Starting phenix.real_space_refine
on Fri Aug 22 23:53:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g46_29714/08_2025/8g46_29714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g46_29714/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g46_29714/08_2025/8g46_29714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g46_29714/08_2025/8g46_29714.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g46_29714/08_2025/8g46_29714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g46_29714/08_2025/8g46_29714.map"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.071
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.68, per 1000 atoms: 0.31
  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: 0.69
  Conformation dependent library (CDL) restraints added in 503.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.23
  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: 1.29

  Time building geometry restraints manager: 0.88 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:             1.750
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.290
-------------------------------------------------------------------------------
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   0.057   8677  Z= 0.485
  Angle     :  0.887  12.016  11757  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.019   0.002   ARG A 753 
 TYR   0.023   0.006   TYR B  76 
 PHE   0.030   0.006   PHE A 942 
 TRP   0.025   0.007   TRP A 953 
 HIS   0.011   0.004   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00759 ( 8672)
  covalent geometry    : angle       0.88286 (11751)
  hydrogen bonds       : bond        0.14245 (  355)
  hydrogen bonds       : angle       7.23257 (  991)
  metal coordination   : bond        0.03020 (    4)
  metal coordination   : angle       3.67620 (    6)
  Misc. bond           : bond        0.04810 (    1)

*********************** 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  : 0.280 
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: 0.6461
  time to fit residues: 81.9022
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  : 0.253 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7588

-------------------------------------------------------------------------------
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 = 0.4124 r_free = 0.4124 target = 0.185544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141048 restraints weight = 27745.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 3.19
r_work: 0.3527 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.0866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8677  Z= 0.131
  Angle     :  0.567   6.513  11757  Z= 0.300
  Chirality :  0.044   0.166   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.933  49.372   1186
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.21 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.25), residues: 1057
  helix:  0.94 (0.36), residues: 219
  sheet:  0.17 (0.26), residues: 368
  loop : -0.38 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 158 
 TYR   0.011   0.001   TYR A 891 
 PHE   0.017   0.002   PHE A 169 
 TRP   0.016   0.002   TRP A 207 
 HIS   0.004   0.001   HIS C 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8672)
  covalent geometry    : angle       0.56391 (11751)
  hydrogen bonds       : bond        0.04341 (  355)
  hydrogen bonds       : angle       5.82012 (  991)
  metal coordination   : bond        0.00343 (    4)
  metal coordination   : angle       2.72005 (    6)
  Misc. bond           : bond        0.00048 (    1)

*********************** 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: 20
    poor density    : 110
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.7561 (mtpm) cc_final: 0.6850 (mppt)
REVERT: A  150 LYS cc_start: 0.6389 (tptt) cc_final: 0.5220 (tptp)
REVERT: A  158 ARG cc_start: 0.7722 (ttt-90) cc_final: 0.7291 (ttp-170)
REVERT: A  210 GLU cc_start: 0.6281 (tm-30) cc_final: 0.5974 (tm-30)
REVERT: A  224 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7516 (mm-30)
REVERT: A  254 LYS cc_start: 0.7076 (mttt) cc_final: 0.6727 (ptpp)
REVERT: A  267 ASN cc_start: 0.8411 (p0) cc_final: 0.8185 (p0)
REVERT: A  847 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7978 (mtm180)
REVERT: A  859 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6875 (pt0)
  outliers start: 20
  outliers final: 7
  residues processed: 119
  average time/residue: 0.6674
  time to fit residues: 83.3123
Evaluate side-chains
  114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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 54 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 50 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 93 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8782

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.185157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140602 restraints weight = 29180.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 3.24
r_work: 0.3520 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8677  Z= 0.130
  Angle     :  0.547   6.009  11757  Z= 0.288
  Chirality :  0.044   0.157   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.529  45.044   1180
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.16 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.25), residues: 1057
  helix:  1.32 (0.36), residues: 219
  sheet:  0.22 (0.26), residues: 368
  loop : -0.43 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 444 
 TYR   0.011   0.001   TYR A 718 
 PHE   0.015   0.002   PHE C 450 
 TRP   0.016   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A1077 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8672)
  covalent geometry    : angle       0.54392 (11751)
  hydrogen bonds       : bond        0.04178 (  355)
  hydrogen bonds       : angle       5.59189 (  991)
  metal coordination   : bond        0.00298 (    4)
  metal coordination   : angle       2.56036 (    6)
  Misc. bond           : bond        0.00002 (    1)

