Starting phenix.real_space_refine
on Wed Mar  4 23:27:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qxb_14197/03_2026/7qxb_14197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qxb_14197/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qxb_14197/03_2026/7qxb_14197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qxb_14197/03_2026/7qxb_14197.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/03_2026/7qxb_14197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qxb_14197/03_2026/7qxb_14197.map"
  }
  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-dev-5986/lib/python3.9/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: {'RNA': 256}
          Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 99, 'rna3p_pyr': 124}
          Link IDs: {'rna2p': 33, 'rna3p': 222}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 643
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "M"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "N"
      Number of atoms: 461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 461
          Classifications: {'DNA': 22}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 21}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 955
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1238
          Classifications: {'peptide': 251}
          Incomplete info: {'truncation_to_alanine': 226}
          Link IDs: {'PTRANS': 9, 'TRANS': 241}
          Chain breaks: 3
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 814
          Unresolved non-hydrogen angles: 1054
          Unresolved non-hydrogen dihedrals: 678
          Unresolved non-hydrogen chiralities: 88
          Planarities with less than four sites: {'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: 3.75, per 1000 atoms: 0.22
  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: 1.48
  Conformation dependent library (CDL) restraints added in 573.0 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: 2.23
  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: 4.04

  Time building geometry restraints manager: 1.95 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     17.990
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.535  17945  Z= 0.703
  Angle     :  1.487  36.960  25661  Z= 0.996
  Chirality :  0.096   0.590   3153
  Planarity :  0.011   0.118   2272
  Dihedral  : 22.182 171.949   8380
  Min Nonbonded Distance : 2.203

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

Rama-Z 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
  covalent geometry    : bond        0.00987 (17944)
  covalent geometry    : angle       1.46121 (25659)
  SS BOND              : bond        0.53508 (    1)
  SS BOND              : angle      31.45145 (    2)
  hydrogen bonds       : bond        0.21906 (  746)
  hydrogen bonds       : angle       8.13514 ( 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  : 0.515 
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: 0.1785
  time to fit residues: 55.7198
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  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue 1074 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   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:    9.9990
   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...

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 GLN
A 482 HIS
A 585 GLN
A 700 GLN
A 969 ASN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  50 HIS
M  64 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.102587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.074255 restraints weight = 86855.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.076064 restraints weight = 44056.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.077124 restraints weight = 29985.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.077744 restraints weight = 24482.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.077963 restraints weight = 22141.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.2943

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= 0.189
  Angle     :  0.782   9.278  25661  Z= 0.405
  Chirality :  0.044   0.327   3153
  Planarity :  0.006   0.064   2272
  Dihedral  : 23.965 171.745   5971
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.11 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.31 (0.21), residues: 1466
  helix:  0.88 (0.20), residues: 617
  sheet: -0.74 (0.35), residues: 199
  loop : -1.04 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 218 
 TYR   0.022   0.002   TYR A 462 
 PHE   0.022   0.002   PHE A 693 
 TRP   0.021   0.002   TRP A 581 
 HIS   0.008   0.002   HIS A 592 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (17944)
  covalent geometry    : angle       0.78173 (25659)
  SS BOND              : bond        0.04425 (    1)
  SS BOND              : angle       3.86786 (    2)
  hydrogen bonds       : bond        0.05386 (  746)
  hydrogen bonds       : angle       4.75008 ( 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
