Starting phenix.real_space_refine
on Thu Mar 13 05:33:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g46_29714/03_2025/8g46_29714.cif"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.071
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
     Zn      1      6.06       5
     S      57      5.16       5
     C    5415      2.51       5
     N    1433      2.21       5
     O    1697      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8603
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6180
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 782, 6150
          Classifications: {'peptide': 782}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755}
          Chain breaks: 6
      Conformer: "B"
        Number of residues, atoms: 782, 6150
          Classifications: {'peptide': 782}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755}
          Chain breaks: 6
          bond proxies already assigned to first conformer: 6221
    Chain: "B"
      Number of atoms: 1260
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 158, 1246
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 17, 'TRANS': 140}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 158, 1246
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 17, 'TRANS': 140}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1266
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 859
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "E"
      Number of atoms: 157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 157
          Classifications: {'peptide': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 17}
    Chain: "B"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {' ZN': 1, 'YK3': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 95
          Classifications: {'water': 95}
          Link IDs: {None: 94}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6635  SG  CYS B 100      40.352  30.235  52.256  1.00 55.81           S
  ATOM   6657  SG  CYS B 103      42.977  32.717  50.994  1.00 59.48           S
  ATOM   7131  SG  CYS B 177      41.272  30.475  48.590  1.00 54.63           S
  ATOM   7143  SG  CYS B 179      39.096  33.155  50.131  1.00 56.71           S

  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  AASN A  16 " occ=0.50
      ... (14 atoms not shown)
      pdb=" ND2BASN A  16 " occ=0.50
    residue:
      pdb=" N  AHIS A 711 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 711 " occ=0.50
    residue:
      pdb=" N  ACYS A 725 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS A 725 " occ=0.50
    residue:
      pdb=" N  ACYS A1008 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS A1008 " occ=0.50
    residue:
      pdb=" N  ATRP B  54 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP B  54 " occ=0.50
  Time building chain proxies: 8.35, per 1000 atoms: 0.97
  Number of scatterers: 8603
  At special positions: 0
  Unit cell: (86.7623, 91.189, 138.997, 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)
     Zn      1     29.99
     S      57     16.00
     O    1697      8.00
     N    1433      7.00
     C    5415      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1001 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 103 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 100 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 177 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 179 "
      Number of angles added : 6


  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 17 sheets defined
      23.5% alpha, 33.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 250 through 256
      removed outlier: 4.073A  pdb=" N   GLN A 255 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 384
    Processing helix  chain 'A' and resid 985 through 990
    Processing helix  chain 'A' and resid 1044 through 1062
    Processing helix  chain 'A' and resid 1069 through 1075
    Processing helix  chain 'A' and resid 1091 through 1096
    Processing helix  chain 'A' and resid 1097 through 1100
    Processing helix  chain 'A' and resid 1101 through 1110
    Processing helix  chain 'A' and resid 1125 through 1138
      removed outlier: 3.887A  pdb=" N   LEU A1129 " --> pdb=" O   THR A1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 61
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 115 through 120
    Processing helix  chain 'B' and resid 130 through 139
    Processing helix  chain 'B' and resid 142 through 158
      removed outlier: 4.215A  pdb=" N   ARG B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 187
    Processing helix  chain 'B' and resid 200 through 216
    Processing helix  chain 'C' and resid 354 through 366
    Processing helix  chain 'C' and resid 369 through 374
    Processing helix  chain 'C' and resid 375 through 378
      removed outlier: 4.311A  pdb=" N   LYS C 378 " --> pdb=" O   PRO C 375 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 375 through 378'
    Processing helix  chain 'C' and resid 389 through 394
    Processing helix  chain 'C' and resid 399 through 409