*********************** 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
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.7572 (mtpm) cc_final: 0.6877 (mppt)
REVERT: A  150 LYS cc_start: 0.6214 (tttt) cc_final: 0.5306 (tptp)
REVERT: A  210 GLU cc_start: 0.6309 (tm-30) cc_final: 0.6096 (tm-30)
REVERT: A  224 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7475 (mm-30)
REVERT: A  254 LYS cc_start: 0.7151 (mttt) cc_final: 0.6734 (ptpp)
REVERT: A  267 ASN cc_start: 0.8447 (p0) cc_final: 0.8205 (p0)
REVERT: A  298 LYS cc_start: 0.7951 (tmtm) cc_final: 0.7693 (tmtm)
REVERT: A  847 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7944 (mtm180)
REVERT: A  859 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6865 (pt0)
REVERT: C  378 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7084 (mmtm)
REVERT: C  407 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4288 (mp)
  outliers start: 17
  outliers final: 6
  residues processed: 113
  average time/residue: 0.6708
  time to fit residues: 79.2232
Evaluate side-chains
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  217 SER
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue 1043 LEU
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 24 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 58 optimal weight:    7.9990
   chunk 88 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
C 428 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.183375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138343 restraints weight = 32539.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 3.58
r_work: 0.3476 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8677  Z= 0.154
  Angle     :  0.573   6.550  11757  Z= 0.301
  Chirality :  0.045   0.167   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.681  53.362   1177
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.38 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1057
  helix:  1.42 (0.36), residues: 220
  sheet:  0.21 (0.26), residues: 366
  loop : -0.44 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 158 
 TYR   0.013   0.002   TYR A 891 
 PHE   0.015   0.002   PHE A 169 
 TRP   0.017   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A1077 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8672)
  covalent geometry    : angle       0.56983 (11751)
  hydrogen bonds       : bond        0.04309 (  355)
  hydrogen bonds       : angle       5.60087 (  991)
  metal coordination   : bond        0.00359 (    4)
  metal coordination   : angle       2.91470 (    6)
  Misc. bond           : bond        0.00019 (    1)

*********************** 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
  127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6941 (mp0) cc_final: 0.6440 (mp0)
REVERT: A   70 LYS cc_start: 0.7551 (mtpm) cc_final: 0.6748 (mppt)
REVERT: A  150 LYS cc_start: 0.6147 (tttt) cc_final: 0.5149 (tptp)
REVERT: A  210 GLU cc_start: 0.6341 (tm-30) cc_final: 0.6052 (tm-30)
REVERT: A  224 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7434 (mm-30)
REVERT: A  254 LYS cc_start: 0.7012 (mttt) cc_final: 0.6569 (ptpp)
REVERT: A  267 ASN cc_start: 0.8487 (p0) cc_final: 0.8198 (p0)
REVERT: A  859 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6856 (pt0)
REVERT: C  360 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5147 (mp)
REVERT: C  364 MET cc_start: 0.6300 (mtp) cc_final: 0.4922 (mmm)
REVERT: C  377 TYR cc_start: 0.7396 (m-10) cc_final: 0.7110 (m-10)
REVERT: C  378 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7091 (mmtm)
REVERT: C  407 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.4143 (mp)
REVERT: C  424 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5202 (tm)
  outliers start: 17
  outliers final: 4
  residues processed: 120
  average time/residue: 0.7022
  time to fit residues: 88.2737
Evaluate side-chains
  115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  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 54 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    1.6586