  158 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.495 
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  605 GLU cc_start: 0.8794 (mp0) cc_final: 0.8573 (mp0)
REVERT: A  903 THR cc_start: 0.9016 (m) cc_final: 0.8693 (p)
REVERT: L   40 TYR cc_start: 0.6669 (m-80) cc_final: 0.5887 (m-80)
REVERT: M   52 ASP cc_start: 0.8563 (t0) cc_final: 0.8151 (p0)
REVERT: O  101 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7900 (tp30)
REVERT: O  103 ILE cc_start: 0.8091 (mm) cc_final: 0.7831 (mt)
  outliers start: 21
  outliers final: 13
  residues processed: 152
  average time/residue: 0.1450
  time to fit residues: 32.4520
Evaluate side-chains
  109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  595 ARG
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 152 optimal weight:   50.0000
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 120 optimal weight:   30.0000
   chunk 153 optimal weight:   40.0000
   chunk 140 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 115 optimal weight:   20.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
A 585 GLN
A 775 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.099084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.070844 restraints weight = 90362.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.072569 restraints weight = 47034.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.073543 restraints weight = 32603.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.074126 restraints weight = 26938.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.074357 restraints weight = 24420.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  17945  Z= 0.236
  Angle     :  0.775   9.729  25661  Z= 0.402
  Chirality :  0.044   0.269   3153
  Planarity :  0.006   0.052   2272
  Dihedral  : 24.055 176.268   5969
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.57 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 14.29 %
    Favored  : 81.89 %
  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: -0.42 (0.21), residues: 1466
  helix:  0.80 (0.20), residues: 615
  sheet: -0.87 (0.36), residues: 190
  loop : -1.09 (0.22), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 865 
 TYR   0.029   0.003   TYR A 894 
 PHE   0.022   0.003   PHE A 575 
 TRP   0.021   0.002   TRP A 581 
 HIS   0.008   0.002   HIS A 687 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (17944)
  covalent geometry    : angle       0.77472 (25659)
  SS BOND              : bond        0.00945 (    1)
  SS BOND              : angle       3.13636 (    2)
  hydrogen bonds       : bond        0.05937 (  746)
  hydrogen bonds       : angle       4.80654 ( 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
  148 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 107
  time to evaluate  : 0.490 
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: 0.8676 (pp) cc_final: 0.8260 (mm)
REVERT: A  412 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6709 (m170)
REVERT: A  507 GLU cc_start: 0.6475 (mt-10) cc_final: 0.6207 (mt-10)
REVERT: A  712 ASP cc_start: 0.7246 (m-30) cc_final: 0.7031 (m-30)
REVERT: A  749 LYS cc_start: 0.6877 (tptp) cc_final: 0.6565 (tptt)
REVERT: A  902 LYS cc_start: 0.8497 (tptt) cc_final: 0.8047 (tptt)
REVERT: L   24 LEU cc_start: 0.6949 (mm) cc_final: 0.6737 (mm)
REVERT: L   40 TYR cc_start: 0.7173 (m-80) cc_final: 0.6511 (m-80)
REVERT: L   52 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8006 (mt)
REVERT: L   75 LYS cc_start: 0.7116 (tppt) cc_final: 0.6811 (tptt)
REVERT: M   52 ASP cc_start: 0.8651 (t0) cc_final: 0.8331 (p0)
REVERT: O  231 GLN cc_start: 0.9102 (pt0) cc_final: 0.8491 (pm20)
  outliers start: 41
  outliers final: 21
  residues processed: 140
  average time/residue: 0.1366
  time to fit residues: 28.7809
Evaluate side-chains
  113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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  412 HIS
Chi-restraints excluded: chain A residue  471 ARG
Chi-restraints excluded: chain A residue  472 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  996 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1079 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 O residue  155 CYS
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  238 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 132 optimal weight:   30.0000
   chunk 169 optimal weight:   50.0000
   chunk 103 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 153 optimal weight:   50.0000
   overall best weight:    6.5992

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 687 HIS
A 754 HIS
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  85 GLN
M  64 ASN
M  83 HIS
M  96 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.095800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.067944 restraints weight = 91401.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.069486 restraints weight = 49777.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.070392 restraints weight = 35383.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.070847 restraints weight = 29604.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.071014 restraints weight = 27163.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.5582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  17945  Z= 0.330