    Processing helix  chain 'C' and resid 414 through 433
    Processing helix  chain 'C' and resid 437 through 455
      removed outlier: 3.628A  pdb=" N   VAL C 449 " --> pdb=" O   LYS C 445 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 6
      removed outlier: 3.775A  pdb=" N   LYS E   6 " --> pdb=" O   ASP E   3 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009
      removed outlier: 6.615A  pdb=" N   GLY A1031 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   PHE A1007 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU A1029 " --> pdb=" O   PHE A1007 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   HIS A1009 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   SER A1027 " --> pdb=" O   HIS A1009 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER A1027 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A1040 " --> pdb=" O   SER A1027 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LEU A1029 " --> pdb=" O   GLY A1038 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLY A1038 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   ILE A1037 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ASN A   4 " --> pdb=" O   ILE A1089 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21
      removed outlier: 6.690A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   GLU A  54 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ILE A  41 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67
      removed outlier: 4.183A  pdb=" N   ASN A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ALA A  86 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   HIS A 105 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ILE A  88 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124
      removed outlier: 4.201A  pdb=" N   LEU A 135 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   LEU A 139 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
      removed outlier: 6.588A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169
      removed outlier: 6.588A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221
    Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263
      removed outlier: 4.257A  pdb=" N   ARG A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ASP A 299 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLU A 288 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU A 297 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 313 through 318
      removed outlier: 6.666A  pdb=" N   VAL A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   SER A 331 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   THR A 352 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   LEU A 333 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 365
      removed outlier: 3.984A  pdb=" N   ASP A 361 " --> pdb=" O   CYS A 378 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 720 through 727
      removed outlier: 6.333A  pdb=" N   SER A 738 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A 723 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ASP A 795 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL A 801 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   SER A 762 " --> pdb=" O   ALA A 804 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   GLN A 806 " --> pdb=" O   SER A 762 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   SER A 764 " --> pdb=" O   GLN A 806 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 819
      removed outlier: 5.549A  pdb=" N   ALA A 813 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG A 847 " --> pdb=" O   THR A 833 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLY A 846 " --> pdb=" O   GLU A 865 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   GLU A 865 " --> pdb=" O   GLY A 846 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ILE A 848 " --> pdb=" O   GLU A 863 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   GLU A 863 " --> pdb=" O   ILE A 848 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   VAL A 850 " --> pdb=" O   VAL A 861 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 870 through 876
      removed outlier: 3.863A  pdb=" N   SER A 872 " --> pdb=" O   SER A 883 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   VAL A 888 " --> pdb=" O   ASN A 904 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASN A 904 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU A 890 " --> pdb=" O   GLU A 902 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 917
      removed outlier: 7.052A  pdb=" N   VAL A 930 " --> pdb=" O   ARG A 947 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ARG A 947 " --> pdb=" O   VAL A 930 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LEU A 932 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN A 941 " --> pdb=" O   LYS A 936 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 954 through 959
