "
            pdb=" C4'   A B 176 "
            pdb=" O3'   A B 176 "
            pdb=" C2'   A B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.15   -0.59 2.00e-01 2.50e+01 8.71e+00
  chirality pdb=" C3'   C B 142 "
            pdb=" C4'   C B 142 "
            pdb=" O3'   C B 142 "
            pdb=" C2'   C B 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.97   -0.51 2.00e-01 2.50e+01 6.49e+00
  chirality pdb=" C3'   G B 292 "
            pdb=" C4'   G B 292 "
            pdb=" O3'   G B 292 "
            pdb=" C2'   G B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.97   -0.50 2.00e-01 2.50e+01 6.34e+00
  ... (remaining 3150 not shown)

  Planarity restraints: 2272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  75 "   -0.220 2.00e-02 2.50e+03   1.00e-01 2.25e+02
        pdb=" N1    C B  75 "    0.114 2.00e-02 2.50e+03
        pdb=" C2    C B  75 "    0.058 2.00e-02 2.50e+03
        pdb=" O2    C B  75 "    0.055 2.00e-02 2.50e+03
        pdb=" N3    C B  75 "   -0.012 2.00e-02 2.50e+03
        pdb=" C4    C B  75 "   -0.057 2.00e-02 2.50e+03
        pdb=" N4    C B  75 "   -0.081 2.00e-02 2.50e+03
        pdb=" C5    C B  75 "    0.037 2.00e-02 2.50e+03
        pdb=" C6    C B  75 "    0.105 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 292 "    0.196 2.00e-02 2.50e+03   8.08e-02 1.96e+02
        pdb=" N9    G B 292 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8    G B 292 "   -0.079 2.00e-02 2.50e+03
        pdb=" N7    G B 292 "   -0.076 2.00e-02 2.50e+03
        pdb=" C5    G B 292 "   -0.035 2.00e-02 2.50e+03
        pdb=" C6    G B 292 "    0.046 2.00e-02 2.50e+03
        pdb=" O6    G B 292 "    0.112 2.00e-02 2.50e+03
        pdb=" N1    G B 292 "    0.036 2.00e-02 2.50e+03
        pdb=" C2    G B 292 "   -0.033 2.00e-02 2.50e+03
        pdb=" N2    G B 292 "   -0.020 2.00e-02 2.50e+03
        pdb=" N3    G B 292 "   -0.069 2.00e-02 2.50e+03
        pdb=" C4    G B 292 "   -0.067 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA N  27 "    0.193 2.00e-02 2.50e+03   7.96e-02 1.74e+02
        pdb=" N9   DA N  27 "   -0.041 2.00e-02 2.50e+03
        pdb=" C8   DA N  27 "   -0.067 2.00e-02 2.50e+03
        pdb=" N7   DA N  27 "   -0.051 2.00e-02 2.50e+03
        pdb=" C5   DA N  27 "   -0.023 2.00e-02 2.50e+03
        pdb=" C6   DA N  27 "    0.044 2.00e-02 2.50e+03
        pdb=" N6   DA N  27 "    0.095 2.00e-02 2.50e+03
        pdb=" N1   DA N  27 "    0.028 2.00e-02 2.50e+03
        pdb=" C2   DA N  27 "   -0.037 2.00e-02 2.50e+03
        pdb=" N3   DA N  27 "   -0.080 2.00e-02 2.50e+03
        pdb=" C4   DA N  27 "   -0.061 2.00e-02 2.50e+03
  ... (remaining 2269 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1283
        2.74 -     3.28: 16577
        3.28 -     3.82: 28842
        3.82 -     4.36: 35195
        4.36 -     4.90: 52349
  Nonbonded interactions: 134246
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 943 "
            pdb=" NZ  LYS A1003 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NZ  LYS A1027 "
            pdb=" OP1   U B 312 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OP2   C B 244 "
            pdb=" NH2 ARG L  43 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NH1 ARG A 481 "
            pdb=" OP2   C B 183 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   TRP A 510 "
            pdb=" O2'   C B 313 "
     model   vdw
     2.314 3.040
  ... (remaining 134241 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:             52.400
  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:             0.020
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     48.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  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:  105.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
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      :  0.011   0.535  17945  Z= 0.703
  Angle     :  1.487  36.960  25661  Z= 0.996
  Chirality :  0.096   0.590   3153
  Planarity :  0.011   0.118   2272
  Dihedral  : 22.182 171.949   8380
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.64 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.01 %
    Favored  : 95.52 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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: -2.07 (0.19), residues: 1466
  helix: -0.97 (0.18), residues: 591
  sheet: -1.19 (0.34), residues: 188
  loop : -1.71 (0.21), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.009   TRP A 510 
