Starting phenix.real_space_refine
on Sat Jun 14 04:37:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qxa_14196/06_2025/7qxa_14196_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qxa_14196/06_2025/7qxa_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_14196/06_2025/7qxa_14196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qxa_14196/06_2025/7qxa_14196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qxa_14196/06_2025/7qxa_14196_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qxa_14196/06_2025/7qxa_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-5710/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: 9.44, per 1000 atoms: 0.61
  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: 3.51
  Conformation dependent library (CDL) restraints added in 1.5 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: 6.60
  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: 8.24

  Time building geometry restraints manager: 4.25 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:             1.420
  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:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     42.910
  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:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.260
-------------------------------------------------------------------------------
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= 0.641
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29839 (  575)
  hydrogen bonds       : angle       8.54143 ( 1569)
  covalent geometry    : bond        0.00974 (16441)
  covalent geometry    : angle       1.18296 (23529)

*********************** 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  : 1.201 
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: 0.3835
  time to fit residues: 83.0373
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  : 1.218 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.146445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.098472 restraints weight = 37263.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.33
r_work: 0.3355 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
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= 0.142
  Angle     :  0.661   8.884  23529  Z= 0.341
  Chirality :  0.039   0.298   2870
  Planarity :  0.005   0.054   2018
  Dihedral  : 23.613 175.647   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05848 (  575)
  hydrogen bonds       : angle       4.51793 ( 1569)
  covalent geometry    : bond        0.00287 (16441)
  covalent geometry    : angle       0.66090 (23529)

*********************** 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  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.7858 (t0) cc_final: 0.7372 (t0)
REVERT: A   99 PHE cc_start: 0.7983 (m-10) cc_final: 0.7668 (m-80)
REVERT: A  139 LEU cc_start: 0.5901 (tp) cc_final: 0.5271 (mp)
REVERT: L   32 ARG cc_start: 0.6235 (mtp180) cc_final: 0.5754 (ttt-90)
REVERT: L   64 LEU cc_start: 0.5495 (tp) cc_final: 0.5051 (tp)
REVERT: L   69 ASN cc_start: 0.7054 (t0) cc_final: 0.6832 (m-40)
REVERT: L   86 LEU cc_start: 0.7296 (mt) cc_final: 0.7026 (tp)
REVERT: M   63 MET cc_start: 0.6855 (mtt) cc_final: 0.6561 (mmp)
REVERT: M  100 ARG cc_start: 0.5198 (ttp-170) cc_final: 0.4995 (mtp-110)
REVERT: M  117 LYS cc_start: 0.6681 (mttt) cc_final: 0.6338 (mtpt)
REVERT: O  100 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7232 (ttp-170)
REVERT: O  170 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7457 (mmmt)
REVERT: O  175 ARG cc_start: 0.6722 (mtt-85) cc_final: 0.6314 (mtt180)
REVERT: O  205 GLN cc_start: 0.7877 (tt0) cc_final: 0.7640 (pp30)
  outliers start: 6
  outliers final: 2
  residues processed: 117
  average time/residue: 0.3560
  time to fit residues: 58.0890
Evaluate side-chains
  93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
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 8 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 143 optimal weight:    9.9990
   chunk 129 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 114 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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**
A1075 HIS
L  74 ASN
M  50 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.142537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.093315 restraints weight = 37100.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.38
r_work: 0.3263 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  16441  Z= 0.222
  Angle     :  0.699   9.425  23529  Z= 0.359
  Chirality :  0.040   0.240   2870
  Planarity :  0.005   0.060   2018
  Dihedral  : 23.641 167.889   5573
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  7.17 %
    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: -0.89 (0.23), residues: 1227
  helix:  0.27 (0.21), residues: 580
  sheet: -1.24 (0.42), residues: 133
  loop : -1.33 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 547 
 HIS   0.008   0.002   HIS A1013 
 PHE   0.021   0.002   PHE A  71 
 TYR   0.016   0.002   TYR A 638 
 ARG   0.007   0.001   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07007 (  575)
  hydrogen bonds       : angle       4.60958 ( 1569)
  covalent geometry    : bond        0.00490 (16441)
  covalent geometry    : angle       0.69945 (23529)

