Starting phenix.real_space_refine
on Tue Jul 29 22:06:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rua_24701/07_2025/7rua_24701.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      64      5.16       5
     C    7350      2.51       5
     N    1992      2.21       5
     O    2188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11603
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2412
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 18, 'TRANS': 286}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2175
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
    Chain: "D"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 790
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 12, 'TRANS': 87}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 392
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 47}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1947  SG  CYS A 283      54.502  65.935  97.337  1.00 99.40           S
  ATOM   1970  SG  CYS A 286      55.392  68.382  94.693  1.00 92.44           S

  Restraints were copied for chains:
    B, F, G, H
  Time building chain proxies: 8.74, per 1000 atoms: 0.75
  Number of scatterers: 11603
  At special positions: 0
  Unit cell: (108.075, 136.125, 112.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      64     16.00
     P       6     15.00
     Mg      2     11.99
     O    2188      8.00
     N    1992      7.00
     C    7350      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.65
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS B 286 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 286 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 283 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS B 283 "
      Number of angles added : 6


  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2760

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 2 sheets defined
      71.4% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 28
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.534A  pdb=" N   ALA A  57 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
    Processing helix  chain 'A' and resid 116 through 133
      removed outlier: 4.177A  pdb=" N   MET A 130 " --> pdb=" O   MET A 126 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   SER A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 152
    Processing helix  chain 'A' and resid 163 through 187
      Proline residue:  A 174  - end of helix
    Processing helix  chain 'A' and resid 211 through 232
      removed outlier: 4.382A  pdb=" N   LYS A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 245 through 263
    Processing helix  chain 'A' and resid 283 through 304
    Processing helix  chain 'A' and resid 321 through 334
      removed outlier: 3.546A  pdb=" N   GLN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 28
    Processing helix  chain 'B' and resid 43 through 57
      removed outlier: 3.534A  pdb=" N   ALA B  57 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 78
    Processing helix  chain 'B' and resid 116 through 133
      removed outlier: 4.178A  pdb=" N   MET B 130 " --> pdb=" O   MET B 126 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   SER B 131 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 152
    Processing helix  chain 'B' and resid 163 through 187
      Proline residue:  B 174  - end of helix
    Processing helix  chain 'B' and resid 211 through 232
      removed outlier: 4.383A  pdb=" N   LYS B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 245 through 263
    Processing helix  chain 'B' and resid 283 through 304
    Processing helix  chain 'B' and resid 321 through 334
      removed outlier: 3.546A  pdb=" N   GLN B 331 " --> pdb=" O   THR B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 37
      removed outlier: 3.619A  pdb=" N   GLN C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 56
    Processing helix  chain 'C' and resid 58 through 76
    Processing helix  chain 'C' and resid 78 through 97
    Processing helix  chain 'C' and resid 101 through 115
    Processing helix  chain 'C' and resid 119 through 133
      removed outlier: 4.382A  pdb=" N   VAL C 123 " --> pdb=" O   SER C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 157
      removed outlier: 3.739A  pdb=" N   HIS C 146 " --> pdb=" O   HIS C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 169
    Processing helix  chain 'C' and resid 172 through 186
    Processing helix  chain 'C' and resid 191 through 206
      removed outlier: 3.821A  pdb=" N   VAL C 196 " --> pdb=" O   VAL C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 223
    Processing helix  chain 'C' and resid 234 through 250
    Processing helix  chain 'C' and resid 251 through 262
    Processing helix  chain 'C' and resid 262 through 267
    Processing helix  chain 'C' and resid 268 through 270
      No H-bonds generated for 'chain 'C' and resid 268 through 270'
    Processing helix  chain 'C' and resid 271 through 284
    Processing helix  chain 'D' and resid 1009 through 1014
      removed outlier: 4.320A  pdb=" N   ALA D1013 " --> pdb=" O   PRO D1009 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL D1014 " --> pdb=" O   TRP D1010 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1009 through 1014'
    Processing helix  chain 'D' and resid 1015 through 1017
      No H-bonds generated for 'chain 'D' and resid 1015 through 1017'
    Processing helix  chain 'D' and resid 1018 through 1032