 HIS   0.014   0.004   HIS A1085 
 PHE   0.063   0.006   PHE A 331 
 TYR   0.068   0.009   TYR A 949 
 ARG   0.014   0.001   ARG O 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21906 (  746)
  hydrogen bonds       : angle       8.13514 ( 1948)
  SS BOND              : bond        0.53508 (    1)
  SS BOND              : angle      31.45145 (    2)
  covalent geometry    : bond        0.00987 (17944)
  covalent geometry    : angle       1.46121 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 224
  time to evaluate  : 1.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 PHE cc_start: 0.8758 (m-10) cc_final: 0.8284 (m-80)
REVERT: A  333 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (m-80)
REVERT: A  536 LEU cc_start: 0.9115 (tp) cc_final: 0.8914 (tp)
REVERT: A  656 SER cc_start: 0.8454 (t) cc_final: 0.7973 (m)
REVERT: A  850 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: A  899 ASN cc_start: 0.8334 (t0) cc_final: 0.8084 (t0)
REVERT: A  902 LYS cc_start: 0.8765 (mttt) cc_final: 0.8536 (tptt)
REVERT: L   89 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6194 (ptm-80)
REVERT: M   49 VAL cc_start: 0.7324 (m) cc_final: 0.7120 (m)
REVERT: M  117 LYS cc_start: 0.7704 (mttt) cc_final: 0.7326 (tppt)
REVERT: O  103 ILE cc_start: 0.7819 (mm) cc_final: 0.7476 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 227
  average time/residue: 0.4539
  time to fit residues: 148.2526
Evaluate side-chains
  125 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue 1074 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 148 optimal weight:   20.0000
   chunk 133 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 71 optimal weight:    0.1980
   chunk 137 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0470
   chunk 83 optimal weight:    0.9990
   chunk 102 optimal weight:    9.9990
   chunk 159 optimal weight:    2.9990
   overall best weight:    0.8282

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 330 HIS
A 482 HIS
A 700 GLN
A 969 ASN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  50 HIS
M  64 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.105605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.077536 restraints weight = 85796.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.079528 restraints weight = 41185.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.080800 restraints weight = 27033.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17945  Z= 0.152
  Angle     :  0.746   9.608  25661  Z= 0.384
  Chirality :  0.043   0.340   3153
  Planarity :  0.005   0.068   2272
  Dihedral  : 23.848 174.937   5971
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.55 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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: -0.09 (0.21), residues: 1466
  helix:  1.14 (0.20), residues: 617
  sheet: -0.50 (0.35), residues: 199
  loop : -1.06 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 581 
 HIS   0.008   0.001   HIS A 592 
 PHE   0.020   0.002   PHE M  71 
 TYR   0.023   0.002   TYR A 462 
 ARG   0.007   0.001   ARG O 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04987 (  746)
  hydrogen bonds       : angle       4.55498 ( 1948)
  SS BOND              : bond        0.01646 (    1)
  SS BOND              : angle       3.75479 (    2)
  covalent geometry    : bond        0.00308 (17944)
  covalent geometry    : angle       0.74520 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7584 (mpt180) cc_final: 0.7364 (mmt180)
REVERT: A  718 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7784 (p0)
REVERT: A  930 TRP cc_start: 0.7688 (t60) cc_final: 0.7244 (t60)
REVERT: L   40 TYR cc_start: 0.6708 (m-80) cc_final: 0.5725 (m-80)
REVERT: M   52 ASP cc_start: 0.8515 (t0) cc_final: 0.8094 (p0)
REVERT: M  122 TYR cc_start: 0.9015 (t80) cc_final: 0.8732 (t80)
REVERT: O  101 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7969 (tp30)
  outliers start: 19
  outliers final: 11
  residues processed: 158
  average time/residue: 0.3071
  time to fit residues: 71.8988
Evaluate side-chains
  114 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  718 ASP
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 157 optimal weight:    0.0570
   chunk 113 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 5 optimal weight:   30.0000
   overall best weight:    3.4106

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