*********************** 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
  112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8169 (mm-30)
REVERT: A   95 ASN cc_start: 0.8093 (t0) cc_final: 0.7647 (t0)
REVERT: A  899 ASN cc_start: 0.8568 (t0) cc_final: 0.8347 (t0)
REVERT: A 1017 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8979 (mp)
REVERT: L   32 ARG cc_start: 0.6244 (mtp180) cc_final: 0.5516 (ttt-90)
REVERT: L   74 ASN cc_start: 0.6888 (t160) cc_final: 0.6605 (t0)
REVERT: L   86 LEU cc_start: 0.7158 (mt) cc_final: 0.6840 (tp)
REVERT: M  100 ARG cc_start: 0.5189 (ttp-170) cc_final: 0.4974 (mtp-110)
REVERT: O  187 CYS cc_start: 0.8110 (p) cc_final: 0.7850 (p)
  outliers start: 28
  outliers final: 16
  residues processed: 96
  average time/residue: 0.3139
  time to fit residues: 44.0465
Evaluate side-chains
  98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  872 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 M residue   45 VAL
Chi-restraints excluded: chain O residue  165 SER
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 130 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 147 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 118 optimal weight:    6.9990
   chunk 95 optimal weight:   30.0000
   chunk 87 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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
A1051 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.142610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.093843 restraints weight = 37005.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.36
r_work: 0.3270 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  16441  Z= 0.217
  Angle     :  0.673   9.933  23529  Z= 0.341
  Chirality :  0.039   0.245   2870
  Planarity :  0.005   0.061   2018
  Dihedral  : 23.669 168.961   5573
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.56 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.31 %
    Favored  : 88.92 %
  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: -0.70 (0.23), residues: 1227
  helix:  0.34 (0.21), residues: 595
  sheet: -1.00 (0.43), residues: 131
  loop : -1.20 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 547 
 HIS   0.009   0.002   HIS A1013 
 PHE   0.020   0.002   PHE A 331 
 TYR   0.016   0.002   TYR A 122 
 ARG   0.007   0.001   ARG O 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05968 (  575)
  hydrogen bonds       : angle       4.44793 ( 1569)
  covalent geometry    : bond        0.00483 (16441)
  covalent geometry    : angle       0.67322 (23529)

*********************** 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
  107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7611 (tpt90)
REVERT: A   79 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8240 (mm-30)
REVERT: A   95 ASN cc_start: 0.8175 (t0) cc_final: 0.7762 (t0)
REVERT: L   32 ARG cc_start: 0.5471 (mtp180) cc_final: 0.5043 (ttt-90)
REVERT: L   64 LEU cc_start: 0.5293 (tp) cc_final: 0.5002 (mt)
REVERT: L   86 LEU cc_start: 0.7045 (mt) cc_final: 0.6734 (tp)
REVERT: M  117 LYS cc_start: 0.6122 (mtmm) cc_final: 0.5910 (mtmm)
REVERT: O   99 ILE cc_start: 0.7966 (tp) cc_final: 0.7697 (pt)
REVERT: O  187 CYS cc_start: 0.8264 (p) cc_final: 0.7814 (p)
REVERT: O  205 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7529 (pm20)
  outliers start: 19
  outliers final: 14
  residues processed: 95
  average time/residue: 0.3363
  time to fit residues: 46.0238
Evaluate side-chains
  95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  131 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 A residue  729 ILE
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  205 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 148 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 120 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   chunk 119 optimal weight:   30.0000
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.143704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.093073 restraints weight = 37621.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.22
r_work: 0.3322 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16441  Z= 0.134
  Angle     :  0.586  10.483  23529  Z= 0.296
  Chirality :  0.036   0.227   2870
  Planarity :  0.004   0.063   2018
  Dihedral  : 23.493 166.687   5573
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.16 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.99 %
    Favored  : 87.62 %
  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: -0.18 (0.24), residues: 1227
  helix:  0.85 (0.21), residues: 595
  sheet: -0.90 (0.43), residues: 133
  loop : -1.01 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 547 
 HIS   0.005   0.001   HIS A1013 
 PHE   0.016   0.001   PHE A 331 
 TYR   0.011   0.001   TYR A 122 
 ARG   0.010   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04774 (  575)
  hydrogen bonds       : angle       4.07104 ( 1569)
  covalent geometry    : bond        0.00287 (16441)
  covalent geometry    : angle       0.58626 (23529)