      removed outlier: 3.535A  pdb=" N   GLN D1023 " --> pdb=" O   VAL D1019 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS D1031 " --> pdb=" O   GLN D1027 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1039 through 1044
    Processing helix  chain 'D' and resid 1062 through 1075
    Processing helix  chain 'D' and resid 1081 through 1088
    Processing helix  chain 'D' and resid 1092 through 1113
      removed outlier: 4.199A  pdb=" N   TYR D1098 " --> pdb=" O   VAL D1094 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 94 through 104
    Processing helix  chain 'E' and resid 108 through 129
    Processing helix  chain 'E' and resid 131 through 140
    Processing helix  chain 'F' and resid 20 through 37
      removed outlier: 3.619A  pdb=" N   GLN F  24 " --> pdb=" O   ARG F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 38 through 56
    Processing helix  chain 'F' and resid 58 through 76
    Processing helix  chain 'F' and resid 78 through 97
    Processing helix  chain 'F' and resid 101 through 115
    Processing helix  chain 'F' and resid 119 through 133
      removed outlier: 4.381A  pdb=" N   VAL F 123 " --> pdb=" O   SER F 119 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 142 through 157
      removed outlier: 3.738A  pdb=" N   HIS F 146 " --> pdb=" O   HIS F 142 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 158 through 169
    Processing helix  chain 'F' and resid 172 through 186
    Processing helix  chain 'F' and resid 191 through 206
      removed outlier: 3.821A  pdb=" N   VAL F 196 " --> pdb=" O   VAL F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 223
    Processing helix  chain 'F' and resid 234 through 250
    Processing helix  chain 'F' and resid 251 through 262
    Processing helix  chain 'F' and resid 262 through 267
    Processing helix  chain 'F' and resid 268 through 270
      No H-bonds generated for 'chain 'F' and resid 268 through 270'
    Processing helix  chain 'F' and resid 271 through 284
    Processing helix  chain 'G' and resid 1009 through 1014
      removed outlier: 4.320A  pdb=" N   ALA G1013 " --> pdb=" O   PRO G1009 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL G1014 " --> pdb=" O   TRP G1010 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 1009 through 1014'
    Processing helix  chain 'G' and resid 1015 through 1017
      No H-bonds generated for 'chain 'G' and resid 1015 through 1017'
    Processing helix  chain 'G' and resid 1018 through 1032
      removed outlier: 3.534A  pdb=" N   GLN G1023 " --> pdb=" O   VAL G1019 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS G1031 " --> pdb=" O   GLN G1027 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1039 through 1044
    Processing helix  chain 'G' and resid 1057 through 1070
    Processing helix  chain 'G' and resid 1076 through 1083
    Processing helix  chain 'G' and resid 1087 through 1108
      removed outlier: 4.199A  pdb=" N   TYR G1093 " --> pdb=" O   VAL G1089 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 104
    Processing helix  chain 'H' and resid 108 through 129
    Processing helix  chain 'H' and resid 131 through 140
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.533A  pdb=" N   VAL A  62 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   MET A  97 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ILE A  64 " --> pdb=" O   MET A  97 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU A  63 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   ASP A 160 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE A  65 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ILE A  34 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TRP A  33 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ILE A 239 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   PHE A  35 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL A 241 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   ILE A 243 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   ASN A 268 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   CYS A 240 " --> pdb=" O   ASN A 268 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE A 269 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   LEU A 312 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87
      removed outlier: 6.534A  pdb=" N   VAL B  62 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   MET B  97 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE B  64 " --> pdb=" O   MET B  97 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU B  63 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   ASP B 160 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE B  65 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ILE B  34 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   TRP B  33 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ILE B 239 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   PHE B  35 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   VAL B 241 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLY B  37 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   ILE B 243 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   ASN B 268 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B 240 " --> pdb=" O   ASN B 268 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE B 269 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   LEU B 312 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL B 271 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)

    718 hydrogen bonds defined for protein.