Flipped N/Q/H residues before XYZ refinement:
A 388 GLN
A 585 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.100331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.072205 restraints weight = 88466.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.073927 restraints weight = 45786.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.074950 restraints weight = 31752.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  17945  Z= 0.206
  Angle     :  0.741   8.998  25661  Z= 0.384
  Chirality :  0.042   0.271   3153
  Planarity :  0.005   0.054   2272
  Dihedral  : 23.918 175.989   5969
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.02 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 13.07 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.21), residues: 1466
  helix:  1.17 (0.21), residues: 615
  sheet: -0.63 (0.36), residues: 194
  loop : -1.01 (0.23), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP O 167 
 HIS   0.007   0.002   HIS A 546 
 PHE   0.021   0.002   PHE A 575 
 TYR   0.025   0.003   TYR A 894 
 ARG   0.006   0.001   ARG L  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05661 (  746)
  hydrogen bonds       : angle       4.58058 ( 1948)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       2.53868 (    2)
  covalent geometry    : bond        0.00439 (17944)
  covalent geometry    : angle       0.74074 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 111
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 LEU cc_start: 0.6927 (mt) cc_final: 0.6689 (mp)
REVERT: A  412 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6691 (m-70)
REVERT: A  712 ASP cc_start: 0.7388 (m-30) cc_final: 0.7128 (m-30)
REVERT: A  749 LYS cc_start: 0.6819 (tptp) cc_final: 0.6551 (tptt)
REVERT: A  902 LYS cc_start: 0.8586 (tptt) cc_final: 0.8123 (tptt)
REVERT: L   24 LEU cc_start: 0.6801 (mm) cc_final: 0.6478 (mm)
REVERT: L   40 TYR cc_start: 0.7107 (m-80) cc_final: 0.6509 (m-80)
REVERT: L   52 LEU cc_start: 0.8602 (tp) cc_final: 0.8320 (mt)
REVERT: L   75 LYS cc_start: 0.7097 (tppt) cc_final: 0.6663 (tptt)
REVERT: M   52 ASP cc_start: 0.8617 (t0) cc_final: 0.8227 (p0)
  outliers start: 38
  outliers final: 21
  residues processed: 139
  average time/residue: 0.3086
  time to fit residues: 64.8035
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 154 optimal weight:   50.0000
   chunk 85 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    0.1980
   chunk 125 optimal weight:    0.3980
   chunk 83 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
A 775 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  85 GLN
M  64 ASN
M  96 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.103079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.074991 restraints weight = 88103.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.076850 restraints weight = 44125.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.077951 restraints weight = 29963.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17945  Z= 0.124
  Angle     :  0.622   9.666  25661  Z= 0.319
  Chirality :  0.038   0.248   3153
  Planarity :  0.004   0.046   2272
  Dihedral  : 23.798 174.209   5969
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.73 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.94 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.39 (0.22), residues: 1466
  helix:  1.55 (0.21), residues: 620
  sheet: -0.25 (0.35), residues: 202
  loop : -0.82 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 581 
 HIS   0.004   0.001   HIS L  83 
 PHE   0.025   0.002   PHE A 809 
 TYR   0.024   0.002   TYR A 462 
 ARG   0.006   0.000   ARG O 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (  746)
  hydrogen bonds       : angle       4.09369 ( 1948)
  SS BOND              : bond        0.00826 (    1)
  SS BOND              : angle       2.03777 (    2)
  covalent geometry    : bond        0.00251 (17944)
  covalent geometry    : angle       0.62197 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6705 (t80)
REVERT: A  749 LYS cc_start: 0.6773 (tptp) cc_final: 0.6501 (tptt)
REVERT: A  902 LYS cc_start: 0.8535 (tptt) cc_final: 0.8011 (tptt)
REVERT: A  970 MET cc_start: 0.7304 (ttm) cc_final: 0.6969 (ptm)
REVERT: L   40 TYR cc_start: 0.7012 (m-80) cc_final: 0.6385 (m-80)
REVERT: L   52 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (mt)
REVERT: L   75 LYS cc_start: 0.7174 (tppt) cc_final: 0.6806 (tptt)
REVERT: M   52 ASP cc_start: 0.8713 (t0) cc_final: 0.8417 (p0)