*********************** 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
  106 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8101 (t0) cc_final: 0.7646 (t0)
REVERT: A  903 THR cc_start: 0.9387 (m) cc_final: 0.9175 (p)
REVERT: A 1017 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8788 (mp)
REVERT: L   32 ARG cc_start: 0.5310 (mtp180) cc_final: 0.4841 (ttt-90)
REVERT: L   74 ASN cc_start: 0.6988 (t160) cc_final: 0.6784 (t0)
REVERT: L   86 LEU cc_start: 0.7048 (mt) cc_final: 0.6717 (tp)
REVERT: M  100 ARG cc_start: 0.5184 (ttp-170) cc_final: 0.4920 (mtp-110)
REVERT: M  117 LYS cc_start: 0.6349 (mtmm) cc_final: 0.6106 (mtmm)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.3163
  time to fit residues: 45.3181
Evaluate side-chains
  88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   56 VAL
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  729 ILE
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 123 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   chunk 36 optimal weight:    0.6980
   chunk 120 optimal weight:    7.9990
   chunk 57 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 116 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.143593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.093135 restraints weight = 37174.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.20
r_work: 0.3309 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16441  Z= 0.151
  Angle     :  0.597  11.072  23529  Z= 0.300
  Chirality :  0.036   0.233   2870
  Planarity :  0.004   0.063   2018
  Dihedral  : 23.461 167.495   5573
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.67 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.89 %
    Favored  : 87.52 %
  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: -0.09 (0.24), residues: 1227
  helix:  0.87 (0.21), residues: 596
  sheet: -0.86 (0.44), residues: 133
  loop : -0.90 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A1013 
 PHE   0.017   0.002   PHE A 159 
 TYR   0.010   0.001   TYR A 122 
 ARG   0.009   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05055 (  575)
  hydrogen bonds       : angle       4.11704 ( 1569)
  covalent geometry    : bond        0.00328 (16441)
  covalent geometry    : angle       0.59743 (23529)

*********************** 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
  96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8117 (t0) cc_final: 0.7664 (t0)
REVERT: A 1017 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: L   32 ARG cc_start: 0.5339 (mtp180) cc_final: 0.4838 (ttt-90)
REVERT: L   64 LEU cc_start: 0.5377 (tp) cc_final: 0.5107 (mt)
REVERT: L   86 LEU cc_start: 0.7047 (mt) cc_final: 0.6708 (tp)
REVERT: M  117 LYS cc_start: 0.6494 (mtmm) cc_final: 0.6240 (mtmm)
  outliers start: 17
  outliers final: 15
  residues processed: 88
  average time/residue: 0.3090
  time to fit residues: 39.3559
Evaluate side-chains
  88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  327 GLU
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 A residue  729 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1017 LEU
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain O residue  174 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 104 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 118 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   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 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.145198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.095107 restraints weight = 37435.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.18
r_work: 0.3351 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  16441  Z= 0.116
  Angle     :  0.569  14.364  23529  Z= 0.282
  Chirality :  0.034   0.223   2870
  Planarity :  0.004   0.063   2018
  Dihedral  : 23.358 166.245   5573
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.99 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.27 %
    Favored  : 86.96 %
  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:  0.27 (0.24), residues: 1227
  helix:  1.18 (0.22), residues: 597
  sheet: -0.67 (0.44), residues: 133
  loop : -0.75 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 547 
 HIS   0.004   0.001   HIS L  83 
 PHE   0.017   0.001   PHE L  26 
 TYR   0.020   0.001   TYR O 235 
 ARG   0.012   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  575)
  hydrogen bonds       : angle       3.89598 ( 1569)
  covalent geometry    : bond        0.00247 (16441)
  covalent geometry    : angle       0.56916 (23529)