    2148 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.40

  Time building geometry restraints manager: 3.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3821
        1.34 -     1.46: 2330
        1.46 -     1.58: 5577
        1.58 -     1.70: 10
        1.70 -     1.82: 106
  Bond restraints: 11844
  Sorted by residual:
  bond pdb=" CA  VAL D1019 "
       pdb=" CB  VAL D1019 "
    ideal  model  delta    sigma   weight residual
    1.539  1.544 -0.005 5.40e-03 3.43e+04 7.45e-01
  bond pdb=" C1' ATP B 401 "
       pdb=" C2' ATP B 401 "
    ideal  model  delta    sigma   weight residual
    1.531  1.521  0.010 1.20e-02 6.94e+03 6.72e-01
  bond pdb=" CD  ARG D1030 "
       pdb=" NE  ARG D1030 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.011 1.40e-02 5.10e+03 6.67e-01
  bond pdb=" CD  ARG G1030 "
       pdb=" NE  ARG G1030 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.011 1.40e-02 5.10e+03 6.67e-01
  bond pdb=" CA  VAL G1019 "
       pdb=" CB  VAL G1019 "
    ideal  model  delta    sigma   weight residual
    1.539  1.543 -0.004 5.40e-03 3.43e+04 6.44e-01
  ... (remaining 11839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 15519
        1.34 -     2.68: 372
        2.68 -     4.02: 99
        4.02 -     5.36: 22
        5.36 -     6.70: 8
  Bond angle restraints: 16020
  Sorted by residual:
  angle pdb=" NE  ARG A 224 "
        pdb=" CZ  ARG A 224 "
        pdb=" NH2 ARG A 224 "
      ideal   model   delta    sigma   weight residual
     119.20  121.62   -2.42 9.00e-01 1.23e+00 7.22e+00
  angle pdb=" NE  ARG B 224 "
        pdb=" CZ  ARG B 224 "
        pdb=" NH2 ARG B 224 "
      ideal   model   delta    sigma   weight residual
     119.20  121.59   -2.39 9.00e-01 1.23e+00 7.07e+00
  angle pdb=" C   ARG G1094 "
        pdb=" N   GLN G1095 "
        pdb=" CA  GLN G1095 "
      ideal   model   delta    sigma   weight residual
     120.72  116.53    4.19 1.67e+00 3.59e-01 6.30e+00
  angle pdb=" C   ARG D1099 "
        pdb=" N   GLN D1100 "
        pdb=" CA  GLN D1100 "
      ideal   model   delta    sigma   weight residual
     120.72  116.54    4.18 1.67e+00 3.59e-01 6.27e+00
  angle pdb=" C1' ATP B 401 "
        pdb=" C2' ATP B 401 "
        pdb=" O2' ATP B 401 "
      ideal   model   delta    sigma   weight residual
     110.58  103.88    6.70 2.79e+00 1.28e-01 5.76e+00
  ... (remaining 16015 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6480
       17.58 -    35.15: 648
       35.15 -    52.73: 136
       52.73 -    70.31: 34
       70.31 -    87.89: 12
  Dihedral angle restraints: 7310
    sinusoidal: 3072
      harmonic: 4238
  Sorted by residual:
  dihedral pdb=" CA  SER F 137 "
           pdb=" C   SER F 137 "
           pdb=" N   GLY F 138 "
           pdb=" CA  GLY F 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.03   18.97     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  SER C 137 "
           pdb=" C   SER C 137 "
           pdb=" N   GLY C 138 "
           pdb=" CA  GLY C 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.05   18.95     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CD  ARG A 224 "
           pdb=" NE  ARG A 224 "
           pdb=" CZ  ARG A 224 "
           pdb=" NH1 ARG A 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -26.87   26.87     1      1.00e+01 1.00e-02 1.04e+01
  ... (remaining 7307 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1568
       0.059 -    0.118: 184
       0.118 -    0.177: 8
       0.177 -    0.236: 2
       0.236 -    0.295: 4
  Chirality restraints: 1766
  Sorted by residual:
  chirality pdb=" C2' ATP A 401 "
            pdb=" C1' ATP A 401 "
            pdb=" C3' ATP A 401 "
            pdb=" O2' ATP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" C2' ATP B 401 "
            pdb=" C1' ATP B 401 "
            pdb=" C3' ATP B 401 "
            pdb=" O2' ATP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" C3' ATP A 401 "
            pdb=" C2' ATP A 401 "
            pdb=" C4' ATP A 401 "
            pdb=" O3' ATP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.91    0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 1763 not shown)

  Planarity restraints: 2072
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 224 "   -0.444 9.50e-02 1.11e+02   1.99e-01 2.51e+01