  Angle     :  0.907   9.371  25661  Z= 0.469
  Chirality :  0.048   0.242   3153
  Planarity :  0.007   0.063   2272
  Dihedral  : 24.733 167.450   5969
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 21.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.80 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.62 %
    Favored  : 78.62 %
  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: -1.43 (0.20), residues: 1466
  helix: -0.25 (0.19), residues: 623
  sheet: -1.03 (0.35), residues: 190
  loop : -1.55 (0.23), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  78 
 TYR   0.028   0.003   TYR A 946 
 PHE   0.032   0.003   PHE A 809 
 TRP   0.023   0.003   TRP O 167 
 HIS   0.015   0.003   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 (17944)
  covalent geometry    : angle       0.90670 (25659)
  SS BOND              : bond        0.00562 (    1)
  SS BOND              : angle       3.34079 (    2)
  hydrogen bonds       : bond        0.07256 (  746)
  hydrogen bonds       : angle       5.41154 ( 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
  151 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 100
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7163 (t80)
REVERT: A  459 TRP cc_start: 0.7184 (OUTLIER) cc_final: 0.6477 (t60)
REVERT: A  749 LYS cc_start: 0.6970 (tptp) cc_final: 0.6676 (tptt)
REVERT: L   40 TYR cc_start: 0.7432 (m-80) cc_final: 0.6735 (m-80)
REVERT: L   51 TYR cc_start: 0.5185 (t80) cc_final: 0.4983 (t80)
REVERT: L   75 LYS cc_start: 0.7757 (tppt) cc_final: 0.7391 (tmtt)
REVERT: L   76 LYS cc_start: 0.6345 (tttt) cc_final: 0.6090 (tttt)
REVERT: O  231 GLN cc_start: 0.8804 (pt0) cc_final: 0.8483 (pm20)
  outliers start: 51
  outliers final: 31
  residues processed: 139
  average time/residue: 0.1309
  time to fit residues: 27.6932
Evaluate side-chains
  122 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  594 LYS
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  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  977 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1079 LEU
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 M residue   42 VAL
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  103 ILE
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  162 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 105 optimal weight:   30.0000
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 174 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 142 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
A 736 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 GLN
** L  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  48 GLN
M  64 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.100433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.072421 restraints weight = 88943.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.074186 restraints weight = 45515.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.075267 restraints weight = 31223.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.075831 restraints weight = 25580.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.076072 restraints weight = 23180.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  17945  Z= 0.138
  Angle     :  0.659  10.978  25661  Z= 0.338
  Chirality :  0.039   0.230   3153
  Planarity :  0.005   0.055   2272
  Dihedral  : 24.189 169.330   5969
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.41 %
    Favored  : 96.52 %
  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: -0.36 (0.21), residues: 1466
  helix:  0.90 (0.20), residues: 629
  sheet: -0.72 (0.34), residues: 204
  loop : -1.21 (0.23), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  72 
 TYR   0.015   0.002   TYR A 552 
 PHE   0.019   0.002   PHE M  71 
 TRP   0.021   0.002   TRP A 581 
 HIS   0.007   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (17944)
  covalent geometry    : angle       0.65867 (25659)
  SS BOND              : bond        0.00936 (    1)
  SS BOND              : angle       1.96113 (    2)
  hydrogen bonds       : bond        0.04412 (  746)
  hydrogen bonds       : angle       4.39311 ( 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
  141 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6601 (t80)
REVERT: A  412 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6761 (m-70)
REVERT: A  459 TRP cc_start: 0.6675 (OUTLIER) cc_final: 0.5985 (t60)
REVERT: A  749 LYS cc_start: 0.6784 (tptp) cc_final: 0.6544 (tptt)
REVERT: A  902 LYS cc_start: 0.8751 (tptt) cc_final: 0.8423 (tptt)
REVERT: L   40 TYR cc_start: 0.7032 (m-80) cc_final: 0.6550 (m-80)
REVERT: L   52 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8076 (mt)
REVERT: L   75 LYS cc_start: 0.7891 (tppt) cc_final: 0.7638 (tmtt)
