Starting phenix.real_space_refine
on Tue Dec 31 13:18:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qxa_14196/12_2024/7qxa_14196_neut.cif"
  }
  resolution = 3.2
  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=   0.003
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     265      5.49       5
     S      42      5.16       5
     C    8869      2.51       5
     N    2831      2.21       5
     O    3569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 129 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 15576
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 954, 7649
          Classifications: {'peptide': 954}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 5371
          Classifications: {'RNA': 253}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 19, 'rna3p_pur': 99, 'rna3p_pyr': 118}
          Link IDs: {'rna2p': 36, 'rna3p': 216}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 632
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
    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: 254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 254
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "O"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 971
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
          Chain breaks: 3
  Time building chain proxies: 9.10, per 1000 atoms: 0.58
  Number of scatterers: 15576
  At special positions: 0
  Unit cell: (166.77, 123.17, 146.06, 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     265     15.00
     O    3569      8.00
     N    2831      7.00
     C    8869      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.92
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2346

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      54.3% alpha, 12.7% beta
      51 base pairs and 131 stacking pairs defined.
    Time for finding SS restraints: 5.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 3.910A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 18
      No H-bonds generated for 'chain 'A' and resid 16 through 18'
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 3.582A  pdb=" N   VAL A  51 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 92
      removed outlier: 3.583A  pdb=" N   VAL A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
      removed outlier: 3.863A  pdb=" N   GLY A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.799A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.725A  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 388
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.657A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.503A  pdb=" N   LEU A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.537A  pdb=" N   ARG A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.938A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.691A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.545A  pdb=" N   LYS A 493 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER A 496 " --> pdb=" O   LYS A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.679A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.542A  pdb=" N   LYS A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.655A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 597
      removed outlier: 3.741A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.681A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 4.112A  pdb=" N   LYS A 659 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.869A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 693 " --> pdb=" O   ALA A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 734
      removed outlier: 3.659A  pdb=" N   GLU A 727 " --> pdb=" O   ASP A 723 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 733 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.570A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 837 through 854
      removed outlier: 3.669A  pdb=" N   CYS A 842 " --> pdb=" O   SER A 838 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A 852 " --> pdb=" O   ASP A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 859
    Processing helix  chain 'A' and resid 876 through 890
      removed outlier: 3.675A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.646A  pdb=" N   TYR A 949 " --> pdb=" O   TYR A 946 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 946 through 950'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.588A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
      removed outlier: 3.604A  pdb=" N   LEU A1007 " --> pdb=" O   LYS A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1028
      removed outlier: 3.554A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1051
      removed outlier: 3.588A  pdb=" N   ASP A1038 " --> pdb=" O   ARG A1034 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   CYS A1043 " --> pdb=" O   THR A1039 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1085
