Starting phenix.real_space_refine
on Sun Oct 25 14:04:48 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qxb_14197/10_2026/7qxb_14197.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     277      5.49       5
     S      42      5.16       5
     C    9714      2.51       5
     N    3124      2.21       5
     O    3896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17053
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 951, 7626
          Classifications: {'peptide': 951}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 893}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 5431
          Classifications: {'RNAv2': 256}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 99, 'rna3p_pyr': 124}
          Link IDs: {'rna2p': 33, 'rna3p': 222}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 643
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "M"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "N"
      Number of atoms: 461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 461
          Classifications: {'DNA': 22}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 21}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 955
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1238
          Classifications: {'peptide': 251}
          Incomplete info: {'truncation_to_alanine': 226}
          Link IDs: {'PTRANS': 9, 'TRANS': 241}
          Chain breaks: 3
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 814
          Unresolved non-hydrogen angles: 1054
          Unresolved non-hydrogen dihedrals: 678
          Unresolved non-hydrogen chiralities: 88
          Planarities with less than four sites: {'ASN:plan1': 11, 'TYR:plan': 13, 'GLN:plan1': 10, 'PHE:plan': 13, 'ASP:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10, 'HIS:plan': 8, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 420
  Time building chain proxies: 3.31, per 1000 atoms: 0.19
  Number of scatterers: 17053
  At special positions: 0
  Unit cell: (166.77, 128.62, 143.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P     277     15.00
     O    3896      8.00
     N    3124      7.00
     C    9714      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 501.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 12 sheets defined
      50.9% alpha, 19.5% beta
      70 base pairs and 135 stacking pairs defined.
    Time for finding SS restraints: 1.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.742A  pdb=" N   ARG A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.559A  pdb=" N   LEU A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
    Processing helix  chain 'A' and resid 383 through 401
      removed outlier: 3.904A  pdb=" N   TRP A 387 " --> pdb=" O   PRO A 383 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG A 390 " --> pdb=" O   TYR A 386 " (cutoff:3.500A)
      Proline residue:  A 391  - end of helix
    Processing helix  chain 'A' and resid 404 through 413
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.554A  pdb=" N   GLN A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.666A  pdb=" N   VAL A 461 " --> pdb=" O   SER A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.852A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.882A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 497 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
    Processing helix  chain 'A' and resid 530 through 551
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 3.786A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 3.792A  pdb=" N   ARG A 657 " --> pdb=" O   ARG A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
    Processing helix  chain 'A' and resid 682 through 688
      removed outlier: 3.742A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 699
    Processing helix  chain 'A' and resid 721 through 734
      removed outlier: 3.529A  pdb=" N   LEU A 725 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 835 through 854
      removed outlier: 3.719A  pdb=" N   THR A 839 " --> pdb=" O   SER A 835 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   LEU A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   LEU A 841 " --> pdb=" O   LEU A 837 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS A 852 " --> pdb=" O   ASP A 848 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 853 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 861
      removed outlier: 4.271A  pdb=" N   ASP A 860 " --> pdb=" O   GLY A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 899 through 902
      removed outlier: 3.699A  pdb=" N   LYS A 902 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 899 through 902'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.521A  pdb=" N   ASN A 969 " --> pdb=" O   LYS A 965 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 980 " --> pdb=" O   GLY A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
      removed outlier: 3.704A  pdb=" N   LEU A 987 " --> pdb=" O   HIS A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1018
      removed outlier: 3.516A  pdb=" N   TYR A1010 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1028
      removed outlier: 3.504A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASN A1028 " --> pdb=" O   VAL A1025 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1024 through 1028'
    Processing helix  chain 'A' and resid 1029 through 1051
      removed outlier: 4.271A  pdb=" N   CYS A1043 " --> pdb=" O   THR A1039 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1085
      removed outlier: 3.758A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS A1081 " --> pdb=" O   ALA A1077 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ARG A1084 " --> pdb=" O   LEU A1080 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   HIS A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.618A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.150A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
    Processing helix  chain 'A' and resid 1124 through 1129