REVERT: M   64 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6679 (m110)
  outliers start: 29
  outliers final: 16
  residues processed: 129
  average time/residue: 0.3044
  time to fit residues: 59.5738
Evaluate side-chains
  112 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   64 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 125 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 133 optimal weight:   30.0000
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 164 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.100867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.072572 restraints weight = 90696.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.074444 restraints weight = 44978.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.075552 restraints weight = 30339.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17945  Z= 0.154
  Angle     :  0.637   9.763  25661  Z= 0.328
  Chirality :  0.038   0.230   3153
  Planarity :  0.004   0.045   2272
  Dihedral  : 23.817 173.174   5969
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.62 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.94 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.35 (0.22), residues: 1466
  helix:  1.48 (0.21), residues: 613
  sheet: -0.26 (0.36), residues: 201
  loop : -0.80 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 581 
 HIS   0.004   0.001   HIS A 534 
 PHE   0.018   0.002   PHE A 487 
 TYR   0.031   0.002   TYR A 462 
 ARG   0.005   0.000   ARG O 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04510 (  746)
  hydrogen bonds       : angle       4.16521 ( 1948)
  SS BOND              : bond        0.00686 (    1)
  SS BOND              : angle       2.21027 (    2)
  covalent geometry    : bond        0.00322 (17944)
  covalent geometry    : angle       0.63691 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6679 (t80)
REVERT: A  459 TRP cc_start: 0.6841 (OUTLIER) cc_final: 0.6047 (t60)
REVERT: A  902 LYS cc_start: 0.8730 (tptt) cc_final: 0.8489 (tptt)
REVERT: L   40 TYR cc_start: 0.6980 (m-80) cc_final: 0.6350 (m-80)
REVERT: L   43 ARG cc_start: 0.2518 (ttp-170) cc_final: 0.2278 (ttp-170)
REVERT: L   52 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: L   75 LYS cc_start: 0.7090 (tppt) cc_final: 0.6821 (tptt)
REVERT: M   52 ASP cc_start: 0.8838 (t0) cc_final: 0.8505 (p0)
REVERT: M  117 LYS cc_start: 0.7386 (ttmt) cc_final: 0.7105 (pptt)
  outliers start: 39
  outliers final: 26
  residues processed: 128
  average time/residue: 0.3060
  time to fit residues: 59.1592
Evaluate side-chains
  123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   25 GLN
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  183 LEU
Chi-restraints excluded: chain O residue  208 ARG
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 166 optimal weight:   50.0000
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 95 optimal weight:   30.0000
   chunk 45 optimal weight:    0.8980
   chunk 124 optimal weight:    8.9990
   chunk 116 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 152 optimal weight:   50.0000
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** 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 = 0.4314 r_free = 0.4314 target = 0.099488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.071468 restraints weight = 92307.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.073178 restraints weight = 48165.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.074127 restraints weight = 33508.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.5335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17945  Z= 0.180
  Angle     :  0.666   9.585  25661  Z= 0.342
  Chirality :  0.039   0.236   3153
  Planarity :  0.005   0.046   2272
  Dihedral  : 23.964 175.740   5969
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.30 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 14.94 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.06 (0.22), residues: 1466
  helix:  1.20 (0.21), residues: 612
  sheet: -0.33 (0.35), residues: 204
  loop : -0.93 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 581 
 HIS   0.006   0.002   HIS A1013 
 PHE   0.018   0.002   PHE A 575 
 TYR   0.023   0.002   TYR A 462 
 ARG   0.006   0.001   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04838 (  746)
  hydrogen bonds       : angle       4.29356 ( 1948)
  SS BOND              : bond        0.00599 (    1)