      removed outlier: 3.897A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS A1075 " --> pdb=" O   GLN A1071 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   THR A1083 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG A1084 " --> pdb=" O   LEU A1080 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   HIS A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.579A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.073A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A1102 " --> pdb=" O   THR A1098 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.894A  pdb=" N   THR A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 38
      removed outlier: 4.389A  pdb=" N   LEU L  34 " --> pdb=" O   ARG L  30 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 73
      removed outlier: 4.489A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU L  56 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR L  60 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE L  63 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 91
      removed outlier: 3.964A  pdb=" N   LEU L  84 " --> pdb=" O   ILE L  80 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG L  89 " --> pdb=" O   GLN L  85 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP L  91 " --> pdb=" O   ALA L  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 91 through 99
      removed outlier: 3.639A  pdb=" N   ASN L  95 " --> pdb=" O   ASP L  91 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS L  96 " --> pdb=" O   GLU L  92 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 50
      removed outlier: 3.662A  pdb=" N   VAL M  45 " --> pdb=" O   TYR M  41 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS M  47 " --> pdb=" O   TYR M  43 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 3.995A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER M  79 " --> pdb=" O   ALA M  75 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   HIS M  83 " --> pdb=" O   SER M  79 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR M  84 " --> pdb=" O   ARG M  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 3.769A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU M 103 " --> pdb=" O   VAL M  99 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 107 through 125
      removed outlier: 3.747A  pdb=" N   SER M 113 " --> pdb=" O   LYS M 109 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU M 114 " --> pdb=" O   HIS M 110 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLY M 115 " --> pdb=" O   ALA M 111 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR M 120 " --> pdb=" O   THR M 116 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER M 125 " --> pdb=" O   LYS M 121 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 98 through 104
      removed outlier: 3.837A  pdb=" N   ILE O 103 " --> pdb=" O   ILE O  99 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 158 through 164
      removed outlier: 3.623A  pdb=" N   LEU O 162 " --> pdb=" O   THR O 158 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 227 through 238
      removed outlier: 3.527A  pdb=" N   LYS O 232 " --> pdb=" O   LEU O 228 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LYS O 233 " --> pdb=" O   ASP O 229 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TYR O 235 " --> pdb=" O   GLN O 231 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ASP O 236 " --> pdb=" O   LYS O 232 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   CYS O 237 " --> pdb=" O   LYS O 233 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU O 238 " --> pdb=" O   LEU O 234 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.778A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.630A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.317A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.778A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.565A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.630A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.317A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A 739 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600
      removed outlier: 7.356A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680
      removed outlier: 3.720A  pdb=" N   LEU A 866 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP A 869 " --> pdb=" O   LEU A 866 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 709 " --> pdb=" O   LEU A 872 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 905 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184
      removed outlier: 7.223A  pdb=" N   LEU O 145 " --> pdb=" O   LEU O 118 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   VAL O 120 " --> pdb=" O   THR O 143 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   THR O 143 " --> pdb=" O   VAL O 120 " (cutoff:3.500A)
      removed outlier: 9.511A  pdb=" N   LEU O 204 " --> pdb=" O   SER O 152 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   ARG O 154 " --> pdb=" O   LEU O 204 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   VAL O 206 " --> pdb=" O   ARG O 154 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU O 156 " --> pdb=" O   VAL O 206 " (cutoff:3.500A)

    453 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      135 hydrogen bonds
      258 hydrogen bond angles
      0 basepair planarities
      51 basepair parallelities
      131 stacking parallelities
  Total time for adding SS restraints: 8.30