      removed outlier: 3.899A  pdb=" N   LYS A1128 " --> pdb=" O   PRO A1124 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   THR A1129 " --> pdb=" O   SER A1125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1124 through 1129'
    Processing helix  chain 'L' and resid 19 through 23
    Processing helix  chain 'L' and resid 27 through 38
      removed outlier: 3.826A  pdb=" N   ARG L  32 " --> pdb=" O   VAL L  28 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ARG L  33 " --> pdb=" O   GLY L  29 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG L  36 " --> pdb=" O   ARG L  32 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS L  37 " --> pdb=" O   ARG L  33 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 73
      removed outlier: 4.571A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL L  55 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LEU L  56 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR L  58 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU L  64 " --> pdb=" O   THR L  60 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA L  67 " --> pdb=" O   ILE L  63 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASP L  73 " --> pdb=" O   ASN L  69 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 90
      removed outlier: 3.816A  pdb=" N   LEU L  84 " --> pdb=" O   ILE L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 92 through 98
      removed outlier: 3.590A  pdb=" N   LEU L  97 " --> pdb=" O   GLU L  93 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 38 through 50
      removed outlier: 3.843A  pdb=" N   TYR M  43 " --> pdb=" O   SER M  39 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL M  45 " --> pdb=" O   TYR M  41 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 4.111A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL M  67 " --> pdb=" O   MET M  63 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE M  74 " --> pdb=" O   ILE M  70 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 4.149A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL M  99 " --> pdb=" O   ILE M  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU M 101 " --> pdb=" O   THR M  97 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 124
      removed outlier: 3.593A  pdb=" N   LYS M 109 " --> pdb=" O   GLY M 105 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS M 121 " --> pdb=" O   LYS M 117 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 98 through 104
    Processing helix  chain 'O' and resid 158 through 165
    Processing helix  chain 'O' and resid 169 through 173
    Processing helix  chain 'O' and resid 223 through 226
    Processing helix  chain 'O' and resid 227 through 238
    Processing helix  chain 'P' and resid 65 through 69
      removed outlier: 3.525A  pdb=" N   LEU P  69 " --> pdb=" O   TYR P  66 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 152 through 156
    Processing helix  chain 'P' and resid 206 through 214
      removed outlier: 3.529A  pdb=" N   GLN P 214 " --> pdb=" O   ILE P 210 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 215 through 217
      No H-bonds generated for 'chain 'P' and resid 215 through 217'
    Processing helix  chain 'P' and resid 225 through 232
      removed outlier: 4.198A  pdb=" N   VAL P 229 " --> pdb=" O   ASN P 225 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 269 through 273
    Processing helix  chain 'P' and resid 282 through 299
      removed outlier: 3.697A  pdb=" N   THR P 298 " --> pdb=" O   SER P 294 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 4.110A  pdb=" N   ALA A 167 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   GLU A 793 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 790 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   LEU A 798 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   TYR A 739 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 600
      removed outlier: 7.101A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE A 633 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 624 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY A 629 " --> pdb=" O   LYS A 626 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 865
    Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 44
      removed outlier: 7.850A  pdb=" N   ARG L  43 " --> pdb=" O   ILE M  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 122
      removed outlier: 6.832A  pdb=" N   LEU O 145 " --> pdb=" O   LEU O 118 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   VAL O 120 " --> pdb=" O   THR O 143 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   THR O 143 " --> pdb=" O   VAL O 120 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL O 206 " --> pdb=" O   CYS O 187 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   CYS O 187 " --> pdb=" O   VAL O 206 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ARG O 208 " --> pdb=" O   GLN O 185 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LEU O 181 " --> pdb=" O   LEU O 212 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG O 180 " --> pdb=" O   LEU O 117 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'P' and resid 21 through 37
      removed outlier: 6.728A  pdb=" N   THR P  48 " --> pdb=" O   LYS P  30 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE P  32 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL P  46 " --> pdb=" O   PHE P  32 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   CYS P  44 " --> pdb=" O   PRO P  34 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   THR P  93 " --> pdb=" O   LYS P  56 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   THR P  58 " --> pdb=" O   THR P  93 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   PHE P  62 " --> pdb=" O   THR P  97 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   SER P  99 " --> pdb=" O   PHE P  62 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ARG P  83 " --> pdb=" O   SER P  98 " (cutoff:3.500A)
      removed outlier: 11.364A  pdb=" N   GLY P 100 " --> pdb=" O   PHE P  81 " (cutoff:3.500A)
      removed outlier: 9.816A  pdb=" N   PHE P  81 " --> pdb=" O   GLY P 100 " (cutoff:3.500A)