  SS BOND              : angle       2.16088 (    2)
  covalent geometry    : bond        0.00381 (17944)
  covalent geometry    : angle       0.66564 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 101
  time to evaluate  : 1.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6909 (t80)
REVERT: A  459 TRP cc_start: 0.6937 (OUTLIER) cc_final: 0.6195 (t60)
REVERT: A  593 LEU cc_start: 0.8519 (pp) cc_final: 0.8130 (tp)
REVERT: A  756 ARG cc_start: 0.8894 (mtp-110) cc_final: 0.8497 (mmp80)
REVERT: A  902 LYS cc_start: 0.8833 (tptt) cc_final: 0.8626 (tptt)
REVERT: L   40 TYR cc_start: 0.7384 (m-80) cc_final: 0.6874 (m-80)
REVERT: L   52 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8046 (mt)
REVERT: L   84 LEU cc_start: 0.8932 (mp) cc_final: 0.8447 (tp)
REVERT: M   52 ASP cc_start: 0.8856 (t0) cc_final: 0.8551 (p0)
REVERT: M  117 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6830 (pptt)
REVERT: M  122 TYR cc_start: 0.8974 (t80) cc_final: 0.8602 (t80)
REVERT: O  101 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8279 (pm20)
REVERT: O  162 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7066 (pp)
  outliers start: 46
  outliers final: 28
  residues processed: 133
  average time/residue: 0.3013
  time to fit residues: 61.3501
Evaluate side-chains
  122 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  959 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  162 LEU
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 161 optimal weight:   50.0000
   chunk 13 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 162 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 117 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0470
   chunk 23 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   overall best weight:    1.2682

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
A 736 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.102073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.073952 restraints weight = 91037.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.075768 restraints weight = 45930.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.077025 restraints weight = 31629.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  17945  Z= 0.118
  Angle     :  0.595   9.542  25661  Z= 0.303
  Chirality :  0.036   0.228   3153
  Planarity :  0.004   0.049   2272
  Dihedral  : 23.798 173.726   5969
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.21 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.81 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.51 (0.22), residues: 1466
  helix:  1.63 (0.22), residues: 611
  sheet: -0.12 (0.35), residues: 212
  loop : -0.74 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 581 
 HIS   0.004   0.001   HIS A1013 
 PHE   0.027   0.001   PHE A 809 
 TYR   0.010   0.001   TYR A 168 
 ARG   0.007   0.000   ARG O 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  746)
  hydrogen bonds       : angle       3.95285 ( 1948)
  SS BOND              : bond        0.00731 (    1)
  SS BOND              : angle       1.64300 (    2)
  covalent geometry    : bond        0.00243 (17944)
  covalent geometry    : angle       0.59518 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6613 (t80)
REVERT: A  593 LEU cc_start: 0.8480 (pp) cc_final: 0.8128 (tp)
REVERT: A  756 ARG cc_start: 0.8827 (mtp-110) cc_final: 0.8511 (mmp80)
REVERT: A  970 MET cc_start: 0.7224 (ttm) cc_final: 0.6888 (ptm)
REVERT: L   40 TYR cc_start: 0.7604 (m-80) cc_final: 0.7298 (m-80)
REVERT: M   52 ASP cc_start: 0.8719 (t0) cc_final: 0.8433 (p0)
REVERT: M  122 TYR cc_start: 0.8824 (t80) cc_final: 0.8460 (t80)
REVERT: O  101 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8300 (pm20)
REVERT: O  209 PHE cc_start: 0.8093 (p90) cc_final: 0.7633 (p90)
  outliers start: 29
  outliers final: 20
  residues processed: 125
  average time/residue: 0.2871
  time to fit residues: 55.1246
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 161 optimal weight:    2.9990
   chunk 170 optimal weight:    4.9990
   chunk 143 optimal weight:    4.9990
   chunk 156 optimal weight:   40.0000
   chunk 83 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 95 optimal weight:   30.0000
   chunk 122 optimal weight:    2.9990