  Time building geometry restraints manager: 4.48 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: 2427
        1.33 -     1.46: 6059
        1.46 -     1.59: 7519
        1.59 -     1.73: 381
        1.73 -     1.86: 55
  Bond restraints: 16441
  Sorted by residual:
  bond pdb=" O3'   A B 176 "
       pdb=" P     U B 177 "
    ideal  model  delta    sigma   weight residual
    1.607  1.697 -0.090 1.50e-02 4.44e+03 3.56e+01
  bond pdb=" CA  ILE A 624 "
       pdb=" C   ILE A 624 "
    ideal  model  delta    sigma   weight residual
    1.524  1.585 -0.060 1.05e-02 9.07e+03 3.31e+01
  bond pdb=" C   SER A 513 "
       pdb=" O   SER A 513 "
    ideal  model  delta    sigma   weight residual
    1.234  1.303 -0.069 1.23e-02 6.61e+03 3.13e+01
  bond pdb=" CA  PHE A1031 "
       pdb=" C   PHE A1031 "
    ideal  model  delta    sigma   weight residual
    1.524  1.467  0.057 1.32e-02 5.74e+03 1.87e+01
  bond pdb=" CA  SER A 513 "
       pdb=" C   SER A 513 "
    ideal  model  delta    sigma   weight residual
    1.523  1.469  0.054 1.30e-02 5.92e+03 1.72e+01
  ... (remaining 16436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 20958
        1.89 -     3.78: 2314
        3.78 -     5.67: 210
        5.67 -     7.56: 38
        7.56 -     9.44: 9
  Bond angle restraints: 23529
  Sorted by residual:
  angle pdb=" O3'   C B  72 "
        pdb=" C3'   C B  72 "
        pdb=" C2'   C B  72 "
      ideal   model   delta    sigma   weight residual
     109.50  118.94   -9.44 1.50e+00 4.44e-01 3.96e+01
  angle pdb=" O3'   G B  44 "
        pdb=" C3'   G B  44 "
        pdb=" C2'   G B  44 "
      ideal   model   delta    sigma   weight residual
     113.70  122.65   -8.95 1.50e+00 4.44e-01 3.56e+01
  angle pdb=" C4'   C B  74 "
        pdb=" C3'   C B  74 "
        pdb=" O3'   C B  74 "
      ideal   model   delta    sigma   weight residual
     109.40  118.02   -8.62 1.50e+00 4.44e-01 3.31e+01
  angle pdb=" N   SER A 838 "
        pdb=" CA  SER A 838 "
        pdb=" C   SER A 838 "
      ideal   model   delta    sigma   weight residual
     111.33  117.93   -6.60 1.21e+00 6.83e-01 2.98e+01
  angle pdb=" O3'   A B 174 "
        pdb=" C3'   A B 174 "
        pdb=" C2'   A B 174 "
      ideal   model   delta    sigma   weight residual
     113.70  121.73   -8.03 1.50e+00 4.44e-01 2.87e+01
  ... (remaining 23524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 9513
       35.95 -    71.89: 700
       71.89 -   107.84: 107
      107.84 -   143.78: 8
      143.78 -   179.73: 10
  Dihedral angle restraints: 10338
    sinusoidal: 6717
      harmonic: 3621
  Sorted by residual:
  dihedral pdb=" C5'   C B  74 "
           pdb=" C4'   C B  74 "
           pdb=" C3'   C B  74 "
           pdb=" O3'   C B  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   74.89   72.11     1      8.00e+00 1.56e-02 1.04e+02
  dihedral pdb=" C4'   C B  74 "
           pdb=" C3'   C B  74 "
           pdb=" C2'   C B  74 "
           pdb=" C1'   C B  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   33.16  -68.16     1      8.00e+00 1.56e-02 9.42e+01
  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   79.66   67.34     1      8.00e+00 1.56e-02 9.22e+01
  ... (remaining 10335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 2208
       0.101 -    0.203: 546
       0.203 -    0.304: 106
       0.304 -    0.405: 6
       0.405 -    0.506: 4
  Chirality restraints: 2870
  Sorted by residual:
  chirality pdb=" C3'   C B  72 "
            pdb=" C4'   C B  72 "
            pdb=" O3'   C B  72 "
            pdb=" C2'   C B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.24   -0.51 2.00e-01 2.50e+01 6.41e+00
  chirality pdb=" C3'   G B 300 "
            pdb=" C4'   G B 300 "
            pdb=" O3'   G B 300 "
            pdb=" C2'   G B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.24   -0.50 2.00e-01 2.50e+01 6.37e+00
  chirality pdb=" C3'   U B  42 "
            pdb=" C4'   U B  42 "
            pdb=" O3'   U B  42 "
            pdb=" C2'   U B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.26   -0.49 2.00e-01 2.50e+01 5.90e+00
  ... (remaining 2867 not shown)

  Planarity restraints: 2018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 177 "   -0.104 2.00e-02 2.50e+03   5.14e-02 5.95e+01
        pdb=" N1    U B 177 "    0.057 2.00e-02 2.50e+03
        pdb=" C2    U B 177 "    0.041 2.00e-02 2.50e+03
        pdb=" O2    U B 177 "    0.037 2.00e-02 2.50e+03
        pdb=" N3    U B 177 "   -0.047 2.00e-02 2.50e+03
        pdb=" C4    U B 177 "   -0.040 2.00e-02 2.50e+03
        pdb=" O4    U B 177 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    U B 177 "    0.011 2.00e-02 2.50e+03
        pdb=" C6    U B 177 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 307 "   -0.068 2.00e-02 2.50e+03   3.50e-02 2.75e+01
        pdb=" N1    U B 307 "    0.061 2.00e-02 2.50e+03
        pdb=" C2    U B 307 "    0.014 2.00e-02 2.50e+03
        pdb=" O2    U B 307 "    0.010 2.00e-02 2.50e+03
        pdb=" N3    U B 307 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    U B 307 "   -0.040 2.00e-02 2.50e+03
        pdb=" O4    U B 307 "   -0.012 2.00e-02 2.50e+03
        pdb=" C5    U B 307 "    0.021 2.00e-02 2.50e+03