      removed outlier: 11.031A  pdb=" N   ALA P 102 " --> pdb=" O   VAL P  79 " (cutoff:3.500A)
      removed outlier: 9.775A  pdb=" N   VAL P  79 " --> pdb=" O   ALA P 102 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ILE P  78 " --> pdb=" O   VAL P  29 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL P  29 " --> pdb=" O   ILE P  78 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   ARG P  80 " --> pdb=" O   GLY P  27 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   GLY P  27 " --> pdb=" O   ARG P  80 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   HIS P  82 " --> pdb=" O   VAL P  25 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL P  25 " --> pdb=" O   HIS P  82 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'P' and resid 204 through 205
      removed outlier: 6.580A  pdb=" N   LYS P 182 " --> pdb=" O   LEU P 169 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   LYS P 171 " --> pdb=" O   LEU P 180 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LEU P 180 " --> pdb=" O   LYS P 171 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLU P 173 " --> pdb=" O   SER P 178 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   SER P 178 " --> pdb=" O   GLU P 173 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   PHE P 263 " --> pdb=" O   ASP P 219 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE P 238 " --> pdb=" O   LEU P 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'P' and resid 204 through 205
      removed outlier: 5.081A  pdb=" N   PHE P 162 " --> pdb=" O   SER P 243 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE P 238 " --> pdb=" O   LEU P 278 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1596 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      186 hydrogen bonds
      352 hydrogen bond angles
      0 basepair planarities
      70 basepair parallelities
      135 stacking parallelities
  Total time for adding SS restraints: 4.59

  Time building geometry restraints manager: 1.68 seconds

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

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

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 24086
        2.96 -     5.93: 1435
        5.93 -     8.89: 126
        8.89 -    11.85: 9
       11.85 -    14.81: 3
  Bond angle restraints: 25659
  Sorted by residual:
  angle pdb=" N   ARG A1084 "
        pdb=" CA  ARG A1084 "
        pdb=" C   ARG A1084 "
      ideal   model   delta    sigma   weight residual
     111.14  119.63   -8.49 1.08e+00 8.57e-01 6.17e+01
  angle pdb=" N   ASP A 516 "
        pdb=" CA  ASP A 516 "
        pdb=" C   ASP A 516 "
      ideal   model   delta    sigma   weight residual
     111.82  120.52   -8.70 1.16e+00 7.43e-01 5.62e+01
  angle pdb=" N   SER A 165 "
        pdb=" CA  SER A 165 "
        pdb=" C   SER A 165 "
      ideal   model   delta    sigma   weight residual
     112.97  120.26   -7.29 1.06e+00 8.90e-01 4.72e+01
  angle pdb=" N   VAL A 888 "
        pdb=" CA  VAL A 888 "
        pdb=" C   VAL A 888 "
      ideal   model   delta    sigma   weight residual
     110.53  104.39    6.14 9.40e-01 1.13e+00 4.27e+01
  angle pdb=" N   GLU O 101 "
        pdb=" CA  GLU O 101 "
        pdb=" C   GLU O 101 "
      ideal   model   delta    sigma   weight residual
     111.28  118.02   -6.74 1.09e+00 8.42e-01 3.83e+01
  ... (remaining 25654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.36: 9495
       34.36 -    68.72: 598
       68.72 -   103.08: 49
      103.08 -   137.44: 2
      137.44 -   171.80: 11
  Dihedral angle restraints: 10155
    sinusoidal: 5831
      harmonic: 4324
  Sorted by residual:
  dihedral pdb=" C4'   G B 251 "
           pdb=" C3'   G B 251 "
           pdb=" C2'   G B 251 "
           pdb=" C1'   G B 251 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -42.82   79.17     1      3.10e+00 1.04e-01 8.11e+02
  dihedral pdb=" C4'   A B  48 "
           pdb=" C3'   A B  48 "
           pdb=" C2'   A B  48 "
           pdb=" C1'   A B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -42.74   79.09     1      3.10e+00 1.04e-01 8.10e+02
  dihedral pdb=" C4'   C B 284 "
           pdb=" C3'   C B 284 "
           pdb=" C2'   C B 284 "
           pdb=" C1'   C B 284 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -41.97   78.32     1      3.10e+00 1.04e-01 7.97e+02
  ... (remaining 10152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 2131
       0.106 -    0.212: 718
       0.212 -    0.318: 277
       0.318 -    0.424: 21
       0.424 -    0.531: 6
  Chirality restraints: 3153
  Sorted by residual:
  chirality pdb=" C3'   C B 142 "
            pdb=" C4'   C B 142 "
            pdb=" O3'   C B 142 "
            pdb=" C2'   C B 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.97   -0.53 2.00e-01 2.50e+01 7.04e+00
  chirality pdb=" C3'   G B 292 "
            pdb=" C4'   G B 292 "
            pdb=" O3'   G B 292 "
            pdb=" C2'   G B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.97   -0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" CA  ASP A1126 "
            pdb=" N   ASP A1126 "
            pdb=" C   ASP A1126 "
            pdb=" CB  ASP A1126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.04e+00
  ... (remaining 3150 not shown)

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

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1283
        2.74 -     3.28: 16577
        3.28 -     3.82: 28842
        3.82 -     4.36: 35195
        4.36 -     4.90: 52349
  Nonbonded interactions: 134246
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 943 "
            pdb=" NZ  LYS A1003 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NZ  LYS A1027 "
            pdb=" OP1   U B 312 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OP2   C B 244 "
            pdb=" NH2 ARG L  43 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NH1 ARG A 481 "
            pdb=" OP2   C B 183 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   TRP A 510 "
            pdb=" O2'   C B 313 "