*********************** 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
  101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8146 (t0) cc_final: 0.7681 (t0)
REVERT: A  903 THR cc_start: 0.9378 (m) cc_final: 0.9169 (p)
REVERT: A  970 MET cc_start: 0.8407 (ttm) cc_final: 0.7933 (ttt)
REVERT: A 1017 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8870 (mp)
REVERT: L   32 ARG cc_start: 0.5438 (mtp180) cc_final: 0.4900 (ttt-90)
REVERT: L   86 LEU cc_start: 0.6945 (mt) cc_final: 0.6618 (tp)
REVERT: M  100 ARG cc_start: 0.5295 (ttp-170) cc_final: 0.5040 (mtm110)
REVERT: M  117 LYS cc_start: 0.6503 (mtmm) cc_final: 0.6217 (mtmm)
REVERT: O  154 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6942 (ptt-90)
  outliers start: 19
  outliers final: 12
  residues processed: 91
  average time/residue: 0.3765
  time to fit residues: 50.9378
Evaluate side-chains
  86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
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 A residue 1017 LEU
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   69 ASN
Chi-restraints excluded: chain L residue   74 ASN
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain O residue  154 ARG
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 111 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 148 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 149 optimal weight:    7.9990
   chunk 105 optimal weight:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 108 optimal weight:    7.9990
   chunk 146 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  74 ASN
O 205 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.140146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.090972 restraints weight = 36811.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.44
r_work: 0.3235 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  16441  Z= 0.306
  Angle     :  0.788  13.407  23529  Z= 0.393
  Chirality :  0.043   0.261   2870
  Planarity :  0.006   0.064   2018
  Dihedral  : 23.705 172.758   5573
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.11 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 10.52 %
    Favored  : 86.22 %
  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: -0.73 (0.23), residues: 1227
  helix:  0.24 (0.20), residues: 603
  sheet: -0.68 (0.48), residues: 119
  loop : -1.22 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 510 
 HIS   0.007   0.002   HIS A 983 
 PHE   0.022   0.003   PHE A 331 
 TYR   0.018   0.003   TYR A 122 
 ARG   0.010   0.001   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07583 (  575)
  hydrogen bonds       : angle       4.70751 ( 1569)
  covalent geometry    : bond        0.00683 (16441)
  covalent geometry    : angle       0.78792 (23529)

*********************** 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
  113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 78
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8032 (t0) cc_final: 0.7628 (t0)
REVERT: L   32 ARG cc_start: 0.5332 (mtp180) cc_final: 0.4906 (ttt-90)
REVERT: M  117 LYS cc_start: 0.6361 (mtmm) cc_final: 0.6104 (mtmm)
REVERT: O  154 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7147 (ptt90)
  outliers start: 35
  outliers final: 25
  residues processed: 102
  average time/residue: 0.3257
  time to fit residues: 47.5198
Evaluate side-chains
  100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   77 LEU
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  729 ILE
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1111 THR
Chi-restraints excluded: chain A residue 1123 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   69 ASN
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue  123 THR
Chi-restraints excluded: chain O residue  154 ARG
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  205 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 116 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 145 optimal weight:   20.0000
   chunk 7 optimal weight:    8.9990
   chunk 80 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 110 optimal weight:   30.0000
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.144023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.096081 restraints weight = 37097.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.34
r_work: 0.3330 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16441  Z= 0.116
  Angle     :  0.590  12.786  23529  Z= 0.294
  Chirality :  0.035   0.225   2870
  Planarity :  0.004   0.063   2018
  Dihedral  : 23.511 168.452   5573
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.24 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.20 %
    Favored  : 86.31 %
  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:  0.04 (0.24), residues: 1227
  helix:  0.87 (0.21), residues: 612
  sheet: -0.49 (0.43), residues: 133
  loop : -0.83 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 581 
 HIS   0.007   0.001   HIS O 190 
 PHE   0.015   0.001   PHE A 331 
 TYR   0.024   0.001   TYR O 235 
 ARG   0.012   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  575)
  hydrogen bonds       : angle       3.98025 ( 1569)
  covalent geometry    : bond        0.00240 (16441)
  covalent geometry    : angle       0.59036 (23529)