REVERT: L   76 LYS cc_start: 0.6863 (tttt) cc_final: 0.6544 (ttpt)
REVERT: M   52 ASP cc_start: 0.8616 (t0) cc_final: 0.8415 (p0)
REVERT: M   64 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6877 (m110)
REVERT: O  101 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8373 (pm20)
  outliers start: 41
  outliers final: 23
  residues processed: 130
  average time/residue: 0.1315
  time to fit residues: 26.1558
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  131 LEU
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  389 MET
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  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  797 SER
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain M residue   48 GLN
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   64 ASN
Chi-restraints excluded: chain O residue  157 VAL
Chi-restraints excluded: chain O residue  208 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 148 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 816 HIS
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 HIS
** L  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  48 GLN
M  64 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.101001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.073176 restraints weight = 88672.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.075020 restraints weight = 44737.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.076101 restraints weight = 30414.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.076558 restraints weight = 24848.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.076898 restraints weight = 22669.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17945  Z= 0.125
  Angle     :  0.619  10.408  25661  Z= 0.316
  Chirality :  0.037   0.223   3153
  Planarity :  0.004   0.050   2272
  Dihedral  : 24.050 171.197   5969
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.55 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.23 %
    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: -0.01 (0.22), residues: 1466
  helix:  1.20 (0.21), residues: 630
  sheet: -0.56 (0.35), residues: 208
  loop : -1.02 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 865 
 TYR   0.025   0.002   TYR A 894 
 PHE   0.016   0.001   PHE M  71 
 TRP   0.019   0.001   TRP A 581 
 HIS   0.007   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (17944)
  covalent geometry    : angle       0.61923 (25659)
  SS BOND              : bond        0.00739 (    1)
  SS BOND              : angle       1.82126 (    2)
  hydrogen bonds       : bond        0.04087 (  746)
  hydrogen bonds       : angle       4.16141 ( 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
  140 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6544 (t80)
REVERT: A  412 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6964 (m-70)
REVERT: A  589 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8266 (mm)
REVERT: A  749 LYS cc_start: 0.7003 (tptp) cc_final: 0.6744 (tptt)
REVERT: A  902 LYS cc_start: 0.8759 (tptt) cc_final: 0.8455 (tptt)
REVERT: L   40 TYR cc_start: 0.7111 (m-80) cc_final: 0.6696 (m-80)
REVERT: L   52 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8166 (mt)
REVERT: L   75 LYS cc_start: 0.7913 (tppt) cc_final: 0.7652 (tmtt)
REVERT: M   64 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6773 (m110)
REVERT: O  101 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8248 (pm20)
REVERT: O  233 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6886 (pttp)
  outliers start: 36
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1277
  time to fit residues: 25.9553
Evaluate side-chains
  120 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  333 TYR
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  412 HIS
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   64 ASN
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  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:
   chunk 116 optimal weight:    9.9990
   chunk 112 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9990
   chunk 146 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 174 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 128 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 736 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1075 HIS
** L  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 116 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.096011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.068279 restraints weight = 91296.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.069793 restraints weight = 49144.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.070704 restraints weight = 34802.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.071057 restraints weight = 29046.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.071436 restraints weight = 26903.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.6135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090  17945  Z= 0.322
  Angle     :  0.836  14.429  25661  Z= 0.427