        pdb=" C6    U B 307 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG N  30 "   -0.036 2.00e-02 2.50e+03   2.63e-02 2.08e+01
        pdb=" N9   DG N  30 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DG N  30 "    0.021 2.00e-02 2.50e+03
        pdb=" N7   DG N  30 "    0.030 2.00e-02 2.50e+03
        pdb=" C5   DG N  30 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DG N  30 "   -0.023 2.00e-02 2.50e+03
        pdb=" O6   DG N  30 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DG N  30 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2   DG N  30 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2   DG N  30 "    0.054 2.00e-02 2.50e+03
        pdb=" N3   DG N  30 "   -0.019 2.00e-02 2.50e+03
        pdb=" C4   DG N  30 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2015 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1975
        2.78 -     3.31: 13932
        3.31 -     3.84: 25459
        3.84 -     4.37: 30664
        4.37 -     4.90: 47163
  Nonbonded interactions: 119193
  Sorted by model distance:
  nonbonded pdb=" OP1   C B 320 "
            pdb=" OH  TYR M  41 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" NH2 ARG A 535 "
            pdb=" O2'   A B 302 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O4'   U B 316 "
            pdb=" O2    U B 316 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   TRP A 510 "
            pdb=" O2'   C B 313 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O4'   U B 194 "
            pdb=" O2    U B 194 "
     model   vdw
     2.366 3.040
  ... (remaining 119188 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     40.760
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
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      :  0.010   0.090  16441  Z= 0.628
  Angle     :  1.183   9.445  23529  Z= 0.779
  Chirality :  0.092   0.506   2870
  Planarity :  0.006   0.051   2018
  Dihedral  : 22.115 179.730   7992
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 0.91
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.03 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.05 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.19), residues: 1227
  helix: -2.02 (0.17), residues: 538
  sheet: -2.06 (0.43), residues: 96
  loop : -2.10 (0.22), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.005   TRP A 547 
 HIS   0.014   0.003   HIS A1013 
 PHE   0.030   0.005   PHE A 870 
 TYR   0.043   0.006   TYR A 949 
 ARG   0.014   0.001   ARG A 669 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8261 (mp0)
REVERT: A   86 GLN cc_start: 0.7885 (tt0) cc_final: 0.7432 (tp-100)
REVERT: A   95 ASN cc_start: 0.7957 (t0) cc_final: 0.7515 (t0)
REVERT: A   99 PHE cc_start: 0.6908 (m-10) cc_final: 0.6657 (m-80)
REVERT: A  142 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6457 (tpt90)
REVERT: A  159 PHE cc_start: 0.7091 (m-80) cc_final: 0.6633 (m-80)
REVERT: A  603 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8410 (tm-30)
REVERT: A  636 MET cc_start: 0.8316 (mmt) cc_final: 0.8096 (mmt)
REVERT: A  743 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6568 (mtp85)
REVERT: A  756 ARG cc_start: 0.6205 (mtp-110) cc_final: 0.5476 (mmt180)
REVERT: A  800 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6871 (mm-30)
REVERT: A  899 ASN cc_start: 0.8230 (t0) cc_final: 0.7853 (t0)
REVERT: A  922 MET cc_start: 0.7350 (mmm) cc_final: 0.7139 (mtp)
REVERT: L   69 ASN cc_start: 0.6793 (t0) cc_final: 0.6586 (m-40)
REVERT: M   63 MET cc_start: 0.7274 (mtt) cc_final: 0.6764 (mmp)
REVERT: M  117 LYS cc_start: 0.6361 (mttt) cc_final: 0.6006 (mtpt)
REVERT: O  165 SER cc_start: 0.4853 (t) cc_final: 0.4564 (m)
REVERT: O  170 LYS cc_start: 0.7804 (ptpt) cc_final: 0.7049 (tppt)
REVERT: O  175 ARG cc_start: 0.7238 (mtt-85) cc_final: 0.6620 (mtt180)
REVERT: O  205 GLN cc_start: 0.8061 (tt0) cc_final: 0.7779 (pp30)
REVERT: O  209 PHE cc_start: 0.7767 (p90) cc_final: 0.7345 (p90)
REVERT: O  219 LEU cc_start: 0.7588 (mt) cc_final: 0.7382 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 160
  average time/residue: 0.3953
  time to fit residues: 85.8534
Evaluate side-chains
  92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.9990
   chunk 113 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 136 optimal weight:    8.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
A 794 GLN
A1013 HIS
L  90 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16441  Z= 0.187
  Angle     :  0.661   8.884  23529  Z= 0.341
  Chirality :  0.039   0.298   2870
  Planarity :  0.005   0.054   2018
  Dihedral  : 23.613 175.646   5573
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.50 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  7.17 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.22), residues: 1227
  helix:  0.01 (0.20), residues: 580
  sheet: -1.73 (0.41), residues: 122
  loop : -1.63 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 547 
 HIS   0.006   0.001   HIS A 546 
 PHE   0.013   0.002   PHE A 331 
 TYR   0.012   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A1084 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8050 (t0) cc_final: 0.7591 (t0)