        pdb=" NE  ARG A 224 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 224 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 224 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 224 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 224 "    0.443 9.50e-02 1.11e+02   1.99e-01 2.50e+01
        pdb=" NE  ARG B 224 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 224 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 224 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 224 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G1051 "   -0.186 9.50e-02 1.11e+02   8.36e-02 4.41e+00
        pdb=" NE  ARG G1051 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG G1051 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG G1051 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG G1051 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2069 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 103
        2.52 -     3.11: 9791
        3.11 -     3.71: 19541
        3.71 -     4.30: 26422
        4.30 -     4.90: 43337
  Nonbonded interactions: 99194
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.920 2.170
  nonbonded pdb=" O2G ATP B 401 "
            pdb="MG    MG B 402 "
     model   vdw
     1.921 2.170
  nonbonded pdb=" OE1 GLU A 245 "
            pdb=" O3' ATP B 401 "
     model   vdw
     1.944 3.040
  nonbonded pdb=" OE1 GLU B 245 "
            pdb=" O3' ATP A 401 "
     model   vdw
     1.946 3.040
  nonbonded pdb=" OG1 THR B  45 "
            pdb="MG    MG B 402 "
     model   vdw
     1.962 2.170
  ... (remaining 99189 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 16 through 339 or resid 401 through 402))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.450
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.590
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
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      :  0.003   0.030  11848  Z= 0.147
  Angle     :  0.568   6.704  16026  Z= 0.294
  Chirality :  0.040   0.295   1766
  Planarity :  0.008   0.199   2072
  Dihedral  : 14.914  87.887   4550
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.23), residues: 1424
  helix:  1.68 (0.17), residues: 944
  sheet:  0.12 (0.61), residues: 82
  loop :  0.34 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  96 
 HIS   0.007   0.001   HIS C  43 
 PHE   0.009   0.001   PHE B 328 
 TYR   0.011   0.001   TYR A 250 
 ARG   0.016   0.001   ARG A 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13505 (  718)
  hydrogen bonds       : angle       5.61979 ( 2148)
  metal coordination   : bond        0.00091 (    4)
  metal coordination   : angle       2.84458 (    6)
  covalent geometry    : bond        0.00331 (11844)
  covalent geometry    : angle       0.56579 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2998 (mmt) cc_final: 0.2411 (mmm)
REVERT: A  121 MET cc_start: 0.1612 (mtt) cc_final: 0.1220 (ptt)
REVERT: A  126 MET cc_start: 0.4497 (ttt) cc_final: 0.4143 (tmm)
REVERT: A  281 ARG cc_start: 0.6460 (ptm160) cc_final: 0.6199 (ptp-170)
REVERT: A  287 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7441 (mt-10)
REVERT: B   89 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7539 (mtmt)
REVERT: B  118 MET cc_start: 0.3322 (mmt) cc_final: 0.2716 (mmm)
REVERT: B  121 MET cc_start: 0.1677 (mtt) cc_final: 0.1408 (ptt)
REVERT: B  126 MET cc_start: 0.4622 (ttt) cc_final: 0.4197 (tmm)
REVERT: B  281 ARG cc_start: 0.6445 (ptm160) cc_final: 0.6182 (ptp-170)
REVERT: B  287 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7434 (mt-10)
REVERT: C   27 GLU cc_start: 0.7266 (tt0) cc_final: 0.6905 (mt-10)
REVERT: C   36 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7983 (ttpt)
REVERT: C   66 MET cc_start: 0.8502 (mmm) cc_final: 0.8278 (mmm)
REVERT: C  128 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7123 (mtp180)
REVERT: C  238 ASN cc_start: 0.7991 (m-40) cc_final: 0.7717 (m110)
REVERT: C  258 LEU cc_start: 0.7103 (mm) cc_final: 0.6882 (mt)
REVERT: D 1042 TYR cc_start: 0.7344 (t80) cc_final: 0.7133 (t80)
REVERT: F   27 GLU cc_start: 0.7259 (tt0) cc_final: 0.6905 (mt-10)
REVERT: F   36 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7993 (ttpt)
REVERT: F   66 MET cc_start: 0.8500 (mmm) cc_final: 0.8259 (mmp)