  Chirality :  0.045   0.245   3153
  Planarity :  0.006   0.056   2272
  Dihedral  : 24.519 165.780   5969
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 18.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.73 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.89 %
    Favored  : 76.19 %
  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: -0.92 (0.21), residues: 1466
  helix:  0.18 (0.20), residues: 637
  sheet: -0.91 (0.34), residues: 209
  loop : -1.26 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 865 
 TYR   0.033   0.003   TYR A 894 
 PHE   0.025   0.003   PHE O 172 
 TRP   0.019   0.003   TRP A 581 
 HIS   0.012   0.002   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00689 (17944)
  covalent geometry    : angle       0.83612 (25659)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       2.41445 (    2)
  hydrogen bonds       : bond        0.06537 (  746)
  hydrogen bonds       : angle       4.98878 ( 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
  135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 93
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7013 (t80)
REVERT: A  412 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6969 (m-70)
REVERT: A  459 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.6308 (t60)
REVERT: A  589 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8355 (mm)
REVERT: A  749 LYS cc_start: 0.6968 (tptp) cc_final: 0.6708 (tptt)
REVERT: L   40 TYR cc_start: 0.7337 (m-80) cc_final: 0.6845 (m-80)
REVERT: L   52 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7884 (mt)
REVERT: L   75 LYS cc_start: 0.7719 (tppt) cc_final: 0.7400 (tmtt)
  outliers start: 42
  outliers final: 28
  residues processed: 127
  average time/residue: 0.1264
  time to fit residues: 24.4549
Evaluate side-chains
  123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
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  176 TYR
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  565 GLU
Chi-restraints excluded: chain A residue  589 ILE
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  675 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain L residue   24 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 O residue  155 CYS
Chi-restraints excluded: chain O residue  174 PHE
Chi-restraints excluded: chain O residue  208 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 107 optimal weight:   30.0000
   chunk 109 optimal weight:   10.0000
   chunk 156 optimal weight:   50.0000
   chunk 5 optimal weight:   20.0000
   chunk 57 optimal weight:    8.9990
   chunk 105 optimal weight:   30.0000
   chunk 73 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 130 optimal weight:    3.9990
   chunk 144 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
A 736 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.098482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.071621 restraints weight = 95780.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.073367 restraints weight = 47858.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.074400 restraints weight = 32502.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.074827 restraints weight = 26479.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.075138 restraints weight = 24170.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.6682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  17945  Z= 0.283
  Angle     :  0.820   9.884  25661  Z= 0.419
  Chirality :  0.044   0.273   3153
  Planarity :  0.006   0.096   2272
  Dihedral  : 24.733 163.544   5969
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.46 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 19.42 %
    Favored  : 75.72 %
  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: -1.20 (0.21), residues: 1466
  helix: -0.09 (0.19), residues: 631
  sheet: -0.98 (0.35), residues: 205
  loop : -1.37 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  15 
 TYR   0.023   0.003   TYR A 894 
 PHE   0.026   0.003   PHE A 331 
 TRP   0.021   0.002   TRP A 581 
 HIS   0.015   0.002   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (17944)
  covalent geometry    : angle       0.81979 (25659)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       2.47990 (    2)
  hydrogen bonds       : bond        0.06316 (  746)
  hydrogen bonds       : angle       5.10496 ( 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
  142 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 90
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7140 (t80)
REVERT: A  390 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.4988 (ptt90)
REVERT: A  459 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.6325 (t60)
REVERT: A  589 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: A  749 LYS cc_start: 0.6962 (tptp) cc_final: 0.6707 (tptt)
REVERT: L   40 TYR cc_start: 0.7353 (m-80) cc_final: 0.6962 (m-80)
REVERT: L   75 LYS cc_start: 0.7741 (tppt) cc_final: 0.7360 (tmtt)
REVERT: O  101 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8616 (pm20)