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.182222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.141590 restraints weight = 28799.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 3.91
r_work: 0.3453 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8677  Z= 0.182
  Angle     :  0.607   7.381  11757  Z= 0.319
  Chirality :  0.046   0.170   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.819  50.047   1177
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1057
  helix:  1.33 (0.36), residues: 220
  sheet:  0.17 (0.26), residues: 373
  loop : -0.48 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 158 
 TYR   0.014   0.002   TYR A 718 
 PHE   0.016   0.002   PHE C 450 
 TRP   0.019   0.003   TRP A 207 
 HIS   0.005   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8672)
  covalent geometry    : angle       0.60266 (11751)
  hydrogen bonds       : bond        0.04574 (  355)
  hydrogen bonds       : angle       5.70358 (  991)
  metal coordination   : bond        0.00464 (    4)
  metal coordination   : angle       3.39944 (    6)
  Misc. bond           : bond        0.00039 (    1)

*********************** 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
  132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6939 (mp0) cc_final: 0.6472 (mp0)
REVERT: A   70 LYS cc_start: 0.7572 (mtpm) cc_final: 0.6810 (mppt)
REVERT: A   99 ASP cc_start: 0.6726 (m-30) cc_final: 0.6411 (m-30)
REVERT: A  150 LYS cc_start: 0.6187 (tttt) cc_final: 0.5191 (tptp)
REVERT: A  210 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6130 (tm-30)
REVERT: A  224 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7448 (mm-30)
REVERT: A  254 LYS cc_start: 0.7067 (mttt) cc_final: 0.6616 (ptpp)
REVERT: A  267 ASN cc_start: 0.8510 (p0) cc_final: 0.8199 (p0)
REVERT: A  859 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6938 (pt0)
REVERT: A 1043 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6732 (mt)
REVERT: A 1106 GLN cc_start: 0.5086 (tp40) cc_final: 0.4772 (tp-100)
REVERT: C  378 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7177 (mmtm)
REVERT: C  383 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7373 (tp30)
REVERT: C  407 LEU cc_start: 0.4632 (OUTLIER) cc_final: 0.4113 (mp)
REVERT: C  421 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5753 (t0)
REVERT: C  424 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5260 (tm)
REVERT: C  425 MET cc_start: 0.5595 (ttp) cc_final: 0.5352 (ttp)
  outliers start: 17
  outliers final: 4
  residues processed: 123
  average time/residue: 0.6748
  time to fit residues: 87.1543
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  151 GLU
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  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 40 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.183047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138450 restraints weight = 27990.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 3.42
r_work: 0.3479 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    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 = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8677  Z= 0.154
  Angle     :  0.573   7.333  11757  Z= 0.302
  Chirality :  0.044   0.167   1324
  Planarity :  0.004   0.036   1500
  Dihedral  :  5.610  50.675   1177
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.25), residues: 1057
  helix:  1.37 (0.36), residues: 220
  sheet:  0.19 (0.26), residues: 373
  loop : -0.47 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 158 
 TYR   0.013   0.002   TYR A 891 
 PHE   0.015   0.002   PHE C 450 
 TRP   0.018   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8672)
  covalent geometry    : angle       0.56972 (11751)
  hydrogen bonds       : bond        0.04300 (  355)
  hydrogen bonds       : angle       5.62809 (  991)
  metal coordination   : bond        0.00368 (    4)
  metal coordination   : angle       2.85137 (    6)
  Misc. bond           : bond        0.00018 (    1)