REVERT: F  128 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7116 (mtp180)
REVERT: F  238 ASN cc_start: 0.8020 (m-40) cc_final: 0.7734 (m110)
REVERT: F  255 PHE cc_start: 0.8342 (t80) cc_final: 0.8094 (t80)
REVERT: F  260 GLU cc_start: 0.8140 (tp30) cc_final: 0.7830 (tm-30)
REVERT: G 1042 TYR cc_start: 0.7279 (t80) cc_final: 0.6991 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2527
  time to fit residues: 93.5770
Evaluate side-chains
  182 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 111 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  54 GLN
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN
** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1024 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.179924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.139207 restraints weight = 16712.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.28
r_work: 0.3364 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11848  Z= 0.165
  Angle     :  0.626   9.953  16026  Z= 0.320
  Chirality :  0.042   0.147   1766
  Planarity :  0.005   0.055   2072
  Dihedral  :  7.847  76.244   1630
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.78 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.23), residues: 1424
  helix:  1.94 (0.17), residues: 976
  sheet: -0.22 (0.60), residues: 74
  loop :  0.35 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP F 241 
 HIS   0.006   0.002   HIS E 106 
 PHE   0.021   0.002   PHE C 239 
 TYR   0.024   0.002   TYR C 272 
 ARG   0.006   0.001   ARG A 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  718)
  hydrogen bonds       : angle       4.41441 ( 2148)
  metal coordination   : bond        0.00270 (    4)
  metal coordination   : angle       3.68716 (    6)
  covalent geometry    : bond        0.00381 (11844)
  covalent geometry    : angle       0.62195 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 1.472 
Fit side-chains
REVERT: A   89 LYS cc_start: 0.8664 (tptt) cc_final: 0.8389 (mtmt)
REVERT: A  118 MET cc_start: 0.3262 (mmt) cc_final: 0.2741 (mpp)
REVERT: A  121 MET cc_start: 0.1681 (mtt) cc_final: 0.1241 (ptt)
REVERT: A  126 MET cc_start: 0.5787 (ttt) cc_final: 0.4944 (tmm)
REVERT: A  128 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7027 (pt0)
REVERT: A  281 ARG cc_start: 0.6662 (ptm160) cc_final: 0.6424 (ptp-170)
REVERT: B   89 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8091 (mttt)
REVERT: B  118 MET cc_start: 0.3467 (mmt) cc_final: 0.3027 (mpp)
REVERT: B  121 MET cc_start: 0.2083 (mtt) cc_final: 0.1684 (ptt)
REVERT: B  126 MET cc_start: 0.5702 (ttt) cc_final: 0.4830 (tmm)
REVERT: B  179 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6896 (ttt-90)
REVERT: B  281 ARG cc_start: 0.6656 (ptm160) cc_final: 0.6434 (ptp-170)
REVERT: C   36 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8377 (ttmt)
REVERT: C  238 ASN cc_start: 0.8076 (m-40) cc_final: 0.7534 (m110)
REVERT: C  271 MET cc_start: 0.6578 (mtt) cc_final: 0.6210 (mmp)
REVERT: D 1042 TYR cc_start: 0.7992 (t80) cc_final: 0.7356 (t80)
REVERT: F   36 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8409 (ttmt)
REVERT: F  238 ASN cc_start: 0.8051 (m-40) cc_final: 0.7481 (m110)
REVERT: F  255 PHE cc_start: 0.8374 (t80) cc_final: 0.8142 (t80)
REVERT: F  271 MET cc_start: 0.6749 (mtt) cc_final: 0.6330 (mmp)
REVERT: G 1042 TYR cc_start: 0.7925 (t80) cc_final: 0.7467 (t80)
  outliers start: 21
  outliers final: 9
  residues processed: 204
  average time/residue: 0.2402
  time to fit residues: 69.7476
Evaluate side-chains
  171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 162
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain G residue 1028 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 138 optimal weight:   30.0000
   chunk 33 optimal weight:    0.8980
   chunk 102 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1027 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.179178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.139226 restraints weight = 16842.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.00
r_work: 0.3357 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11848  Z= 0.157
  Angle     :  0.566   6.697  16026  Z= 0.294
  Chirality :  0.041   0.144   1766