      removed outlier: 6.869A  pdb=" N   ALA A 968 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   VAL A 957 " --> pdb=" O   LEU A 966 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   LEU A 966 " --> pdb=" O   VAL A 957 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   ILE A 959 " --> pdb=" O   ASN A 964 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   ASN A 964 " --> pdb=" O   ILE A 959 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ASN A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   GLN A 978 " --> pdb=" O   GLU A 994 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   GLU A 994 " --> pdb=" O   GLN A 978 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077
    Processing sheet with id=AB8, first strand: chain 'B' and resid 66 through 67

    364 hydrogen bonds defined for protein.
    991 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 2.28 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: 1820
        1.33 -     1.46: 2666
        1.46 -     1.58: 4100
        1.58 -     1.71: 1
        1.71 -     1.84: 85
  Bond restraints: 8672
  Sorted by residual:
  bond pdb=" C   PHE C 450 "
       pdb=" O   PHE C 450 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.033 1.15e-02 7.56e+03 8.26e+00
  bond pdb=" CA  SER A 379 "
       pdb=" CB  SER A 379 "
    ideal  model  delta    sigma   weight residual
    1.533  1.488  0.045 1.60e-02 3.91e+03 7.95e+00
  bond pdb=" C21 YK3 B1002 "
       pdb=" C4  YK3 B1002 "
    ideal  model  delta    sigma   weight residual
    1.370  1.423 -0.053 2.00e-02 2.50e+03 7.10e+00
  bond pdb=" CA  ALA B 148 "
       pdb=" CB  ALA B 148 "
    ideal  model  delta    sigma   weight residual
    1.528  1.487  0.041 1.56e-02 4.11e+03 7.03e+00
  bond pdb=" CG  HIS A 789 "
       pdb=" CD2 HIS A 789 "
    ideal  model  delta    sigma   weight residual
    1.354  1.325  0.029 1.10e-02 8.26e+03 6.79e+00
  ... (remaining 8667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 11542
        2.40 -     4.81: 201
        4.81 -     7.21: 5
        7.21 -     9.61: 1
        9.61 -    12.02: 2
  Bond angle restraints: 11751
  Sorted by residual:
  angle pdb=" N   MET C 442 "
        pdb=" CA  MET C 442 "
        pdb=" C   MET C 442 "
      ideal   model   delta    sigma   weight residual
     113.38  105.14    8.24 1.23e+00 6.61e-01 4.48e+01
  angle pdb=" N   ALA C 441 "
        pdb=" CA  ALA C 441 "
        pdb=" C   ALA C 441 "
      ideal   model   delta    sigma   weight residual
     113.97  108.17    5.80 1.28e+00 6.10e-01 2.06e+01
  angle pdb=" C9  YK3 B1002 "
        pdb=" N   YK3 B1002 "
        pdb=" S   YK3 B1002 "
      ideal   model   delta    sigma   weight residual
     118.17  130.19  -12.02 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" N   ALA C 443 "
        pdb=" CA  ALA C 443 "
        pdb=" C   ALA C 443 "
      ideal   model   delta    sigma   weight residual
     111.24  106.18    5.06 1.29e+00 6.01e-01 1.54e+01
  angle pdb=" N   PHE C 454 "
        pdb=" CA  PHE C 454 "
        pdb=" C   PHE C 454 "
      ideal   model   delta    sigma   weight residual
     111.69  106.94    4.75 1.23e+00 6.61e-01 1.49e+01
  ... (remaining 11746 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 4702
       17.61 -    35.21: 383
       35.21 -    52.81: 114
       52.81 -    70.42: 30
       70.42 -    88.02: 16
  Dihedral angle restraints: 5245
    sinusoidal: 2134
      harmonic: 3111
  Sorted by residual:
  dihedral pdb=" CA  GLN A 332 "
           pdb=" C   GLN A 332 "
           pdb=" N   LEU A 333 "
           pdb=" CA  LEU A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.05   17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PRO A 223 "
           pdb=" C   PRO A 223 "
           pdb=" N   GLU A 224 "
           pdb=" CA  GLU A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CG  ARG C 444 "
           pdb=" CD  ARG C 444 "
           pdb=" NE  ARG C 444 "
           pdb=" CZ  ARG C 444 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   40.84   49.16     2      1.50e+01 4.44e-03 1.22e+01
  ... (remaining 5242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 581
       0.037 -    0.074: 416
       0.074 -    0.111: 233
       0.111 -    0.148: 81
       0.148 -    0.185: 13
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CA  TRP C 374 "
            pdb=" N   TRP C 374 "
            pdb=" C   TRP C 374 "
            pdb=" CB  TRP C 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.55e-01
  chirality pdb=" CA  VAL A 874 "
            pdb=" N   VAL A 874 "
            pdb=" C   VAL A 874 "
            pdb=" CB  VAL A 874 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.44e-01
  chirality pdb=" CB  VAL C 439 "
            pdb=" CA  VAL C 439 "
            pdb=" CG1 VAL C 439 "
            pdb=" CG2 VAL C 439 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.99e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 441 "   -0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   ALA C 441 "    0.069 2.00e-02 2.50e+03
        pdb=" O   ALA C 441 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   MET C 442 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 440 "    0.020 2.00e-02 2.50e+03   3.97e-02 1.57e+01