     model   vdw
     2.314 3.040
  ... (remaining 134241 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.600
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.535  17945  Z= 0.698
  Angle     :  1.549  36.960  25661  Z= 0.912
  Chirality :  0.118   0.531   3153
  Planarity :  0.011   0.118   2272
  Dihedral  : 19.469 171.805   7346
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.64 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.01 %
    Favored  : 95.52 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.19), residues: 1466
  helix: -0.97 (0.18), residues: 591
  sheet: -1.19 (0.34), residues: 188
  loop : -1.71 (0.21), residues: 687

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00987 /  0.67 (17944)
  covalent geometry    : angle       1.52380 /  0.90 (25659)
  SS BOND              : bond        0.53508 / 28.16 (    1)
  SS BOND              : angle      31.45145 / 17.92 (    2)
  hydrogen bonds       : bond        0.21906 / 15.01 (  746)
  hydrogen bonds       : angle       8.13514 /  5.91 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 224
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 PHE cc_start: 0.8758 (m-10) cc_final: 0.8285 (m-80)
REVERT: A  333 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (m-80)
REVERT: A  536 LEU cc_start: 0.9115 (tp) cc_final: 0.8895 (tt)
REVERT: A  656 SER cc_start: 0.8454 (t) cc_final: 0.7973 (m)
REVERT: A  850 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: A  899 ASN cc_start: 0.8334 (t0) cc_final: 0.8084 (t0)
REVERT: A  902 LYS cc_start: 0.8765 (mttt) cc_final: 0.8536 (tptt)
REVERT: L   89 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6194 (ptm-80)
REVERT: M   49 VAL cc_start: 0.7324 (m) cc_final: 0.7120 (m)
REVERT: M  117 LYS cc_start: 0.7704 (mttt) cc_final: 0.7326 (tppt)
REVERT: O  103 ILE cc_start: 0.7819 (mm) cc_final: 0.7475 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 227
  average time/residue: 0.1701
  time to fit residues: 53.9324
Evaluate side-chains
  127 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue 1074 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149]
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  53 GLN
A 330 HIS
A 388 GLN
A 482 HIS
A 585 GLN
** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 700 GLN
A 969 ASN
A1013 HIS
M  50 HIS
M  64 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.102614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.073938 restraints weight = 87352.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.075878 restraints weight = 43459.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.077030 restraints weight = 29085.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.077621 restraints weight = 23509.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.078005 restraints weight = 21170.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103  17945  Z= 0.264
  Angle     :  1.423  21.343  25661  Z= 0.593
  Chirality :  0.127   1.798   3153
  Planarity :  0.007   0.096   2272
  Dihedral  : 20.020 174.890   4937
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.11 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.21), residues: 1466
  helix:  0.69 (0.20), residues: 606
  sheet: -0.88 (0.35), residues: 196
  loop : -1.19 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 175 
 TYR   0.020   0.003   TYR A1002 
 PHE   0.029   0.003   PHE A 331 
 TRP   0.029   0.002   TRP A 547 
 HIS   0.007   0.002   HIS M 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.26 (17944)
  covalent geometry    : angle       1.42311 /  0.59 (25659)
  SS BOND              : bond        0.00181 /  0.10 (    1)
  SS BOND              : angle       3.97690 /  2.34 (    2)
  hydrogen bonds       : bond        0.07096 /  4.83 (  746)
  hydrogen bonds       : angle       5.13442 /  3.75 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7505 (mpt180) cc_final: 0.7289 (mmt180)
REVERT: A  605 GLU cc_start: 0.8812 (mp0) cc_final: 0.8562 (mp0)
REVERT: A  809 PHE cc_start: 0.8721 (t80) cc_final: 0.8417 (t80)
REVERT: A  902 LYS cc_start: 0.8629 (mttt) cc_final: 0.8415 (tptt)
REVERT: A  903 THR cc_start: 0.8944 (m) cc_final: 0.8626 (p)
REVERT: A  930 TRP cc_start: 0.7779 (t60) cc_final: 0.7458 (t60)
REVERT: M   52 ASP cc_start: 0.8502 (t0) cc_final: 0.8092 (p0)
REVERT: M  117 LYS cc_start: 0.7303 (mttt) cc_final: 0.6987 (tppt)
REVERT: O  103 ILE cc_start: 0.7924 (mm) cc_final: 0.7592 (mt)
  outliers start: 26
  outliers final: 13
  residues processed: 150
  average time/residue: 0.1379
  time to fit residues: 31.0882
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain M residue   69 ASP
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  183 LEU
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [152, 35, 33, 59, 91, 120, 153, 140, 114, 90, 115]
   chunk 152 optimal weight:   50.0000
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 120 optimal weight:    9.9990
   chunk 153 optimal weight:   50.0000
   chunk 140 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 775 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.100962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.072935 restraints weight = 90641.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.074724 restraints weight = 45961.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.075785 restraints weight = 31442.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.076368 restraints weight = 25777.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.076596 restraints weight = 23345.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  17945  Z= 0.234
  Angle     :  1.162  16.107  25661  Z= 0.490
  Chirality :  0.094   1.285   3153
  Planarity :  0.006   0.125   2272
  Dihedral  : 19.948 171.762   4935
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 12.98 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.21), residues: 1466
  helix:  0.93 (0.20), residues: 607
  sheet: -0.74 (0.36), residues: 192
  loop : -1.15 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.058   0.001   ARG L  72 