  Planarity :  0.005   0.057   2072
  Dihedral  :  7.570  80.869   1630
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.42 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.22), residues: 1424
  helix:  1.86 (0.16), residues: 976
  sheet: -0.78 (0.56), residues: 76
  loop :  0.25 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F 241 
 HIS   0.005   0.001   HIS E 106 
 PHE   0.020   0.001   PHE C 255 
 TYR   0.019   0.002   TYR A 336 
 ARG   0.006   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  718)
  hydrogen bonds       : angle       4.24683 ( 2148)
  metal coordination   : bond        0.00092 (    4)
  metal coordination   : angle       3.69551 (    6)
  covalent geometry    : bond        0.00367 (11844)
  covalent geometry    : angle       0.56183 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 1.275 
Fit side-chains
REVERT: A   89 LYS cc_start: 0.8665 (tptt) cc_final: 0.8464 (mtmt)
REVERT: A  118 MET cc_start: 0.3245 (mmt) cc_final: 0.2674 (mpp)
REVERT: A  121 MET cc_start: 0.1833 (mtt) cc_final: 0.1374 (ptt)
REVERT: A  126 MET cc_start: 0.5776 (ttt) cc_final: 0.5110 (tmm)
REVERT: A  128 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7047 (pt0)
REVERT: A  157 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8403 (t)
REVERT: A  281 ARG cc_start: 0.6790 (ptm160) cc_final: 0.6567 (ptp-170)
REVERT: B   78 ASP cc_start: 0.8024 (t0) cc_final: 0.7785 (m-30)
REVERT: B  118 MET cc_start: 0.3293 (mmt) cc_final: 0.2788 (mpp)
REVERT: B  121 MET cc_start: 0.1790 (mtt) cc_final: 0.1441 (ptt)
REVERT: B  126 MET cc_start: 0.5813 (ttt) cc_final: 0.5098 (tmm)
REVERT: B  128 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6917 (pt0)
REVERT: B  179 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6867 (ttt-90)
REVERT: C   36 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8347 (ttmt)
REVERT: C  238 ASN cc_start: 0.8045 (m-40) cc_final: 0.7411 (m110)
REVERT: C  277 ASP cc_start: 0.7654 (t0) cc_final: 0.7322 (t0)
REVERT: D 1024 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6255 (tp-100)
REVERT: D 1042 TYR cc_start: 0.7950 (t80) cc_final: 0.7503 (t80)
REVERT: F   36 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8376 (ttmt)
REVERT: F  238 ASN cc_start: 0.8067 (m-40) cc_final: 0.7409 (m110)
REVERT: F  271 MET cc_start: 0.6641 (mtt) cc_final: 0.6350 (mmp)
REVERT: F  277 ASP cc_start: 0.7670 (t70) cc_final: 0.7333 (t0)
REVERT: G 1026 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7802 (tp)
REVERT: G 1042 TYR cc_start: 0.7965 (t80) cc_final: 0.7657 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 188
  average time/residue: 0.2356
  time to fit residues: 64.0702
Evaluate side-chains
  175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLN
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue 1026 ILE
Chi-restraints excluded: chain G residue 1044 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0570
   chunk 55 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A 267 HIS
A 299 GLN
B 267 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.178965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.137816 restraints weight = 16657.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.14
r_work: 0.3348 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11848  Z= 0.153
  Angle     :  0.579  11.576  16026  Z= 0.295
  Chirality :  0.040   0.139   1766
  Planarity :  0.005   0.061   2072
  Dihedral  :  7.406  86.849   1630
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.13 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.22), residues: 1424
  helix:  1.83 (0.16), residues: 976
  sheet: -1.14 (0.53), residues: 76
  loop :  0.10 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 241 
 HIS   0.004   0.001   HIS C  43 
 PHE   0.019   0.001   PHE F 255 
 TYR   0.020   0.002   TYR B 336 
 ARG   0.005   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  718)
  hydrogen bonds       : angle       4.18425 ( 2148)
  metal coordination   : bond        0.00093 (    4)
  metal coordination   : angle       3.70709 (    6)
  covalent geometry    : bond        0.00358 (11844)
  covalent geometry    : angle       0.57460 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.290 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.8320 (t0) cc_final: 0.8048 (m-30)