        pdb=" C   VAL C 440 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   VAL C 440 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ALA C 441 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 442 "   -0.014 2.00e-02 2.50e+03   2.85e-02 8.13e+00
        pdb=" C   MET C 442 "    0.049 2.00e-02 2.50e+03
        pdb=" O   MET C 442 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ALA C 443 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 723
        2.75 -     3.28: 8308
        3.28 -     3.82: 15182
        3.82 -     4.36: 18809
        4.36 -     4.90: 31145
  Nonbonded interactions: 74167
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  62 "
            pdb=" OE2 GLU C 438 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" ND1 HIS C 369 "
            pdb=" OH  TYR C 372 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG1 THR A 118 "
            pdb=" NH2 ARG A 134 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OE2 GLU B 193 "
            pdb=" OH  TYR B 199 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" ND2 ASN A 950 "
            pdb=" OE1 GLU A 994 "
     model   vdw
     2.306 3.120
  ... (remaining 74162 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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     28.170
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.050
  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:12.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
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      :  0.008   0.053   8672  Z= 0.499
  Angle     :  0.883  12.016  11751  Z= 0.556
  Chirality :  0.061   0.185   1324
  Planarity :  0.006   0.057   1500
  Dihedral  : 15.573  88.024   3235
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.42 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.25), residues: 1057
  helix:  0.23 (0.37), residues: 217
  sheet:  0.00 (0.26), residues: 384
  loop : -0.34 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.007   TRP A 953 
 HIS   0.011   0.004   HIS B 138 
 PHE   0.030   0.006   PHE A 942 
 TYR   0.023   0.006   TYR B  76 
 ARG   0.019   0.002   ARG A 753 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  150 LYS cc_start: 0.5626 (tptt) cc_final: 0.4650 (tptp)
REVERT: A  224 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6971 (mm-30)
REVERT: A  254 LYS cc_start: 0.6884 (mttt) cc_final: 0.6222 (ptpp)
REVERT: A  267 ASN cc_start: 0.8138 (p0) cc_final: 0.7689 (p0)
REVERT: A  847 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7938 (mtm180)
  outliers start: 14
  outliers final: 8
  residues processed: 121
  average time/residue: 1.7643
  time to fit residues: 224.0089
Evaluate side-chains
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1071 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   58 CYS
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 43 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:    0.1980
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 396 HIS
C 428 ASN
C 447 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.186435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142414 restraints weight = 26239.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.69
r_work: 0.3551 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.0884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8672  Z= 0.161
  Angle     :  0.550   6.466  11751  Z= 0.292
  Chirality :  0.044   0.163   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.823  48.892   1186
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.21 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1057
  helix:  0.95 (0.36), residues: 219
  sheet:  0.18 (0.26), residues: 368
  loop : -0.38 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 207 
 HIS   0.004   0.001   HIS C 369 
 PHE   0.016   0.002   PHE C 450 
 TYR   0.011   0.001   TYR C 372 
 ARG   0.006   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.7572 (mtpm) cc_final: 0.6820 (mppt)
REVERT: A  150 LYS cc_start: 0.6379 (tptt) cc_final: 0.5208 (tptp)
REVERT: A  158 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7462 (ttp-170)
REVERT: A  210 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5935 (tm-30)
REVERT: A  224 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7611 (mm-30)
REVERT: A  254 LYS cc_start: 0.7149 (mttt) cc_final: 0.6697 (ptpp)
REVERT: A  267 ASN cc_start: 0.8493 (p0) cc_final: 0.8235 (p0)
REVERT: A  847 ARG cc_start: 0.8320 (mtm180) cc_final: 0.8085 (mtm180)
REVERT: A  859 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6933 (pt0)
  outliers start: 21
  outliers final: 7
  residues processed: 120
  average time/residue: 1.6088
  time to fit residues: 202.8839
Evaluate side-chains
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1071 SER
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 950 ASN