*********************** 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
  95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 ASN cc_start: 0.8062 (t0) cc_final: 0.7598 (t0)
REVERT: A  970 MET cc_start: 0.8378 (ttm) cc_final: 0.8031 (ttt)
REVERT: L   32 ARG cc_start: 0.5317 (mtp180) cc_final: 0.4792 (ttt-90)
REVERT: L   86 LEU cc_start: 0.7007 (mt) cc_final: 0.6638 (tp)
REVERT: M  117 LYS cc_start: 0.6343 (mtmm) cc_final: 0.6056 (mtmm)
REVERT: O  154 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7001 (ptt-90)
REVERT: O  170 LYS cc_start: 0.7833 (tttt) cc_final: 0.7479 (tppt)
  outliers start: 16
  outliers final: 10
  residues processed: 86
  average time/residue: 0.2782
  time to fit residues: 35.8037
Evaluate side-chains
  88 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  538 GLU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain O residue  154 ARG
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 28 optimal weight:    0.6980
   chunk 149 optimal weight:    5.9990
   chunk 136 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   chunk 48 optimal weight:    0.7980
   chunk 117 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0270
   overall best weight:    2.5042

-------------------------------------------------------------------------------
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**
** O 205 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 = 0.4319 r_free = 0.4319 target = 0.142430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.093593 restraints weight = 37313.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.33
r_work: 0.3285 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  16441  Z= 0.182
  Angle     :  0.635  12.813  23529  Z= 0.316
  Chirality :  0.037   0.239   2870
  Planarity :  0.005   0.063   2018
  Dihedral  : 23.564 170.425   5573
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.46 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.20 %
    Favored  : 86.31 %
  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: -0.15 (0.24), residues: 1227
  helix:  0.69 (0.21), residues: 613
  sheet: -0.50 (0.43), residues: 138
  loop : -0.91 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A1013 
 PHE   0.017   0.002   PHE A 331 
 TYR   0.010   0.001   TYR A 638 
 ARG   0.012   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05524 (  575)
  hydrogen bonds       : angle       4.19456 ( 1569)
  covalent geometry    : bond        0.00402 (16441)
  covalent geometry    : angle       0.63470 (23529)

********************** 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
  93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ARG cc_start: 0.6441 (ptm160) cc_final: 0.6190 (ptm160)
REVERT: A   95 ASN cc_start: 0.8078 (t0) cc_final: 0.7655 (t0)
REVERT: L   32 ARG cc_start: 0.5319 (mtp180) cc_final: 0.4796 (ttt-90)
REVERT: L   86 LEU cc_start: 0.7040 (mt) cc_final: 0.6681 (tp)
REVERT: M  117 LYS cc_start: 0.6404 (mtmm) cc_final: 0.6107 (mtmm)
REVERT: O  154 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6966 (ptt-90)
REVERT: O  170 LYS cc_start: 0.7677 (tttt) cc_final: 0.7275 (tppt)
REVERT: O  190 HIS cc_start: 0.7115 (m90) cc_final: 0.6812 (m90)
  outliers start: 16
  outliers final: 14
  residues processed: 86
  average time/residue: 0.3079
  time to fit residues: 39.4531
Evaluate side-chains
  93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   77 LEU
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  729 ILE
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain O residue  154 ARG
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 98 optimal weight:   30.0000
   chunk 58 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 128 optimal weight:    8.9990
   chunk 143 optimal weight:    7.9990
   chunk 119 optimal weight:   30.0000
   chunk 111 optimal weight:   20.0000
   chunk 41 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 44 optimal weight:    0.7980
   overall best weight:    3.7386

-------------------------------------------------------------------------------
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**
** O 205 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 = 0.4299 r_free = 0.4299 target = 0.140871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.092034 restraints weight = 37139.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.46
r_work: 0.3243 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  16441  Z= 0.251
  Angle     :  0.727  12.555  23529  Z= 0.361
  Chirality :  0.040   0.249   2870
  Planarity :  0.005   0.067   2018
  Dihedral  : 23.738 173.872   5573
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.95 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.73 %
    Favored  : 86.50 %
  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: -0.59 (0.23), residues: 1227
  helix:  0.26 (0.20), residues: 613
  sheet: -0.64 (0.43), residues: 138
  loop : -1.04 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 510 
 HIS   0.005   0.001   HIS A1013 
 PHE   0.021   0.002   PHE A 331 
 TYR   0.014   0.002   TYR A 638 
 ARG   0.010   0.001   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06626 (  575)
  hydrogen bonds       : angle       4.50592 ( 1569)
  covalent geometry    : bond        0.00561 (16441)
  covalent geometry    : angle       0.72695 (23529)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9773.91 seconds
wall clock time: 167 minutes 16.24 seconds (10036.24 seconds total)