REVERT: A   89 LYS cc_start: 0.8839 (tptt) cc_final: 0.8488 (mtmt)
REVERT: A  118 MET cc_start: 0.3239 (mmt) cc_final: 0.2596 (mpp)
REVERT: A  121 MET cc_start: 0.1957 (mtt) cc_final: 0.1471 (ptt)
REVERT: A  126 MET cc_start: 0.6110 (ttt) cc_final: 0.5061 (tmm)
REVERT: A  128 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7024 (pt0)
REVERT: A  157 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8496 (t)
REVERT: A  306 ASP cc_start: 0.7100 (t70) cc_final: 0.6637 (m-30)
REVERT: B   78 ASP cc_start: 0.8310 (t0) cc_final: 0.8060 (m-30)
REVERT: B  118 MET cc_start: 0.3314 (mmt) cc_final: 0.2732 (mpp)
REVERT: B  121 MET cc_start: 0.1946 (mtt) cc_final: 0.1513 (ptt)
REVERT: B  126 MET cc_start: 0.6156 (ttt) cc_final: 0.5064 (tmm)
REVERT: B  128 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6986 (pt0)
REVERT: B  157 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8455 (t)
REVERT: B  179 ARG cc_start: 0.7317 (mtm110) cc_final: 0.6954 (ttt-90)
REVERT: B  306 ASP cc_start: 0.7057 (t70) cc_final: 0.6585 (m-30)
REVERT: C   36 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8514 (ttmt)
REVERT: C  238 ASN cc_start: 0.8096 (m-40) cc_final: 0.7449 (m110)
REVERT: C  260 GLU cc_start: 0.7841 (tp30) cc_final: 0.7415 (tm-30)
REVERT: C  277 ASP cc_start: 0.7724 (t0) cc_final: 0.7415 (t0)
REVERT: D 1024 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6234 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8040 (t80) cc_final: 0.7489 (t80)
REVERT: F   36 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8510 (ttmt)
REVERT: F  238 ASN cc_start: 0.8154 (m-40) cc_final: 0.7453 (m110)
REVERT: F  251 LYS cc_start: 0.7349 (mptt) cc_final: 0.7087 (mmtp)
REVERT: F  271 MET cc_start: 0.6772 (mtt) cc_final: 0.6520 (mmp)
REVERT: F  277 ASP cc_start: 0.7784 (t70) cc_final: 0.7474 (t0)
REVERT: G 1026 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7835 (tp)
REVERT: G 1042 TYR cc_start: 0.8056 (t80) cc_final: 0.7632 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 182
  average time/residue: 0.2238
  time to fit residues: 59.1048
Evaluate side-chains
  177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue 1026 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 133 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 135 optimal weight:   50.0000
   chunk 62 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0980
   chunk 100 optimal weight:   10.0000
   chunk 139 optimal weight:   40.0000
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
G1024 GLN
G1027 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.176782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.134436 restraints weight = 16587.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 3.06
r_work: 0.3305 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11848  Z= 0.198
  Angle     :  0.587   6.491  16026  Z= 0.304
  Chirality :  0.042   0.161   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  7.290  89.756   1630
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.58 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.22), residues: 1424
  helix:  1.73 (0.16), residues: 976
  sheet: -1.50 (0.49), residues: 78
  loop :  0.04 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 241 
 HIS   0.005   0.001   HIS F 165 
 PHE   0.016   0.002   PHE F 255 
 TYR   0.023   0.002   TYR F 272 
 ARG   0.006   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04165 (  718)
  hydrogen bonds       : angle       4.23939 ( 2148)
  metal coordination   : bond        0.00199 (    4)
  metal coordination   : angle       4.12259 (    6)
  covalent geometry    : bond        0.00479 (11844)
  covalent geometry    : angle       0.58207 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8044 (t0) cc_final: 0.7774 (m-30)
REVERT: A   89 LYS cc_start: 0.8737 (tptt) cc_final: 0.8454 (mtmt)
REVERT: A  118 MET cc_start: 0.3290 (mmt) cc_final: 0.2627 (mpp)
REVERT: A  121 MET cc_start: 0.1958 (mtt) cc_final: 0.1460 (ptt)
REVERT: A  126 MET cc_start: 0.5915 (ttt) cc_final: 0.5371 (tmm)
REVERT: A  306 ASP cc_start: 0.6632 (t70) cc_final: 0.6419 (m-30)
REVERT: B   78 ASP cc_start: 0.8020 (t0) cc_final: 0.7755 (m-30)
REVERT: B  118 MET cc_start: 0.3501 (mmt) cc_final: 0.2887 (mpp)
REVERT: B  121 MET cc_start: 0.2098 (mtt) cc_final: 0.1652 (ptt)