 TYR   0.020   0.003   TYR A 462 
 PHE   0.024   0.002   PHE A 575 
 TRP   0.036   0.003   TRP A 387 
 HIS   0.005   0.002   HIS A 546 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00495 /  0.23 (17944)
  covalent geometry    : angle       1.16166 /  0.49 (25659)
  SS BOND              : bond        0.01083 /  0.57 (    1)
  SS BOND              : angle       3.59454 /  2.10 (    2)
  hydrogen bonds       : bond        0.06114 /  4.13 (  746)
  hydrogen bonds       : angle       4.86065 /  3.56 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8541 (mp)
REVERT: A  366 LEU cc_start: 0.6811 (mt) cc_final: 0.6565 (mp)
REVERT: A  411 THR cc_start: 0.9025 (m) cc_final: 0.8784 (p)
REVERT: A  872 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5566 (mp)
REVERT: A  930 TRP cc_start: 0.7696 (t60) cc_final: 0.7285 (t60)
REVERT: L   85 GLN cc_start: 0.7403 (mm110) cc_final: 0.7059 (pp30)
REVERT: M   52 ASP cc_start: 0.8574 (t0) cc_final: 0.8206 (p0)
REVERT: O  101 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8415 (pm20)
  outliers start: 36
  outliers final: 19
  residues processed: 132
  average time/residue: 0.1265
  time to fit residues: 25.6794
Evaluate side-chains
  111 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain M residue  120 THR
Chi-restraints excluded: chain M residue  121 LYS
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [100, 106, 74, 91, 132, 169, 103, 113, 78, 76, 153]
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   10.0000
   chunk 74 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 132 optimal weight:   30.0000
   chunk 169 optimal weight:   50.0000
   chunk 103 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 153 optimal weight:   40.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 ASN
M  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.097810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.069789 restraints weight = 91383.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.071386 restraints weight = 49351.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.072297 restraints weight = 34990.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.072681 restraints weight = 29183.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.072971 restraints weight = 26924.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080  17945  Z= 0.322
  Angle     :  1.221  14.056  25661  Z= 0.522
  Chirality :  0.089   1.310   3153
  Planarity :  0.007   0.057   2272
  Dihedral  : 19.808 170.865   4935
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.91 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.31 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.21), residues: 1466
  helix:  0.18 (0.20), residues: 621
  sheet: -0.91 (0.38), residues: 181
  loop : -1.31 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 756 
 TYR   0.022   0.003   TYR A 462 
 PHE   0.027   0.004   PHE A 809 
 TRP   0.022   0.003   TRP O 167 
 HIS   0.012   0.002   HIS A 687 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00691 /  0.32 (17944)
  covalent geometry    : angle       1.22058 /  0.52 (25659)
  SS BOND              : bond        0.00381 /  0.20 (    1)
  SS BOND              : angle       3.06550 /  1.80 (    2)
  hydrogen bonds       : bond        0.07027 /  4.71 (  746)
  hydrogen bonds       : angle       5.22249 /  3.83 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 97
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6710 (m170)
REVERT: A  756 ARG cc_start: 0.8926 (mtp-110) cc_final: 0.8653 (mmm160)
REVERT: A  872 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5643 (mp)
REVERT: L   52 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8042 (mt)
REVERT: L   75 LYS cc_start: 0.7143 (tppt) cc_final: 0.6708 (tptt)
REVERT: L   85 GLN cc_start: 0.7363 (mm110) cc_final: 0.7143 (pp30)
REVERT: M   52 ASP cc_start: 0.8687 (t0) cc_final: 0.8329 (p0)
REVERT: M  122 TYR cc_start: 0.8933 (t80) cc_final: 0.8590 (t80)
  outliers start: 46
  outliers final: 34
  residues processed: 134
  average time/residue: 0.1350
  time to fit residues: 27.1908
Evaluate side-chains
  123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 86
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [27, 105, 48, 26, 174, 86, 18, 17, 142, 30, 5]
   chunk 27 optimal weight:    0.0980
   chunk 105 optimal weight:   20.0000
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 174 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 142 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.100819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.072730 restraints weight = 88402.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.074489 restraints weight = 45310.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.075532 restraints weight = 31084.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.075992 restraints weight = 25631.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.076102 restraints weight = 23472.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17945  Z= 0.173
  Angle     :  1.026  13.357  25661  Z= 0.430
  Chirality :  0.080   1.272   3153
  Planarity :  0.005   0.052   2272
  Dihedral  : 19.606 167.936   4935
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.68 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.09 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.21), residues: 1466
  helix:  0.93 (0.21), residues: 618
  sheet: -0.49 (0.36), residues: 199
  loop : -1.16 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 865 
 TYR   0.031   0.002   TYR A 462 
 PHE   0.025   0.002   PHE A 809 
 TRP   0.023   0.002   TRP A 581 
 HIS   0.005   0.001   HIS A 983 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 (17944)
  covalent geometry    : angle       1.02619 /  0.43 (25659)
  SS BOND              : bond        0.01107 /  0.58 (    1)
  SS BOND              : angle       2.90069 /  1.70 (    2)
  hydrogen bonds       : bond        0.05111 /  3.40 (  746)
  hydrogen bonds       : angle       4.59662 /  3.36 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8550 (pp) cc_final: 0.8281 (mm)