  outliers start: 52
  outliers final: 36
  residues processed: 130
  average time/residue: 0.1266
  time to fit residues: 25.2297
Evaluate side-chains
  123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 83
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  390 ARG
Chi-restraints excluded: chain A residue  407 VAL
Chi-restraints excluded: chain A residue  459 TRP
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  589 ILE
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  675 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1078 PHE
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain L residue   28 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   92 SER
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  183 LEU
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:
   chunk 149 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 107 optimal weight:   30.0000
   chunk 156 optimal weight:   50.0000
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 119 optimal weight:   20.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 736 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.102641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.076141 restraints weight = 93553.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.078043 restraints weight = 45449.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.079145 restraints weight = 30264.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.079608 restraints weight = 24455.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.079741 restraints weight = 22260.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.6745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17945  Z= 0.135
  Angle     :  0.652  11.770  25661  Z= 0.330
  Chirality :  0.038   0.248   3153
  Planarity :  0.005   0.060   2272
  Dihedral  : 24.348 167.760   5969
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.48 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.48 %
    Favored  : 75.72 %
  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: -0.34 (0.22), residues: 1466
  helix:  0.87 (0.21), residues: 627
  sheet: -0.79 (0.34), residues: 218
  loop : -1.10 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 390 
 TYR   0.014   0.001   TYR A 894 
 PHE   0.020   0.002   PHE M  71 
 TRP   0.024   0.002   TRP A 581 
 HIS   0.007   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (17944)
  covalent geometry    : angle       0.65222 (25659)
  SS BOND              : bond        0.00727 (    1)
  SS BOND              : angle       1.64558 (    2)
  hydrogen bonds       : bond        0.04321 (  746)
  hydrogen bonds       : angle       4.40633 ( 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
  133 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8639 (pp) cc_final: 0.8236 (mm)
REVERT: A  736 GLN cc_start: 0.8471 (tp40) cc_final: 0.8196 (mp10)
REVERT: A  749 LYS cc_start: 0.6766 (tptp) cc_final: 0.6511 (tptt)
REVERT: A  849 MET cc_start: 0.8096 (mmm) cc_final: 0.7746 (mmm)
REVERT: A  902 LYS cc_start: 0.8886 (tptt) cc_final: 0.8620 (tptt)
REVERT: A  903 THR cc_start: 0.9176 (m) cc_final: 0.8863 (p)
REVERT: A  970 MET cc_start: 0.7115 (ttm) cc_final: 0.6746 (ptm)
REVERT: L   24 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6166 (tp)
REVERT: L   40 TYR cc_start: 0.7106 (m-80) cc_final: 0.6760 (m-80)
REVERT: L   51 TYR cc_start: 0.5481 (t80) cc_final: 0.4253 (m-80)
REVERT: O  101 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8419 (pm20)
  outliers start: 30
  outliers final: 22
  residues processed: 128
  average time/residue: 0.1279
  time to fit residues: 25.0720
Evaluate side-chains
  119 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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  333 TYR
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  740 CYS
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain A residue 1001 ILE
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1079 LEU
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain O residue  120 VAL
Chi-restraints excluded: chain O residue  155 CYS
Chi-restraints excluded: chain O residue  183 LEU
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:
   chunk 124 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0770
   chunk 147 optimal weight:    8.9990
   chunk 52 optimal weight:    0.3980
   chunk 113 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 152 optimal weight:    0.6980
   chunk 166 optimal weight:   50.0000
   chunk 44 optimal weight:    0.0980
   overall best weight:    0.2596

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 506 GLN
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 GLN
M  64 ASN
O 116 GLN