REVERT: A  139 LEU cc_start: 0.5516 (tp) cc_final: 0.4974 (mp)
REVERT: A  603 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8237 (mm-30)
REVERT: A  684 ASP cc_start: 0.7685 (p0) cc_final: 0.7401 (m-30)
REVERT: A  685 ASP cc_start: 0.7685 (t0) cc_final: 0.7446 (t0)
REVERT: A  889 ARG cc_start: 0.8913 (ttt-90) cc_final: 0.8459 (ptp-170)
REVERT: A  922 MET cc_start: 0.7049 (mmm) cc_final: 0.6825 (mtp)
REVERT: L   32 ARG cc_start: 0.6191 (mtp180) cc_final: 0.5659 (ttt-90)
REVERT: L   64 LEU cc_start: 0.5036 (tp) cc_final: 0.4544 (tp)
REVERT: L   69 ASN cc_start: 0.6799 (t0) cc_final: 0.6561 (m-40)
REVERT: L   86 LEU cc_start: 0.7522 (mt) cc_final: 0.7285 (tp)
REVERT: M   63 MET cc_start: 0.7024 (mtt) cc_final: 0.6646 (mmp)
REVERT: M  100 ARG cc_start: 0.5520 (ttp-170) cc_final: 0.5271 (mtp-110)
REVERT: M  117 LYS cc_start: 0.6587 (mttt) cc_final: 0.6220 (mtpt)
REVERT: O  119 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7783 (mm-30)
REVERT: O  165 SER cc_start: 0.4579 (t) cc_final: 0.3799 (m)
REVERT: O  170 LYS cc_start: 0.7673 (ptpt) cc_final: 0.7028 (mmmt)
REVERT: O  175 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6397 (mtt180)
REVERT: O  205 GLN cc_start: 0.8030 (tt0) cc_final: 0.7753 (pp30)
  outliers start: 6
  outliers final: 2
  residues processed: 117
  average time/residue: 0.3488
  time to fit residues: 56.9610
Evaluate side-chains
  97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  538 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 113 optimal weight:    9.9990
   chunk 92 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 136 optimal weight:    3.9990
   chunk 147 optimal weight:    6.9990
   chunk 121 optimal weight:   20.0000
   chunk 135 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0470
   chunk 109 optimal weight:    9.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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**
A1023 GLN
L  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  16441  Z= 0.145
  Angle     :  0.554   9.117  23529  Z= 0.286
  Chirality :  0.035   0.210   2870
  Planarity :  0.004   0.058   2018
  Dihedral  : 23.409 169.903   5573
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.42 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.19 %
    Favored  : 90.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.21 (0.23), residues: 1227
  helix:  1.05 (0.21), residues: 580
  sheet: -1.14 (0.45), residues: 120
  loop : -1.22 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A 151 
 PHE   0.017   0.001   PHE A  71 
 TYR   0.008   0.001   TYR L  40 
 ARG   0.006   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8294 (mm-30)
REVERT: A   91 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.6913 (ptm160)
REVERT: A   95 ASN cc_start: 0.8195 (t0) cc_final: 0.7780 (t0)
REVERT: A  139 LEU cc_start: 0.5134 (tp) cc_final: 0.4881 (mp)
REVERT: A  603 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8238 (mm-30)
REVERT: A  889 ARG cc_start: 0.8926 (ttt-90) cc_final: 0.8445 (ptp-170)
REVERT: A  903 THR cc_start: 0.8913 (m) cc_final: 0.8669 (p)
REVERT: L   32 ARG cc_start: 0.6050 (mtp180) cc_final: 0.5510 (ttt-90)
REVERT: L   64 LEU cc_start: 0.4856 (tp) cc_final: 0.4398 (tp)
REVERT: L   69 ASN cc_start: 0.6675 (t0) cc_final: 0.6457 (m-40)
REVERT: L   86 LEU cc_start: 0.7319 (mt) cc_final: 0.7098 (tp)
REVERT: M   63 MET cc_start: 0.6895 (mtt) cc_final: 0.6598 (mmp)
REVERT: O  119 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7931 (mm-30)
REVERT: O  165 SER cc_start: 0.3378 (t) cc_final: 0.3100 (m)
REVERT: O  170 LYS cc_start: 0.7578 (ptpt) cc_final: 0.6894 (mmmt)
REVERT: O  187 CYS cc_start: 0.6787 (p) cc_final: 0.6119 (p)
REVERT: O  205 GLN cc_start: 0.8031 (tt0) cc_final: 0.7785 (pp30)
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 0.3296
  time to fit residues: 47.5053
Evaluate side-chains
  90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  538 GLU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    0.5980
   chunk 102 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 65 optimal weight:    0.1980
   chunk 91 optimal weight:    0.8980
   chunk 136 optimal weight:    7.9990
   chunk 144 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0030
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 608 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  16441  Z= 0.126
  Angle     :  0.533   9.002  23529  Z= 0.270
  Chirality :  0.034   0.212   2870
  Planarity :  0.004   0.078   2018
  Dihedral  : 23.282 169.099   5573
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.10 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.85 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.24 (0.23), residues: 1227
  helix:  1.36 (0.22), residues: 582
  sheet: -0.83 (0.44), residues: 133
  loop : -0.93 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 547 
 HIS   0.003   0.001   HIS L  83 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.007   0.001   TYR A 325 
 ARG   0.006   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.5101 (mt)
REVERT: A   79 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8356 (mm-30)
REVERT: A   91 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.6989 (ptm160)