REVERT: A  176 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7358 (t80)
REVERT: A  411 THR cc_start: 0.9015 (m) cc_final: 0.8787 (p)
REVERT: A  462 TYR cc_start: 0.8305 (t80) cc_final: 0.8095 (t80)
REVERT: A  605 GLU cc_start: 0.8719 (mp0) cc_final: 0.8493 (mp0)
REVERT: A  903 THR cc_start: 0.9063 (m) cc_final: 0.8663 (p)
REVERT: L   52 LEU cc_start: 0.8330 (tp) cc_final: 0.7973 (mt)
REVERT: L   75 LYS cc_start: 0.7222 (tppt) cc_final: 0.6845 (tptt)
REVERT: M   52 ASP cc_start: 0.8700 (t0) cc_final: 0.8388 (p0)
  outliers start: 33
  outliers final: 24
  residues processed: 129
  average time/residue: 0.1392
  time to fit residues: 26.8978
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   64 ASN
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain O residue  104 LEU
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [91, 74, 24, 70, 106, 148, 71, 12, 2, 72, 149]
   chunk 91 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 70 optimal weight:    0.4980
   chunk 106 optimal weight:    9.9990
   chunk 148 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    2.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.100610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.072551 restraints weight = 89390.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.074318 restraints weight = 45310.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.075389 restraints weight = 30969.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.075817 restraints weight = 25400.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.076205 restraints weight = 23308.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  17945  Z= 0.177
  Angle     :  1.002  13.237  25661  Z= 0.421
  Chirality :  0.077   1.184   3153
  Planarity :  0.005   0.058   2272
  Dihedral  : 19.528 167.943   4935
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.09 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 17.74 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.22), residues: 1466
  helix:  0.96 (0.21), residues: 618
  sheet: -0.49 (0.35), residues: 207
  loop : -1.11 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 390 
 TYR   0.019   0.002   TYR A 462 
 PHE   0.020   0.002   PHE M  71 
 TRP   0.022   0.002   TRP A 581 
 HIS   0.004   0.001   HIS A 534 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.18 (17944)
  covalent geometry    : angle       1.00194 /  0.42 (25659)
  SS BOND              : bond        0.00826 /  0.43 (    1)
  SS BOND              : angle       2.49662 /  1.44 (    2)
  hydrogen bonds       : bond        0.05007 /  3.35 (  746)
  hydrogen bonds       : angle       4.52764 /  3.29 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 94
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8587 (pp) cc_final: 0.8260 (mm)
REVERT: A  176 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (t80)
REVERT: A  412 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6732 (m170)
REVERT: A  749 LYS cc_start: 0.6213 (tptp) cc_final: 0.5911 (tptt)
REVERT: A  903 THR cc_start: 0.9087 (m) cc_final: 0.8692 (p)
REVERT: L   52 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7992 (mt)
REVERT: L   75 LYS cc_start: 0.7273 (tppt) cc_final: 0.6768 (tptt)
REVERT: M   52 ASP cc_start: 0.8800 (t0) cc_final: 0.8465 (p0)
REVERT: O  103 ILE cc_start: 0.7543 (tp) cc_final: 0.7175 (pt)
  outliers start: 41
  outliers final: 28
  residues processed: 125
  average time/residue: 0.1308
  time to fit residues: 24.7066
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Chi-restraints excluded: chain O residue  233 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [116, 112, 82, 146, 0, 109, 174, 19, 128, 5, 75]
   chunk 116 optimal weight:   10.0000
   chunk 112 optimal weight:   10.0000
   chunk 82 optimal weight:    0.7980
   chunk 146 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 109 optimal weight:    8.9990
   chunk 174 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 128 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0870
   chunk 75 optimal weight:   10.0000
   overall best weight:    5.1764

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 687 HIS
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  83 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.097823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.069881 restraints weight = 90784.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.071479 restraints weight = 47742.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.072265 restraints weight = 33565.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.072820 restraints weight = 28355.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 65)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.073204 restraints weight = 25861.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  17945  Z= 0.276
  Angle     :  1.102  12.564  25661  Z= 0.469
  Chirality :  0.079   1.136   3153
  Planarity :  0.006   0.070   2272
  Dihedral  : 19.638 169.480   4935
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.98 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.65 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.21), residues: 1466
  helix:  0.33 (0.20), residues: 622
  sheet: -0.77 (0.36), residues: 199
  loop : -1.38 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 865 
 TYR   0.037   0.003   TYR A 462 
 PHE   0.021   0.003   PHE A 331 
 TRP   0.022   0.002   TRP A 581 
 HIS   0.008   0.002   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00595 /  0.28 (17944)
  covalent geometry    : angle       1.10213 /  0.47 (25659)
  SS BOND              : bond        0.00470 /  0.25 (    1)
  SS BOND              : angle       2.84738 /  1.67 (    2)
  hydrogen bonds       : bond        0.06242 /  4.16 (  746)
  hydrogen bonds       : angle       4.87360 /  3.53 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 88
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7567 (t80)
REVERT: A  412 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6903 (m-70)
REVERT: A  459 TRP cc_start: 0.7229 (OUTLIER) cc_final: 0.6465 (t60)