** C 428 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 = 0.4076 r_free = 0.4076 target = 0.181124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.135930 restraints weight = 32598.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 3.69
r_work: 0.3447 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3450
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8672  Z= 0.315
  Angle     :  0.649   6.786  11751  Z= 0.344
  Chirality :  0.047   0.171   1324
  Planarity :  0.004   0.045   1500
  Dihedral  :  6.176  52.079   1180
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.06 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.25), residues: 1057
  helix:  1.08 (0.36), residues: 220
  sheet:  0.17 (0.26), residues: 373
  loop : -0.44 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 207 
 HIS   0.006   0.001   HIS A1077 
 PHE   0.020   0.003   PHE A 169 
 TYR   0.017   0.002   TYR A 718 
 ARG   0.005   0.001   ARG C 444 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.7588 (mtpm) cc_final: 0.6838 (mppt)
REVERT: A  150 LYS cc_start: 0.6236 (tttt) cc_final: 0.5235 (tptp)
REVERT: A  210 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6118 (tm-30)
REVERT: A  224 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7447 (mm-30)
REVERT: A  254 LYS cc_start: 0.7156 (mttt) cc_final: 0.6733 (ptpp)
REVERT: A  267 ASN cc_start: 0.8475 (p0) cc_final: 0.8200 (p0)
REVERT: A  859 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6948 (pt0)
REVERT: A 1106 GLN cc_start: 0.5017 (tp40) cc_final: 0.4666 (tp-100)
REVERT: C  377 TYR cc_start: 0.7388 (m-10) cc_final: 0.7180 (m-10)
REVERT: C  378 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7085 (mmtm)
REVERT: C  407 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4164 (mp)
  outliers start: 17
  outliers final: 7
  residues processed: 123
  average time/residue: 1.7769
  time to fit residues: 229.4330
Evaluate side-chains
  121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1071 SER
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.183011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138273 restraints weight = 30616.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 3.63
r_work: 0.3475 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3475
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8672  Z= 0.219
  Angle     :  0.573   6.697  11751  Z= 0.304
  Chirality :  0.045   0.166   1324
  Planarity :  0.004   0.038   1500
  Dihedral  :  5.929  59.388   1180
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.69 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.25), residues: 1057
  helix:  1.32 (0.36), residues: 220
  sheet:  0.19 (0.26), residues: 366
  loop : -0.47 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.016   0.002   PHE C 450 
 TYR   0.012   0.002   TYR A 891 
 ARG   0.004   0.000   ARG C 444 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.115 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7040 (mp0) cc_final: 0.6541 (mp0)
REVERT: A   70 LYS cc_start: 0.7584 (mtpm) cc_final: 0.6793 (mppt)
REVERT: A  150 LYS cc_start: 0.6205 (tttt) cc_final: 0.5193 (tptp)
REVERT: A  210 GLU cc_start: 0.6376 (tm-30) cc_final: 0.6102 (tm-30)
REVERT: A  224 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7462 (mm-30)
REVERT: A  254 LYS cc_start: 0.7126 (mttt) cc_final: 0.6710 (ptpp)
REVERT: A  267 ASN cc_start: 0.8477 (p0) cc_final: 0.8192 (p0)
REVERT: A  859 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6922 (pt0)
REVERT: A 1106 GLN cc_start: 0.5003 (tp40) cc_final: 0.4647 (tp-100)
REVERT: C  360 ILE cc_start: 0.5407 (OUTLIER) cc_final: 0.5203 (mp)
REVERT: C  364 MET cc_start: 0.6352 (mtp) cc_final: 0.4921 (mmm)
REVERT: C  378 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7119 (mmtm)
REVERT: C  407 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4150 (mp)
REVERT: C  424 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.5086 (tm)
  outliers start: 17
  outliers final: 5
  residues processed: 123
  average time/residue: 1.6960
  time to fit residues: 219.0228
Evaluate side-chains
  120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 92 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.183919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139340 restraints weight = 26367.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 3.17
r_work: 0.3500 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8672  Z= 0.187
  Angle     :  0.549   6.612  11751  Z= 0.291
  Chirality :  0.044   0.160   1324
  Planarity :  0.004   0.036   1500
  Dihedral  :  5.589  49.104   1179
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.01 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1057
  helix:  1.44 (0.36), residues: 221
  sheet:  0.19 (0.26), residues: 368
  loop : -0.49 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.015   0.002   PHE C 450 
 TYR   0.012   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.7576 (mtpm) cc_final: 0.6812 (mppt)
REVERT: A  150 LYS cc_start: 0.6224 (tttt) cc_final: 0.5204 (tptp)
REVERT: A  210 GLU cc_start: 0.6352 (tm-30) cc_final: 0.6086 (tm-30)
REVERT: A  224 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7471 (mm-30)