** O 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.103868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.076669 restraints weight = 89347.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.078557 restraints weight = 43536.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.079732 restraints weight = 29032.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.080313 restraints weight = 23497.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.080680 restraints weight = 21192.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.7063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  17945  Z= 0.118
  Angle     :  0.609  10.903  25661  Z= 0.306
  Chirality :  0.037   0.204   3153
  Planarity :  0.005   0.070   2272
  Dihedral  : 23.979 176.846   5969
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.34 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 22.13 %
    Favored  : 76.28 %
  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:  0.22 (0.22), residues: 1466
  helix:  1.30 (0.21), residues: 626
  sheet: -0.36 (0.35), residues: 219
  loop : -0.82 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 390 
 TYR   0.024   0.002   TYR A 462 
 PHE   0.021   0.002   PHE M  71 
 TRP   0.020   0.002   TRP A 581 
 HIS   0.009   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (17944)
  covalent geometry    : angle       0.60921 (25659)
  SS BOND              : bond        0.00574 (    1)
  SS BOND              : angle       1.39122 (    2)
  hydrogen bonds       : bond        0.03795 (  746)
  hydrogen bonds       : angle       4.06007 ( 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
  142 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 LEU cc_start: 0.8474 (pp) cc_final: 0.8115 (mm)
REVERT: A  593 LEU cc_start: 0.8505 (pp) cc_final: 0.8122 (tp)
REVERT: A  712 ASP cc_start: 0.6632 (m-30) cc_final: 0.6365 (m-30)
REVERT: A  749 LYS cc_start: 0.7087 (tptp) cc_final: 0.6747 (tptt)
REVERT: A  769 LEU cc_start: 0.9248 (mt) cc_final: 0.9044 (mt)
REVERT: A  902 LYS cc_start: 0.8792 (tptt) cc_final: 0.8461 (tptt)
REVERT: A  970 MET cc_start: 0.7186 (ttm) cc_final: 0.6636 (ptm)
REVERT: L   40 TYR cc_start: 0.6842 (m-80) cc_final: 0.6611 (m-80)
REVERT: L   51 TYR cc_start: 0.5713 (t80) cc_final: 0.4410 (m-80)
REVERT: L   75 LYS cc_start: 0.6115 (tttt) cc_final: 0.5357 (tmtt)
REVERT: M  122 TYR cc_start: 0.8751 (t80) cc_final: 0.8375 (t80)
REVERT: O  143 THR cc_start: 0.7624 (m) cc_final: 0.7366 (m)
  outliers start: 17
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1232
  time to fit residues: 25.9315
Evaluate side-chains
  120 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 TYR
Chi-restraints excluded: chain A residue  459 TRP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  996 THR
Chi-restraints excluded: chain L residue   24 LEU
Chi-restraints excluded: chain M residue   57 SER
Chi-restraints excluded: chain M residue   64 ASN
Chi-restraints excluded: chain M residue   92 SER
Chi-restraints excluded: chain O residue  120 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:
   chunk 133 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 96 optimal weight:   30.0000
   chunk 32 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   chunk 98 optimal weight:   20.0000
   chunk 64 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 174 optimal weight:    8.9990
   chunk 129 optimal weight:    0.7980
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 482 HIS
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1085 HIS
** L  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  64 ASN
O 116 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.099219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.073014 restraints weight = 90946.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.074635 restraints weight = 50739.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.074455 restraints weight = 35114.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.074660 restraints weight = 28531.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.074766 restraints weight = 27262.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.7095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17945  Z= 0.184
  Angle     :  0.671  12.591  25661  Z= 0.338
  Chirality :  0.039   0.240   3153
  Planarity :  0.005   0.063   2272
  Dihedral  : 24.138 172.526   5968
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.89 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 22.78 %
    Favored  : 75.63 %
  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: -0.03 (0.22), residues: 1466
  helix:  1.01 (0.21), residues: 630
  sheet: -0.38 (0.35), residues: 217
  loop : -0.90 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1084 
 TYR   0.015   0.002   TYR A 462 
 PHE   0.023   0.002   PHE A 464 
 TRP   0.016   0.002   TRP A 581 
 HIS   0.006   0.001   HIS A1075 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (17944)
  covalent geometry    : angle       0.67071 (25659)
  SS BOND              : bond        0.00424 (    1)
  SS BOND              : angle       1.89864 (    2)
  hydrogen bonds       : bond        0.04740 (  746)
  hydrogen bonds       : angle       4.30631 ( 1948)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4031.45 seconds
wall clock time: 69 minutes 47.21 seconds (4187.21 seconds total)