*********************** 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
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6888 (mp0) cc_final: 0.6384 (mp0)
REVERT: A   70 LYS cc_start: 0.7606 (mtpm) cc_final: 0.6810 (mppt)
REVERT: A  150 LYS cc_start: 0.6207 (tttt) cc_final: 0.5177 (tptp)
REVERT: A  210 GLU cc_start: 0.6390 (tm-30) cc_final: 0.6103 (tm-30)
REVERT: A  224 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7478 (mm-30)
REVERT: A  254 LYS cc_start: 0.7066 (mttt) cc_final: 0.6630 (ptpp)
REVERT: A  267 ASN cc_start: 0.8489 (p0) cc_final: 0.8179 (p0)
REVERT: A  859 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6895 (pt0)
REVERT: A  994 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8265 (mt-10)
REVERT: A 1106 GLN cc_start: 0.4997 (tp40) cc_final: 0.4683 (tp-100)
REVERT: C  378 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7114 (mmtm)
REVERT: C  383 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7337 (tp30)
REVERT: C  407 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4086 (mp)
REVERT: C  421 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.5795 (t0)
REVERT: C  424 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.5214 (tm)
  outliers start: 19
  outliers final: 3
  residues processed: 123
  average time/residue: 0.6672
  time to fit residues: 85.9595
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  : 0.339 
-------------------------------------------------------------------------------
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  859 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.181972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.137153 restraints weight = 26631.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.78
r_work: 0.3481 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8677  Z= 0.188
  Angle     :  0.614   7.981  11757  Z= 0.322
  Chirality :  0.046   0.169   1324
  Planarity :  0.004   0.037   1500
  Dihedral  :  5.627  52.870   1175
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.91 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.25), residues: 1057
  helix:  1.29 (0.36), residues: 220
  sheet:  0.13 (0.26), residues: 373
  loop : -0.51 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 158 
 TYR   0.014   0.002   TYR A 718 
 PHE   0.016   0.002   PHE C 450 
 TRP   0.019   0.003   TRP A 207 
 HIS   0.005   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8672)
  covalent geometry    : angle       0.60915 (11751)
  hydrogen bonds       : bond        0.04587 (  355)
  hydrogen bonds       : angle       5.71380 (  991)
  metal coordination   : bond        0.00495 (    4)
  metal coordination   : angle       3.34228 (    6)
  Misc. bond           : bond        0.00044 (    1)

*********************** 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
  136 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6925 (mp0) cc_final: 0.6431 (mp0)
REVERT: A   70 LYS cc_start: 0.7686 (mtpm) cc_final: 0.6915 (mppt)
REVERT: A   99 ASP cc_start: 0.6813 (m-30) cc_final: 0.6481 (m-30)
REVERT: A  150 LYS cc_start: 0.6196 (tttt) cc_final: 0.5206 (tptp)
REVERT: A  210 GLU cc_start: 0.6408 (tm-30) cc_final: 0.6101 (tm-30)
REVERT: A  224 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7615 (mm-30)
REVERT: A  254 LYS cc_start: 0.7173 (mttt) cc_final: 0.6678 (ptpp)
REVERT: A  267 ASN cc_start: 0.8593 (p0) cc_final: 0.8294 (p0)
REVERT: A  859 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6994 (pt0)
REVERT: A  863 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7562 (mt-10)
REVERT: A  994 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8328 (mt-10)
REVERT: A 1106 GLN cc_start: 0.5200 (tp40) cc_final: 0.4872 (tp-100)
REVERT: C  378 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7226 (mmtm)
REVERT: C  383 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7467 (tp30)
REVERT: C  407 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4031 (mp)
REVERT: C  421 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.5890 (t0)
REVERT: C  424 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5240 (tm)
REVERT: C  425 MET cc_start: 0.5529 (ttp) cc_final: 0.5184 (ttp)
  outliers start: 19
  outliers final: 4
  residues processed: 126
  average time/residue: 0.6788
  time to fit residues: 89.6806
Evaluate side-chains
  126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
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  439 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.183505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138622 restraints weight = 27590.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 3.37
r_work: 0.3492 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3494
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8677  Z= 0.140
  Angle     :  0.559   7.785  11757  Z= 0.294
  Chirality :  0.044   0.162   1324
  Planarity :  0.004   0.036   1500
  Dihedral  :  5.403  53.183   1175
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.65 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.25), residues: 1057
  helix:  1.43 (0.36), residues: 220
  sheet:  0.19 (0.26), residues: 373
  loop : -0.48 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 158 
 TYR   0.012   0.002   TYR A 891 
 PHE   0.014   0.002   PHE C 450 
 TRP   0.018   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8672)
  covalent geometry    : angle       0.55622 (11751)
  hydrogen bonds       : bond        0.04140 (  355)
  hydrogen bonds       : angle       5.54703 (  991)
  metal coordination   : bond        0.00326 (    4)
  metal coordination   : angle       2.56339 (    6)
  Misc. bond           : bond        0.00013 (    1)