REVERT: A   95 ASN cc_start: 0.8251 (t0) cc_final: 0.7842 (t0)
REVERT: A  372 MET cc_start: 0.2087 (tmm) cc_final: 0.0784 (tpp)
REVERT: A  512 MET cc_start: 0.7129 (mmt) cc_final: 0.6392 (mmt)
REVERT: A  603 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7983 (mm-30)
REVERT: A  889 ARG cc_start: 0.8952 (ttt-90) cc_final: 0.8477 (ptp-170)
REVERT: A  903 THR cc_start: 0.8910 (m) cc_final: 0.8681 (p)
REVERT: L   32 ARG cc_start: 0.6061 (mtp180) cc_final: 0.5522 (ttt-90)
REVERT: L   64 LEU cc_start: 0.4852 (tp) cc_final: 0.4407 (tp)
REVERT: L   69 ASN cc_start: 0.6673 (t0) cc_final: 0.6369 (m-40)
REVERT: L   86 LEU cc_start: 0.7309 (mt) cc_final: 0.7105 (tp)
REVERT: O  119 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7980 (mm-30)
REVERT: O  187 CYS cc_start: 0.7041 (p) cc_final: 0.6388 (p)
REVERT: O  205 GLN cc_start: 0.8008 (tt0) cc_final: 0.7759 (pp30)
  outliers start: 10
  outliers final: 4
  residues processed: 100
  average time/residue: 0.3145
  time to fit residues: 46.7888
Evaluate side-chains
  90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 120 optimal weight:    0.0040
   chunk 82 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 59 optimal weight:    7.9990
   chunk 123 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0970
   chunk 130 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    2.6196

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 ASN
A1075 HIS
L  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16441  Z= 0.269
  Angle     :  0.645  10.580  23529  Z= 0.326
  Chirality :  0.038   0.237   2870
  Planarity :  0.005   0.070   2018
  Dihedral  : 23.445 165.695   5573
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.32 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.29 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.10 (0.23), residues: 1227
  helix:  0.91 (0.21), residues: 591
  sheet: -0.85 (0.42), residues: 133
  loop : -0.95 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 547 
 HIS   0.011   0.002   HIS A 879 
 PHE   0.017   0.002   PHE A 331 
 TYR   0.013   0.002   TYR A 638 
 ARG   0.006   0.001   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8557 (mm-30)
REVERT: A   91 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.7263 (ptm160)
REVERT: A   95 ASN cc_start: 0.8408 (t0) cc_final: 0.8016 (t0)
REVERT: A  372 MET cc_start: 0.1564 (tmm) cc_final: 0.0437 (tpp)
REVERT: A  603 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8354 (mm-30)
REVERT: A  889 ARG cc_start: 0.8936 (ttt-90) cc_final: 0.8447 (ptp-170)
REVERT: A  899 ASN cc_start: 0.8210 (t0) cc_final: 0.7701 (t0)
REVERT: L   32 ARG cc_start: 0.6092 (mtp180) cc_final: 0.5419 (ttt-90)
REVERT: L   74 ASN cc_start: 0.7010 (t0) cc_final: 0.6761 (t0)
REVERT: L   86 LEU cc_start: 0.7429 (mt) cc_final: 0.7203 (tp)
REVERT: M  100 ARG cc_start: 0.4994 (ttm110) cc_final: 0.4510 (ptt180)
REVERT: M  117 LYS cc_start: 0.5706 (mtmm) cc_final: 0.5505 (mtmm)
  outliers start: 20
  outliers final: 14
  residues processed: 87
  average time/residue: 0.3023
  time to fit residues: 39.3169
Evaluate side-chains
  88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  189 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 145 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 76 optimal weight:    0.8980
   chunk 139 optimal weight:    8.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  16441  Z= 0.141
  Angle     :  0.541  10.984  23529  Z= 0.271
  Chirality :  0.033   0.223   2870
  Planarity :  0.004   0.061   2018
  Dihedral  : 23.264 166.270   5573
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.34 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.24 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.34 (0.24), residues: 1227
  helix:  1.31 (0.21), residues: 597
  sheet: -0.57 (0.44), residues: 133
  loop : -0.84 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 459 
 HIS   0.013   0.001   HIS O 190 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.007   0.001   TYR L  51 
 ARG   0.005   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.7894 (m) cc_final: 0.6927 (p)
REVERT: A   79 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8513 (mm-30)
REVERT: A   91 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7231 (ptm160)
REVERT: A   95 ASN cc_start: 0.8361 (t0) cc_final: 0.7941 (t0)
REVERT: A  603 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8230 (mm-30)
REVERT: A  889 ARG cc_start: 0.8932 (ttt-90) cc_final: 0.8444 (ptp-170)
REVERT: A  903 THR cc_start: 0.8944 (m) cc_final: 0.8659 (p)
REVERT: L   32 ARG cc_start: 0.6068 (mtp180) cc_final: 0.5429 (ttt-90)
REVERT: L   74 ASN cc_start: 0.6936 (t0) cc_final: 0.6724 (t0)
REVERT: L   86 LEU cc_start: 0.7290 (mt) cc_final: 0.7078 (tp)
REVERT: M  100 ARG cc_start: 0.5002 (ttm110) cc_final: 0.4648 (ptt180)
REVERT: M  117 LYS cc_start: 0.5808 (mtmm) cc_final: 0.5592 (mtmm)
  outliers start: 11
  outliers final: 8
  residues processed: 83
  average time/residue: 0.2928
  time to fit residues: 36.4427
Evaluate side-chains
  87 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  538 GLU
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  205 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   chunk 105 optimal weight:   20.0000