REVERT: A  462 TYR cc_start: 0.8443 (t80) cc_final: 0.8222 (t80)
REVERT: A  749 LYS cc_start: 0.6413 (tptp) cc_final: 0.6177 (tptt)
REVERT: L   52 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8000 (mt)
REVERT: L   75 LYS cc_start: 0.7098 (tppt) cc_final: 0.6842 (tmtt)
REVERT: M   52 ASP cc_start: 0.8817 (t0) cc_final: 0.8464 (p0)
REVERT: O  101 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8179 (pm20)
  outliers start: 44
  outliers final: 35
  residues processed: 124
  average time/residue: 0.1411
  time to fit residues: 26.0865
Evaluate side-chains
  122 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 83
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  162 LEU
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Chi-restraints excluded: chain O residue  233 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [107, 109, 156, 5, 57, 105, 73, 11, 130, 144, 87]
   chunk 107 optimal weight:   30.0000
   chunk 109 optimal weight:    7.9990
   chunk 156 optimal weight:   40.0000
   chunk 5 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 73 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 144 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    3.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 500 HIS
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.099322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.071348 restraints weight = 90265.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.073042 restraints weight = 46297.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.074068 restraints weight = 31962.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.074492 restraints weight = 26353.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.074791 restraints weight = 24216.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  17945  Z= 0.203
  Angle     :  1.003  12.925  25661  Z= 0.422
  Chirality :  0.075   1.135   3153
  Planarity :  0.005   0.071   2272
  Dihedral  : 19.569 170.711   4935
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.23 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.11 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.22), residues: 1466
  helix:  0.68 (0.21), residues: 621
  sheet: -0.62 (0.36), residues: 197
  loop : -1.33 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 865 
 TYR   0.028   0.002   TYR A 462 
 PHE   0.021   0.002   PHE M  71 
 TRP   0.025   0.002   TRP A 581 
 HIS   0.006   0.001   HIS A1013 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.20 (17944)
  covalent geometry    : angle       1.00249 /  0.42 (25659)
  SS BOND              : bond        0.00638 /  0.34 (    1)
  SS BOND              : angle       2.33709 /  1.35 (    2)
  hydrogen bonds       : bond        0.05121 /  3.39 (  746)
  hydrogen bonds       : angle       4.61195 /  3.34 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 95
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8721 (pp) cc_final: 0.8380 (mm)
REVERT: A  412 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6788 (m170)
REVERT: A  459 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6422 (t60)
REVERT: A  462 TYR cc_start: 0.8372 (t80) cc_final: 0.8148 (t80)
REVERT: A  749 LYS cc_start: 0.6296 (tptp) cc_final: 0.6051 (tptt)
REVERT: L   24 LEU cc_start: 0.7708 (mm) cc_final: 0.7088 (tp)
REVERT: L   52 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8014 (mt)
REVERT: L   75 LYS cc_start: 0.7193 (tppt) cc_final: 0.6848 (tmtt)
REVERT: M   52 ASP cc_start: 0.8829 (t0) cc_final: 0.8465 (p0)
REVERT: O  101 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8102 (pm20)
  outliers start: 40
  outliers final: 29
  residues processed: 128
  average time/residue: 0.1279
  time to fit residues: 24.5377
Evaluate side-chains
  120 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 88
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   71 PHE
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  186 ASP
Chi-restraints excluded: chain O residue  208 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [149, 22, 107, 156, 0, 50, 48, 86, 82, 34, 119]
   chunk 149 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 107 optimal weight:   20.0000
   chunk 156 optimal weight:   50.0000
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 119 optimal weight:   20.0000
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.100193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.072161 restraints weight = 90175.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.073901 restraints weight = 45977.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.074952 restraints weight = 31648.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.075370 restraints weight = 26100.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.075672 restraints weight = 23985.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17945  Z= 0.171
  Angle     :  0.963  12.424  25661  Z= 0.405
  Chirality :  0.072   1.034   3153
  Planarity :  0.005   0.072   2272
  Dihedral  : 19.479 173.780   4935
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.16 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.86 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.22), residues: 1466
  helix:  0.96 (0.21), residues: 620
  sheet: -0.50 (0.36), residues: 198
  loop : -1.27 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 865 
 TYR   0.028   0.002   TYR A 462 
 PHE   0.033   0.002   PHE A 809 
 TRP   0.023   0.002   TRP A 581 
 HIS   0.007   0.001   HIS M  50 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.17 (17944)
  covalent geometry    : angle       0.96325 /  0.40 (25659)
  SS BOND              : bond        0.00653 /  0.34 (    1)
  SS BOND              : angle       2.11293 /  1.21 (    2)
  hydrogen bonds       : bond        0.04751 /  3.15 (  746)
  hydrogen bonds       : angle       4.44827 /  3.22 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8720 (pp) cc_final: 0.8306 (mm)
REVERT: A  362 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: A  412 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6694 (m-70)