REVERT: A  254 LYS cc_start: 0.7026 (mttt) cc_final: 0.6624 (ptpp)
REVERT: A  267 ASN cc_start: 0.8453 (p0) cc_final: 0.8171 (p0)
REVERT: A  859 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6868 (pt0)
REVERT: A 1106 GLN cc_start: 0.5119 (tp40) cc_final: 0.4752 (tp-100)
REVERT: C  364 MET cc_start: 0.6309 (mtp) cc_final: 0.4951 (mmm)
REVERT: C  378 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7154 (mmtm)
REVERT: C  383 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7292 (tp30)
REVERT: C  407 LEU cc_start: 0.4676 (OUTLIER) cc_final: 0.4161 (mp)
REVERT: C  421 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.5900 (t0)
REVERT: C  424 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5208 (tm)
REVERT: C  425 MET cc_start: 0.5502 (ttp) cc_final: 0.5219 (ttp)
  outliers start: 16
  outliers final: 4
  residues processed: 116
  average time/residue: 1.6707
  time to fit residues: 203.8959
Evaluate side-chains
  114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 98 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 39 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.183185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138508 restraints weight = 30097.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 3.43
r_work: 0.3481 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8672  Z= 0.218
  Angle     :  0.571   7.102  11751  Z= 0.302
  Chirality :  0.045   0.166   1324
  Planarity :  0.004   0.036   1500
  Dihedral  :  5.432  50.799   1175
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.01 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.25), residues: 1057
  helix:  1.38 (0.36), residues: 221
  sheet:  0.20 (0.26), residues: 366
  loop : -0.51 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.015   0.002   PHE C 450 
 TYR   0.013   0.002   TYR A 891 
 ARG   0.006   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 1.822 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6884 (mp0) cc_final: 0.6418 (mp0)
REVERT: A   70 LYS cc_start: 0.7596 (mtpm) cc_final: 0.6822 (mppt)
REVERT: A  150 LYS cc_start: 0.6209 (tttt) cc_final: 0.5215 (tptp)
REVERT: A  210 GLU cc_start: 0.6363 (tm-30) cc_final: 0.6081 (tm-30)
REVERT: A  224 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7455 (mm-30)
REVERT: A  254 LYS cc_start: 0.7047 (mttt) cc_final: 0.6608 (ptpp)
REVERT: A  267 ASN cc_start: 0.8473 (p0) cc_final: 0.8149 (p0)
REVERT: A  859 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6888 (pt0)
REVERT: A  863 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7330 (mt-10)
REVERT: A  994 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8253 (mt-10)
REVERT: A 1106 GLN cc_start: 0.5063 (tp40) cc_final: 0.4702 (tp-100)
REVERT: B  126 LYS cc_start: 0.7762 (mptt) cc_final: 0.7435 (mptt)
REVERT: C  364 MET cc_start: 0.6284 (mtp) cc_final: 0.4925 (mmm)
REVERT: C  378 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7165 (mmtm)
REVERT: C  383 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7342 (tp30)
REVERT: C  407 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4088 (mp)
REVERT: C  421 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.5957 (t0)
REVERT: C  424 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5225 (tm)
REVERT: C  438 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6283 (mt-10)
REVERT: E    1 MET cc_start: 0.3475 (OUTLIER) cc_final: 0.3204 (ttt)
  outliers start: 21
  outliers final: 4
  residues processed: 124
  average time/residue: 1.8082
  time to fit residues: 236.6404
Evaluate side-chains
  126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  438 GLU
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain E residue    1 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.184602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.140060 restraints weight = 25688.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.76
r_work: 0.3519 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8672  Z= 0.173
  Angle     :  0.534   6.793  11751  Z= 0.282
  Chirality :  0.044   0.160   1324
  Planarity :  0.003   0.035   1500
  Dihedral  :  5.245  50.257   1175
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.91 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1057
  helix:  1.49 (0.36), residues: 221
  sheet:  0.19 (0.26), residues: 368
  loop : -0.49 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 207 
 HIS   0.003   0.001   HIS A 789 
 PHE   0.014   0.002   PHE C 450 
 TYR   0.012   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.811 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6875 (mp0) cc_final: 0.6405 (mp0)
REVERT: A   70 LYS cc_start: 0.7681 (mtpm) cc_final: 0.6890 (mppt)
REVERT: A  150 LYS cc_start: 0.6201 (tttt) cc_final: 0.5167 (tptp)
REVERT: A  210 GLU cc_start: 0.6320 (tm-30) cc_final: 0.6054 (tm-30)
REVERT: A  224 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7520 (mm-30)
REVERT: A  254 LYS cc_start: 0.7132 (mttt) cc_final: 0.6665 (ptpp)
REVERT: A  267 ASN cc_start: 0.8548 (p0) cc_final: 0.8246 (p0)