   chunk 157 optimal weight:    6.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** 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 = 0.4321 r_free = 0.4321 target = 0.099809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.071769 restraints weight = 90959.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.073541 restraints weight = 46874.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.074481 restraints weight = 32361.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.5775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17945  Z= 0.164
  Angle     :  0.650   9.747  25661  Z= 0.331
  Chirality :  0.038   0.229   3153
  Planarity :  0.004   0.046   2272
  Dihedral  : 23.903 176.496   5969
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.96 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.62 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.22), residues: 1466
  helix:  1.39 (0.21), residues: 610
  sheet: -0.21 (0.35), residues: 214
  loop : -0.80 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 581 
 HIS   0.006   0.001   HIS L  83 
 PHE   0.016   0.002   PHE A 575 
 TYR   0.022   0.002   TYR A 552 
 ARG   0.005   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  746)
  hydrogen bonds       : angle       4.14219 ( 1948)
  SS BOND              : bond        0.00519 (    1)
  SS BOND              : angle       1.97365 (    2)
  covalent geometry    : bond        0.00347 (17944)
  covalent geometry    : angle       0.64957 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6801 (t80)
REVERT: A  593 LEU cc_start: 0.8533 (pp) cc_final: 0.8168 (tp)
REVERT: A  756 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8529 (mmp80)
REVERT: A  902 LYS cc_start: 0.8410 (tptt) cc_final: 0.8171 (tptt)
REVERT: L   40 TYR cc_start: 0.7408 (m-80) cc_final: 0.6909 (m-80)
REVERT: M   52 ASP cc_start: 0.8735 (t0) cc_final: 0.8453 (p0)
REVERT: M  122 TYR cc_start: 0.8949 (t80) cc_final: 0.8561 (t80)
REVERT: O  101 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8418 (pm20)
  outliers start: 33
  outliers final: 25
  residues processed: 124
  average time/residue: 0.2806
  time to fit residues: 53.3463
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 111 optimal weight:   40.0000
   chunk 84 optimal weight:    0.0170
   chunk 146 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 163 optimal weight:   50.0000
   chunk 29 optimal weight:    0.0030
   chunk 128 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 107 optimal weight:   30.0000
   chunk 121 optimal weight:    5.9990
   chunk 161 optimal weight:   40.0000
   overall best weight:    1.5632

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

Flipped N/Q/H residues before XYZ refinement:
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** 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 = 0.4354 r_free = 0.4354 target = 0.101563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.073631 restraints weight = 90977.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.075434 restraints weight = 45850.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.076458 restraints weight = 31307.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  17945  Z= 0.124
  Angle     :  0.619  12.614  25661  Z= 0.308
  Chirality :  0.037   0.225   3153
  Planarity :  0.004   0.049   2272
  Dihedral  : 23.794 175.953   5969
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.62 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.83 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.51 (0.22), residues: 1466
  helix:  1.55 (0.22), residues: 612
  sheet: -0.03 (0.36), residues: 212
  loop : -0.69 (0.25), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 581 
 HIS   0.008   0.001   HIS L  83 
 PHE   0.013   0.001   PHE A 464 
 TYR   0.020   0.002   TYR A 552 
 ARG   0.006   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  746)
  hydrogen bonds       : angle       3.97883 ( 1948)
  SS BOND              : bond        0.00624 (    1)
  SS BOND              : angle       1.62537 (    2)
  covalent geometry    : bond        0.00260 (17944)
  covalent geometry    : angle       0.61845 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6563 (t80)
REVERT: A  593 LEU cc_start: 0.8507 (pp) cc_final: 0.8183 (tp)
REVERT: A  756 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8548 (mmp80)
REVERT: L   40 TYR cc_start: 0.7389 (m-80) cc_final: 0.7005 (m-80)
REVERT: M   52 ASP cc_start: 0.8702 (t0) cc_final: 0.8436 (p0)
REVERT: O  209 PHE cc_start: 0.8168 (p90) cc_final: 0.7697 (p90)
  outliers start: 24
  outliers final: 22
  residues processed: 117
  average time/residue: 0.3049