REVERT: A  459 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.6356 (t60)
REVERT: A  749 LYS cc_start: 0.6217 (tptp) cc_final: 0.5997 (tptt)
REVERT: A  902 LYS cc_start: 0.8623 (tptt) cc_final: 0.8251 (tptt)
REVERT: L   24 LEU cc_start: 0.7902 (mm) cc_final: 0.7310 (tp)
REVERT: L   52 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8030 (mt)
REVERT: M   52 ASP cc_start: 0.8723 (t0) cc_final: 0.8408 (p0)
REVERT: O  101 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8143 (pm20)
  outliers start: 37
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1323
  time to fit residues: 26.1209
Evaluate side-chains
  121 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  403 CYS
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue  106 GLU
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [124, 21, 72, 84, 147, 52, 113, 77, 152, 166, 44]
   chunk 124 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0060
   chunk 72 optimal weight:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 147 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 113 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 152 optimal weight:   50.0000
   chunk 166 optimal weight:   50.0000
   chunk 44 optimal weight:    0.0030
   overall best weight:    0.5006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.102407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.074626 restraints weight = 88360.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.076461 restraints weight = 44377.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.077561 restraints weight = 30178.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.078009 restraints weight = 24679.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.078346 restraints weight = 22612.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.5451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17945  Z= 0.142
  Angle     :  0.937  12.220  25661  Z= 0.391
  Chirality :  0.069   0.960   3153
  Planarity :  0.005   0.072   2272
  Dihedral  : 19.319 174.774   4935
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.45 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.22), residues: 1466
  helix:  1.22 (0.21), residues: 614
  sheet: -0.33 (0.36), residues: 204
  loop : -1.02 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 865 
 TYR   0.042   0.002   TYR A 462 
 PHE   0.022   0.002   PHE A 809 
 TRP   0.016   0.002   TRP A 547 
 HIS   0.005   0.001   HIS A 534 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.14 (17944)
  covalent geometry    : angle       0.93663 /  0.39 (25659)
  SS BOND              : bond        0.00665 /  0.35 (    1)
  SS BOND              : angle       1.59650 /  0.89 (    2)
  hydrogen bonds       : bond        0.04223 /  2.85 (  746)
  hydrogen bonds       : angle       4.25308 /  3.08 ( 1948)

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

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8619 (pp) cc_final: 0.8245 (mm)
REVERT: A  362 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: A  390 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.4243 (ptt90)
REVERT: A  459 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.6075 (t60)
REVERT: A  749 LYS cc_start: 0.5966 (tptp) cc_final: 0.5727 (tptt)
REVERT: A  903 THR cc_start: 0.9152 (m) cc_final: 0.8873 (p)
REVERT: A  970 MET cc_start: 0.7267 (ttm) cc_final: 0.6956 (ptm)
REVERT: L   24 LEU cc_start: 0.7893 (mm) cc_final: 0.7241 (tp)
REVERT: L   52 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7981 (mt)
REVERT: M   52 ASP cc_start: 0.8676 (t0) cc_final: 0.8421 (p0)
REVERT: O  101 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8207 (pm20)
  outliers start: 23
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1390
  time to fit residues: 24.7684
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   80 ILE
Chi-restraints excluded: chain M residue  106 GLU
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  208 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks: [133, 34, 96, 32, 42, 127, 98, 64, 88, 174, 129]
   chunk 133 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0670
   chunk 96 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 127 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0970
   chunk 174 optimal weight:    7.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    2.0120

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.101225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.073568 restraints weight = 89375.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.075260 restraints weight = 45040.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.076316 restraints weight = 30965.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.076750 restraints weight = 25435.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.077079 restraints weight = 23291.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.5551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  17945  Z= 0.159
  Angle     :  0.929  12.629  25661  Z= 0.389
  Chirality :  0.069   0.878   3153
  Planarity :  0.005   0.071   2272
  Dihedral  : 19.288 177.735   4935
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.92 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.22), residues: 1466
  helix:  1.29 (0.21), residues: 613
  sheet: -0.33 (0.36), residues: 204
  loop : -1.00 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 865 
 TYR   0.027   0.002   TYR A 462 
 PHE   0.027   0.002   PHE A 809 
 TRP   0.017   0.002   TRP A 547 
 HIS   0.005   0.001   HIS L  83 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.16 (17944)
  covalent geometry    : angle       0.92929 /  0.39 (25659)
  SS BOND              : bond        0.00491 /  0.26 (    1)
  SS BOND              : angle       1.96050 /  1.13 (    2)
  hydrogen bonds       : bond        0.04415 /  2.94 (  746)
  hydrogen bonds       : angle       4.24751 /  3.07 ( 1948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3971.06 seconds
wall clock time: 68 minutes 39.77 seconds (4119.77 seconds total)