REVERT: A  859 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6937 (pt0)
REVERT: A  994 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8363 (mt-10)
REVERT: A 1106 GLN cc_start: 0.5251 (tp40) cc_final: 0.4870 (tp-100)
REVERT: B  126 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7473 (mptt)
REVERT: C  364 MET cc_start: 0.6172 (mtp) cc_final: 0.4868 (mmm)
REVERT: C  378 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7235 (mmtm)
REVERT: C  383 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7429 (tp30)
REVERT: C  407 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4152 (mp)
REVERT: C  421 ASP cc_start: 0.6349 (OUTLIER) cc_final: 0.5887 (t0)
REVERT: C  424 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5367 (tm)
REVERT: C  425 MET cc_start: 0.5485 (ttp) cc_final: 0.5179 (ttp)
  outliers start: 20
  outliers final: 5
  residues processed: 121
  average time/residue: 2.0617
  time to fit residues: 262.3935
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  766 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 82 optimal weight:    0.0670
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.185146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.140749 restraints weight = 25803.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.76
r_work: 0.3528 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8672  Z= 0.163
  Angle     :  0.525   6.626  11751  Z= 0.277
  Chirality :  0.043   0.158   1324
  Planarity :  0.003   0.035   1500
  Dihedral  :  5.130  49.541   1175
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.97 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1057
  helix:  1.52 (0.36), residues: 221
  sheet:  0.20 (0.26), residues: 368
  loop : -0.48 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 207 
 HIS   0.003   0.001   HIS A 789 
 PHE   0.014   0.002   PHE C 450 
 TYR   0.012   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6855 (mp0) cc_final: 0.6398 (mp0)
REVERT: A   70 LYS cc_start: 0.7682 (mtpm) cc_final: 0.6873 (mppt)
REVERT: A  150 LYS cc_start: 0.6217 (tttt) cc_final: 0.5125 (tptp)
REVERT: A  210 GLU cc_start: 0.6327 (tm-30) cc_final: 0.6047 (tm-30)
REVERT: A  224 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7531 (mm-30)
REVERT: A  254 LYS cc_start: 0.7133 (mttt) cc_final: 0.6628 (ptpp)
REVERT: A  267 ASN cc_start: 0.8552 (p0) cc_final: 0.8251 (p0)
REVERT: A  859 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6918 (pt0)
REVERT: A  863 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7482 (mt-10)
REVERT: A  969 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7385 (pp20)
REVERT: A  994 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8366 (mt-10)
REVERT: A 1106 GLN cc_start: 0.5194 (tp40) cc_final: 0.4802 (tp-100)
REVERT: B  126 LYS cc_start: 0.7753 (mptt) cc_final: 0.7423 (mptt)
REVERT: C  364 MET cc_start: 0.6111 (mtp) cc_final: 0.4846 (mmm)
REVERT: C  378 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7183 (mmtm)
REVERT: C  383 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7449 (tp30)
REVERT: C  407 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4064 (mp)
REVERT: C  421 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.6091 (t0)
REVERT: C  424 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5271 (tm)
REVERT: C  428 ASN cc_start: 0.6693 (m110) cc_final: 0.6475 (m-40)
  outliers start: 16
  outliers final: 5
  residues processed: 118
  average time/residue: 1.6123
  time to fit residues: 199.9622
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  766 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain A residue  969 GLU
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.184033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.139165 restraints weight = 33786.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.61
r_work: 0.3485 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8672  Z= 0.196
  Angle     :  0.551   7.049  11751  Z= 0.291
  Chirality :  0.044   0.163   1324
  Planarity :  0.004   0.035   1500
  Dihedral  :  5.284  50.588   1175
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.76 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.25), residues: 1057
  helix:  1.45 (0.36), residues: 221
  sheet:  0.20 (0.26), residues: 366
  loop : -0.49 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 
 PHE   0.014   0.002   PHE A1030 
 TYR   0.013   0.002   TYR A 891 
 ARG   0.006   0.000   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.365 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6741 (mp0) cc_final: 0.6305 (mp0)
REVERT: A   70 LYS cc_start: 0.7626 (mtpm) cc_final: 0.6837 (mppt)
REVERT: A  150 LYS cc_start: 0.6111 (tttt) cc_final: 0.5094 (tptp)
REVERT: A  210 GLU cc_start: 0.6303 (tm-30) cc_final: 0.6038 (tm-30)
REVERT: A  224 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7415 (mm-30)
REVERT: A  254 LYS cc_start: 0.7039 (mttt) cc_final: 0.6584 (ptpp)
REVERT: A  267 ASN cc_start: 0.8486 (p0) cc_final: 0.8182 (p0)
REVERT: A  859 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6861 (pt0)