  time to fit residues: 54.5102
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   25 GLN
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 157 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 94 optimal weight:    0.2980
   chunk 160 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 129 optimal weight:    0.9980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** 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 = 0.4331 r_free = 0.4331 target = 0.100255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.072240 restraints weight = 90093.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.073997 restraints weight = 46382.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.075045 restraints weight = 31977.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.6121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  17945  Z= 0.158
  Angle     :  0.647  11.120  25661  Z= 0.326
  Chirality :  0.038   0.226   3153
  Planarity :  0.004   0.047   2272
  Dihedral  : 23.866 177.650   5969
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.02 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.55 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.38 (0.22), residues: 1466
  helix:  1.42 (0.21), residues: 619
  sheet: -0.14 (0.35), residues: 219
  loop : -0.75 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 581 
 HIS   0.007   0.001   HIS L  83 
 PHE   0.029   0.002   PHE A 809 
 TYR   0.016   0.002   TYR A 552 
 ARG   0.006   0.000   ARG A 865 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04329 (  746)
  hydrogen bonds       : angle       4.10785 ( 1948)
  SS BOND              : bond        0.00479 (    1)
  SS BOND              : angle       1.78861 (    2)
  covalent geometry    : bond        0.00339 (17944)
  covalent geometry    : angle       0.64681 (25659)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6706 (t80)
REVERT: A  593 LEU cc_start: 0.8520 (pp) cc_final: 0.8190 (tp)
REVERT: A  756 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8520 (mmp80)
REVERT: L   40 TYR cc_start: 0.7285 (m-80) cc_final: 0.6796 (m-80)
REVERT: M   52 ASP cc_start: 0.8742 (t0) cc_final: 0.8477 (p0)
REVERT: O  101 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8566 (pm20)
  outliers start: 26
  outliers final: 24
  residues processed: 118
  average time/residue: 0.2876
  time to fit residues: 52.1720
Evaluate side-chains
  117 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   25 GLN
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  235 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   chunk 95 optimal weight:   30.0000
   chunk 113 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0980
   chunk 123 optimal weight:   30.0000
   chunk 40 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 135 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 585 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.101661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.075696 restraints weight = 89961.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.076846 restraints weight = 54032.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.078870 restraints weight = 34611.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.6369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17945  Z= 0.136
  Angle     :  0.627  11.438  25661  Z= 0.314
  Chirality :  0.037   0.225   3153
  Planarity :  0.004   0.049   2272
  Dihedral  : 23.833 178.137   5969
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.89 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.55 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    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:  0.48 (0.22), residues: 1466
  helix:  1.45 (0.21), residues: 622
  sheet: -0.14 (0.35), residues: 222
  loop : -0.62 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 581 
 HIS   0.006   0.001   HIS L  83 
 PHE   0.024   0.002   PHE A 809 
 TYR   0.018   0.001   TYR A 552 
 ARG   0.009   0.000   ARG A 858 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  746)
  hydrogen bonds       : angle       4.06752 ( 1948)
  SS BOND              : bond        0.00544 (    1)
  SS BOND              : angle       1.62444 (    2)
  covalent geometry    : bond        0.00289 (17944)
  covalent geometry    : angle       0.62678 (25659)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8150.69 seconds
wall clock time: 142 minutes 52.12 seconds (8572.12 seconds total)