   chunk 122 optimal weight:    0.0170
   chunk 81 optimal weight:    0.8980
   chunk 144 optimal weight:    0.0570
   chunk 90 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.7738

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  16441  Z= 0.135
  Angle     :  0.533  10.662  23529  Z= 0.265
  Chirality :  0.033   0.217   2870
  Planarity :  0.004   0.059   2018
  Dihedral  : 23.168 165.960   5573
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.18 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.80 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.64 (0.24), residues: 1227
  helix:  1.51 (0.21), residues: 600
  sheet: -0.38 (0.47), residues: 121
  loop : -0.65 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 547 
 HIS   0.003   0.001   HIS A 983 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.008   0.001   TYR A 325 
 ARG   0.006   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.7928 (m) cc_final: 0.7063 (p)
REVERT: A   79 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8503 (mm-30)
REVERT: A   91 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.7203 (ptm160)
REVERT: A   95 ASN cc_start: 0.8338 (t0) cc_final: 0.7942 (t0)
REVERT: A  139 LEU cc_start: 0.5444 (tp) cc_final: 0.5171 (mp)
REVERT: A  512 MET cc_start: 0.6983 (mmt) cc_final: 0.6286 (mmt)
REVERT: A  603 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8331 (mm-30)
REVERT: A  889 ARG cc_start: 0.8950 (ttt-90) cc_final: 0.8451 (ptp-170)
REVERT: A  903 THR cc_start: 0.8933 (m) cc_final: 0.8642 (p)
REVERT: A  972 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7590 (mtp85)
REVERT: L   32 ARG cc_start: 0.5929 (mtp180) cc_final: 0.5374 (ttt-90)
REVERT: L   74 ASN cc_start: 0.7125 (t0) cc_final: 0.6901 (t0)
REVERT: L   86 LEU cc_start: 0.7273 (mt) cc_final: 0.7059 (tp)
REVERT: M  100 ARG cc_start: 0.5156 (ttm110) cc_final: 0.4809 (ptt180)
REVERT: M  117 LYS cc_start: 0.5862 (mtmm) cc_final: 0.5657 (mtmm)
REVERT: O  119 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (mm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 83
  average time/residue: 0.3511
  time to fit residues: 41.5004
Evaluate side-chains
  85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  119 GLU
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 98 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 113 optimal weight:    9.9990
   chunk 131 optimal weight:    5.9990
   chunk 138 optimal weight:    1.9990
   chunk 126 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  16441  Z= 0.134
  Angle     :  0.526  10.693  23529  Z= 0.260
  Chirality :  0.033   0.219   2870
  Planarity :  0.004   0.058   2018
  Dihedral  : 23.100 166.041   5573
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.42 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.80 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.79 (0.24), residues: 1227
  helix:  1.62 (0.21), residues: 602
  sheet: -0.25 (0.45), residues: 131
  loop : -0.58 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 547 
 HIS   0.003   0.001   HIS A 879 
 PHE   0.011   0.001   PHE A 331 
 TYR   0.007   0.001   TYR A 325 
 ARG   0.005   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.7767 (m) cc_final: 0.7086 (p)
REVERT: A   79 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8480 (mm-30)
REVERT: A   91 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.7119 (ptm160)
REVERT: A   95 ASN cc_start: 0.8325 (t0) cc_final: 0.7941 (t0)
REVERT: A  139 LEU cc_start: 0.5241 (tp) cc_final: 0.5029 (mm)
REVERT: A  603 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8351 (mm-30)
REVERT: A  889 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8456 (ptp-170)
REVERT: A  903 THR cc_start: 0.8939 (m) cc_final: 0.8642 (p)
REVERT: L   32 ARG cc_start: 0.5893 (mtp180) cc_final: 0.5373 (ttt-90)
REVERT: L   74 ASN cc_start: 0.7110 (t0) cc_final: 0.6886 (t0)
REVERT: L   86 LEU cc_start: 0.7277 (mt) cc_final: 0.7062 (tp)
REVERT: M  100 ARG cc_start: 0.5236 (ttm110) cc_final: 0.4857 (ptt180)
REVERT: M  117 LYS cc_start: 0.5866 (mtmm) cc_final: 0.5655 (mtmm)
REVERT: O  170 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7299 (tttt)
  outliers start: 11
  outliers final: 10
  residues processed: 84
  average time/residue: 0.3409
  time to fit residues: 41.3255
Evaluate side-chains
  87 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   66 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 138 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 58 optimal weight:   10.0000
   chunk 105 optimal weight:   20.0000
   chunk 41 optimal weight:    3.9990
   chunk 121 optimal weight:   10.0000
   chunk 127 optimal weight:    0.0980
   chunk 88 optimal weight:    0.6980
   chunk 142 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16441  Z= 0.193
  Angle     :  0.574  11.061  23529  Z= 0.286
  Chirality :  0.034   0.229   2870
  Planarity :  0.004   0.056   2018
  Dihedral  : 23.187 166.548   5573
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.67 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.52 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1227
  helix:  1.35 (0.21), residues: 606
  sheet: -0.21 (0.45), residues: 131