*********************** 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
  123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6844 (mp0) cc_final: 0.6382 (mp0)
REVERT: A   70 LYS cc_start: 0.7604 (mtpm) cc_final: 0.6812 (mppt)
REVERT: A  150 LYS cc_start: 0.6209 (tttt) cc_final: 0.5199 (tptp)
REVERT: A  210 GLU cc_start: 0.6362 (tm-30) cc_final: 0.6083 (tm-30)
REVERT: A  224 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7424 (mm-30)
REVERT: A  254 LYS cc_start: 0.7057 (mttt) cc_final: 0.6632 (ptpp)
REVERT: A  267 ASN cc_start: 0.8496 (p0) cc_final: 0.8182 (p0)
REVERT: A  859 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6872 (pt0)
REVERT: A  863 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7331 (mt-10)
REVERT: A  961 ASP cc_start: 0.7700 (p0) cc_final: 0.7489 (p0)
REVERT: A  994 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8262 (mt-10)
REVERT: A 1106 GLN cc_start: 0.4984 (tp40) cc_final: 0.4672 (tp-100)
REVERT: C  378 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7162 (mmtm)
REVERT: C  407 LEU cc_start: 0.4604 (OUTLIER) cc_final: 0.4110 (mp)
REVERT: C  421 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.5848 (t0)
REVERT: C  424 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5278 (tm)
  outliers start: 14
  outliers final: 4
  residues processed: 119
  average time/residue: 0.6953
  time to fit residues: 86.7302
Evaluate side-chains
  120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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 100 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 88 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4106 r_free = 0.4106 target = 0.184258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.139877 restraints weight = 29843.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.56
r_work: 0.3493 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8677  Z= 0.128
  Angle     :  0.544   7.656  11757  Z= 0.286
  Chirality :  0.044   0.164   1324
  Planarity :  0.004   0.035   1500
  Dihedral  :  5.290  53.146   1175
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.25), residues: 1057
  helix:  1.44 (0.36), residues: 221
  sheet:  0.17 (0.26), residues: 368
  loop : -0.49 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 158 
 TYR   0.012   0.001   TYR A 891 
 PHE   0.013   0.002   PHE C 450 
 TRP   0.017   0.002   TRP A 207 
 HIS   0.004   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8672)
  covalent geometry    : angle       0.54170 (11751)
  hydrogen bonds       : bond        0.03998 (  355)
  hydrogen bonds       : angle       5.46478 (  991)
  metal coordination   : bond        0.00295 (    4)
  metal coordination   : angle       2.27387 (    6)
  Misc. bond           : bond        0.00013 (    1)

*********************** 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
  121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6767 (mp0) cc_final: 0.6347 (mp0)
REVERT: A   70 LYS cc_start: 0.7594 (mtpm) cc_final: 0.6808 (mppt)
REVERT: A  150 LYS cc_start: 0.6194 (tttt) cc_final: 0.5172 (tptp)
REVERT: A  210 GLU cc_start: 0.6322 (tm-30) cc_final: 0.6046 (tm-30)
REVERT: A  224 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7409 (mm-30)
REVERT: A  254 LYS cc_start: 0.7047 (mttt) cc_final: 0.6602 (ptpp)
REVERT: A  267 ASN cc_start: 0.8478 (p0) cc_final: 0.8174 (p0)
REVERT: A  298 LYS cc_start: 0.7993 (tmtm) cc_final: 0.7070 (ttpp)
REVERT: A  859 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6838 (pt0)
REVERT: A  994 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (mt-10)
REVERT: A 1106 GLN cc_start: 0.4903 (tp40) cc_final: 0.4603 (tp-100)
REVERT: C  364 MET cc_start: 0.6233 (mtp) cc_final: 0.4886 (mmm)
REVERT: C  378 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7070 (mmtm)
REVERT: C  383 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7330 (tp30)
REVERT: C  407 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.4065 (mp)
REVERT: C  421 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.5992 (t0)
REVERT: C  424 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5192 (tm)
REVERT: C  425 MET cc_start: 0.5422 (ttp) cc_final: 0.5113 (ttp)
REVERT: C  428 ASN cc_start: 0.6681 (m110) cc_final: 0.6441 (m-40)
  outliers start: 13
  outliers final: 4
  residues processed: 118
  average time/residue: 0.7196
  time to fit residues: 88.9939
Evaluate side-chains
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0570
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 24 optimal weight:    0.2980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.185387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.141035 restraints weight = 29778.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 3.64
r_work: 0.3507 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8677  Z= 0.113
  Angle     :  0.526   6.708  11757  Z= 0.278
  Chirality :  0.043   0.159   1324
  Planarity :  0.003   0.035   1500
  Dihedral  :  5.118  52.609   1175
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 15.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1057
  helix:  1.48 (0.36), residues: 221
  sheet:  0.21 (0.26), residues: 368
  loop : -0.48 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 158 
 TYR   0.013   0.001   TYR A 193 
 PHE   0.012   0.002   PHE C 450 
 TRP   0.016   0.002   TRP A 207 
 HIS   0.004   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8672)
  covalent geometry    : angle       0.52482 (11751)
  hydrogen bonds       : bond        0.03781 (  355)
  hydrogen bonds       : angle       5.36569 (  991)
  metal coordination   : bond        0.00235 (    4)
  metal coordination   : angle       1.89567 (    6)
  Misc. bond           : bond        0.00003 (    1)