REVERT: A  863 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7297 (mt-10)
REVERT: A  969 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7315 (pp20)
REVERT: A  994 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8275 (mt-10)
REVERT: A 1106 GLN cc_start: 0.4935 (tp40) cc_final: 0.4574 (tp-100)
REVERT: B  126 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7353 (mptt)
REVERT: C  364 MET cc_start: 0.6197 (mtp) cc_final: 0.4889 (mmm)
REVERT: C  378 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7070 (mmtm)
REVERT: C  383 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7379 (tp30)
REVERT: C  407 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4087 (mp)
REVERT: C  421 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.6110 (t0)
REVERT: C  424 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5336 (tm)
REVERT: C  425 MET cc_start: 0.5473 (ttp) cc_final: 0.5238 (ttp)
  outliers start: 17
  outliers final: 5
  residues processed: 118
  average time/residue: 1.7391
  time to fit residues: 215.7207
Evaluate side-chains
  121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  766 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain A residue  969 GLU
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  421 ASP
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 20 optimal weight:    0.2980
   chunk 84 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.183143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.142862 restraints weight = 30724.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 4.00
r_work: 0.3464 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8672  Z= 0.222
  Angle     :  0.575   7.548  11751  Z= 0.304
  Chirality :  0.045   0.168   1324
  Planarity :  0.004   0.036   1500
  Dihedral  :  5.439  52.247   1175
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.86 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.25), residues: 1057
  helix:  1.38 (0.36), residues: 221
  sheet:  0.17 (0.26), residues: 366
  loop : -0.50 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 207 
 HIS   0.005   0.001   HIS A 789 
 PHE   0.015   0.002   PHE A1030 
 TYR   0.013   0.002   TYR A 891 
 ARG   0.006   0.001   ARG A 158 

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6782 (mp0) cc_final: 0.6341 (mp0)
REVERT: A   70 LYS cc_start: 0.7645 (mtpm) cc_final: 0.6853 (mppt)
REVERT: A  150 LYS cc_start: 0.6141 (tttt) cc_final: 0.5141 (tptp)
REVERT: A  210 GLU cc_start: 0.6374 (tm-30) cc_final: 0.6093 (tm-30)
REVERT: A  224 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7451 (mm-30)
REVERT: A  254 LYS cc_start: 0.7079 (mttt) cc_final: 0.6611 (ptpp)
REVERT: A  267 ASN cc_start: 0.8515 (p0) cc_final: 0.8186 (p0)
REVERT: A  859 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6906 (pt0)
REVERT: A  863 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7372 (mt-10)
REVERT: A  969 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7484 (pp20)
REVERT: A  994 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8292 (mt-10)
REVERT: A 1106 GLN cc_start: 0.5075 (tp40) cc_final: 0.4717 (tp-100)
REVERT: B  126 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7389 (mptt)
REVERT: C  364 MET cc_start: 0.6247 (mtp) cc_final: 0.5002 (mmm)
REVERT: C  378 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7127 (mmtm)
REVERT: C  383 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7428 (tp30)
REVERT: C  407 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4041 (mp)
REVERT: C  424 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5368 (tm)
REVERT: C  425 MET cc_start: 0.5524 (ttp) cc_final: 0.5230 (ttp)
  outliers start: 17
  outliers final: 4
  residues processed: 119
  average time/residue: 1.6342
  time to fit residues: 204.4309
Evaluate side-chains
  120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  863 GLU
Chi-restraints excluded: chain A residue  969 GLU
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  383 GLU
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0060
   chunk 59 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.184847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145257 restraints weight = 29409.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 3.93
r_work: 0.3489 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8672  Z= 0.166
  Angle     :  0.532   6.587  11751  Z= 0.281
  Chirality :  0.043   0.163   1324
  Planarity :  0.003   0.035   1500
  Dihedral  :  5.202  51.087   1175
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.29 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1057
  helix:  1.50 (0.36), residues: 220
  sheet:  0.20 (0.26), residues: 368
  loop : -0.48 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 207 
 HIS   0.003   0.001   HIS A 789 
 PHE   0.012   0.002   PHE A1030 
 TYR   0.012   0.001   TYR A 891 
 ARG   0.007   0.000   ARG A 158 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9712.40 seconds
wall clock time: 169 minutes 45.66 seconds (10185.66 seconds total)