  loop : -0.65 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 547 
 HIS   0.006   0.001   HIS A 879 
 PHE   0.014   0.002   PHE A 331 
 TYR   0.011   0.001   TYR A 638 
 ARG   0.007   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.7937 (m) cc_final: 0.7080 (p)
REVERT: A   91 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7186 (ptm160)
REVERT: A   95 ASN cc_start: 0.8379 (t0) cc_final: 0.7964 (t0)
REVERT: A  603 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8402 (mm-30)
REVERT: A  889 ARG cc_start: 0.8954 (ttt-90) cc_final: 0.8503 (ptp-170)
REVERT: A  903 THR cc_start: 0.8934 (m) cc_final: 0.8614 (p)
REVERT: A  970 MET cc_start: 0.7172 (ttm) cc_final: 0.6888 (ttt)
REVERT: L   32 ARG cc_start: 0.5753 (mtp180) cc_final: 0.5229 (ttt-90)
REVERT: L   74 ASN cc_start: 0.7112 (t0) cc_final: 0.6876 (t0)
REVERT: L   86 LEU cc_start: 0.7221 (mt) cc_final: 0.6997 (tp)
REVERT: M  100 ARG cc_start: 0.5262 (ttm110) cc_final: 0.5039 (mtm110)
REVERT: M  117 LYS cc_start: 0.5985 (mtmm) cc_final: 0.5783 (mtmm)
REVERT: O  170 LYS cc_start: 0.7494 (ptpt) cc_final: 0.7266 (tttt)
  outliers start: 15
  outliers final: 12
  residues processed: 81
  average time/residue: 0.3215
  time to fit residues: 38.3220
Evaluate side-chains
  85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  719 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   66 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 149 optimal weight:    9.9990
   chunk 137 optimal weight:    8.9990
   chunk 118 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0470
   chunk 72 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 126 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8480

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  16441  Z= 0.136
  Angle     :  0.539  10.985  23529  Z= 0.266
  Chirality :  0.033   0.219   2870
  Planarity :  0.004   0.056   2018
  Dihedral  : 23.145 165.224   5573
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.26 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.89 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.77 (0.24), residues: 1227
  helix:  1.52 (0.21), residues: 608
  sheet: -0.09 (0.46), residues: 121
  loop : -0.54 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 581 
 HIS   0.003   0.001   HIS A 983 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.008   0.001   TYR A 325 
 ARG   0.007   0.000   ARG L  82 

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 CYS cc_start: 0.7833 (m) cc_final: 0.7110 (p)
REVERT: A   91 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7209 (ptm160)
REVERT: A   95 ASN cc_start: 0.8317 (t0) cc_final: 0.7903 (t0)
REVERT: A  512 MET cc_start: 0.6932 (mmt) cc_final: 0.6220 (mmt)
REVERT: A  603 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8398 (mm-30)
REVERT: A  889 ARG cc_start: 0.8938 (ttt-90) cc_final: 0.8472 (ptp-170)
REVERT: A  903 THR cc_start: 0.8908 (m) cc_final: 0.8613 (p)
REVERT: A  970 MET cc_start: 0.7184 (ttm) cc_final: 0.6904 (ttt)
REVERT: L   32 ARG cc_start: 0.5747 (mtp180) cc_final: 0.5228 (ttt-90)
REVERT: L   74 ASN cc_start: 0.7166 (t0) cc_final: 0.6950 (t0)
REVERT: L   86 LEU cc_start: 0.7274 (mt) cc_final: 0.7067 (tp)
REVERT: M  100 ARG cc_start: 0.5305 (ttm110) cc_final: 0.4896 (ptt180)
REVERT: M  117 LYS cc_start: 0.5916 (mtmm) cc_final: 0.5710 (mtmm)
REVERT: O  119 GLU cc_start: 0.7945 (pp20) cc_final: 0.7351 (mm-30)
REVERT: O  170 LYS cc_start: 0.7515 (ptpt) cc_final: 0.7280 (tttt)
  outliers start: 12
  outliers final: 12
  residues processed: 78
  average time/residue: 0.3436
  time to fit residues: 38.7653
Evaluate side-chains
  84 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   66 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 119 optimal weight:   20.0000
   chunk 49 optimal weight:    0.0060
   chunk 122 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0980
   chunk 86 optimal weight:    4.9990
   overall best weight:    2.8202

-------------------------------------------------------------------------------
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**
M  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.143558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.095507 restraints weight = 36891.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.32
r_work: 0.3304 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16441  Z= 0.280
  Angle     :  0.637  11.188  23529  Z= 0.318
  Chirality :  0.037   0.237   2870
  Planarity :  0.005   0.056   2018
  Dihedral  : 23.300 169.235   5573
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.48 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.89 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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:  0.28 (0.24), residues: 1227
  helix:  1.03 (0.21), residues: 605
  sheet: -0.25 (0.44), residues: 131
  loop : -0.68 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 690 
 HIS   0.008   0.001   HIS A 879 
 PHE   0.025   0.002   PHE L  26 
 TYR   0.014   0.002   TYR A 638 
 ARG   0.009   0.000   ARG L  82 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2685.67 seconds
wall clock time: 50 minutes 36.38 seconds (3036.38 seconds total)