********************** 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
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.6686 (mp0) cc_final: 0.6287 (mp0)
REVERT: A   70 LYS cc_start: 0.7588 (mtpm) cc_final: 0.6780 (mppt)
REVERT: A  150 LYS cc_start: 0.6279 (tttt) cc_final: 0.5269 (tptp)
REVERT: A  210 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5981 (tm-30)
REVERT: A  224 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7408 (mm-30)
REVERT: A  254 LYS cc_start: 0.7009 (mttt) cc_final: 0.6562 (ptpp)
REVERT: A  267 ASN cc_start: 0.8479 (p0) cc_final: 0.8171 (p0)
REVERT: A  298 LYS cc_start: 0.8014 (tmtm) cc_final: 0.7106 (ttpp)
REVERT: A  859 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6812 (pt0)
REVERT: A  969 GLU cc_start: 0.7746 (pp20) cc_final: 0.7259 (pp20)
REVERT: A  994 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (mt-10)
REVERT: A 1106 GLN cc_start: 0.4972 (tp40) cc_final: 0.4661 (tp-100)
REVERT: B  126 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7424 (mptt)
REVERT: C  364 MET cc_start: 0.6134 (mtp) cc_final: 0.4833 (mmm)
REVERT: C  378 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7047 (mmtm)
REVERT: C  383 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7318 (tp30)
REVERT: C  407 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4038 (mp)
REVERT: C  421 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.6127 (t0)
REVERT: C  424 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5186 (tm)
REVERT: C  425 MET cc_start: 0.5400 (ttp) cc_final: 0.5127 (ttp)
REVERT: C  428 ASN cc_start: 0.6539 (m110) cc_final: 0.6329 (m-40)
  outliers start: 11
  outliers final: 4
  residues processed: 115
  average time/residue: 0.7063
  time to fit residues: 85.1189
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.182257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.137209 restraints weight = 28118.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.24
r_work: 0.3473 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    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 = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8677  Z= 0.187
  Angle     :  0.613   7.883  11757  Z= 0.322
  Chirality :  0.046   0.171   1324
  Planarity :  0.004   0.039   1500
  Dihedral  :  5.590  54.953   1175
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.97 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.25), residues: 1057
  helix:  1.28 (0.36), residues: 221
  sheet:  0.14 (0.26), residues: 373
  loop : -0.51 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 158 
 TYR   0.014   0.002   TYR A 718 
 PHE   0.016   0.002   PHE A1030 
 TRP   0.018   0.003   TRP A 207 
 HIS   0.006   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8672)
  covalent geometry    : angle       0.60913 (11751)
  hydrogen bonds       : bond        0.04481 (  355)
  hydrogen bonds       : angle       5.63168 (  991)
  metal coordination   : bond        0.00466 (    4)
  metal coordination   : angle       3.21878 (    6)
  Misc. bond           : bond        0.00031 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3798.14 seconds
wall clock time: 65 minutes 12.93 seconds (3912.93 seconds total)