REVERT: B  126 MET cc_start: 0.6004 (ttt) cc_final: 0.5459 (tmm)
REVERT: B  128 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6848 (pt0)
REVERT: B  179 ARG cc_start: 0.7305 (mtm110) cc_final: 0.7002 (ttt-90)
REVERT: B  306 ASP cc_start: 0.6738 (t70) cc_final: 0.6497 (m-30)
REVERT: C  238 ASN cc_start: 0.7871 (m-40) cc_final: 0.7390 (m110)
REVERT: C  244 LEU cc_start: 0.8764 (mp) cc_final: 0.8403 (mp)
REVERT: C  260 GLU cc_start: 0.7406 (tp30) cc_final: 0.7037 (tm-30)
REVERT: C  277 ASP cc_start: 0.7275 (t0) cc_final: 0.6979 (t0)
REVERT: D 1024 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6258 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8007 (t80) cc_final: 0.7547 (t80)
REVERT: F   36 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8441 (ttmt)
REVERT: F  238 ASN cc_start: 0.7923 (m-40) cc_final: 0.7417 (m110)
REVERT: F  244 LEU cc_start: 0.8848 (mp) cc_final: 0.8483 (mp)
REVERT: F  251 LYS cc_start: 0.7355 (mptt) cc_final: 0.7132 (mmtp)
REVERT: F  271 MET cc_start: 0.6856 (mtt) cc_final: 0.6638 (mmp)
REVERT: F  277 ASP cc_start: 0.7378 (t70) cc_final: 0.7116 (t0)
REVERT: G 1042 TYR cc_start: 0.8019 (t80) cc_final: 0.7573 (t80)
  outliers start: 34
  outliers final: 25
  residues processed: 191
  average time/residue: 0.2090
  time to fit residues: 59.6604
Evaluate side-chains
  179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue 1023 GLN
Chi-restraints excluded: chain H residue   95 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 128 optimal weight:    8.9990
   chunk 99 optimal weight:   50.0000
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
F 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.178327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.136318 restraints weight = 16631.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.87
r_work: 0.3359 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11848  Z= 0.149
  Angle     :  0.582  13.558  16026  Z= 0.295
  Chirality :  0.040   0.157   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  7.061  84.652   1630
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.97 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.22), residues: 1424
  helix:  1.81 (0.17), residues: 976
  sheet: -1.69 (0.46), residues: 88
  loop :  0.05 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 241 
 HIS   0.005   0.001   HIS B 308 
 PHE   0.029   0.001   PHE F 112 
 TYR   0.028   0.002   TYR F 272 
 ARG   0.005   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  718)
  hydrogen bonds       : angle       4.20351 ( 2148)
  metal coordination   : bond        0.00200 (    4)
  metal coordination   : angle       4.01531 (    6)
  covalent geometry    : bond        0.00350 (11844)
  covalent geometry    : angle       0.57696 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8182 (t0) cc_final: 0.7907 (m-30)
REVERT: A   89 LYS cc_start: 0.8743 (tptt) cc_final: 0.8444 (mtmt)
REVERT: A  118 MET cc_start: 0.2997 (mmt) cc_final: 0.2130 (mpp)
REVERT: A  121 MET cc_start: 0.1958 (mtt) cc_final: 0.1477 (ptt)
REVERT: A  126 MET cc_start: 0.6221 (ttt) cc_final: 0.5271 (tmm)
REVERT: A  157 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8474 (t)
REVERT: A  306 ASP cc_start: 0.7010 (t70) cc_final: 0.6734 (m-30)
REVERT: B   78 ASP cc_start: 0.8182 (t0) cc_final: 0.7928 (m-30)
REVERT: B  118 MET cc_start: 0.3285 (mmt) cc_final: 0.2577 (mpp)
REVERT: B  121 MET cc_start: 0.2090 (mtt) cc_final: 0.1642 (ptt)
REVERT: B  126 MET cc_start: 0.6266 (ttt) cc_final: 0.5359 (tmm)
REVERT: B  128 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6897 (pt0)
REVERT: B  306 ASP cc_start: 0.7041 (t70) cc_final: 0.6775 (m-30)
REVERT: C   36 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8547 (ttmt)
REVERT: C  238 ASN cc_start: 0.8028 (m-40) cc_final: 0.7353 (m110)
REVERT: C  260 GLU cc_start: 0.7713 (tp30) cc_final: 0.7258 (tm-30)
REVERT: C  277 ASP cc_start: 0.7705 (t0) cc_final: 0.7390 (t0)
REVERT: D 1024 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6392 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8047 (t80) cc_final: 0.7546 (t80)
REVERT: F   36 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8523 (ttmt)
REVERT: F   87 MET cc_start: 0.8989 (mmm) cc_final: 0.8625 (mmm)
REVERT: F  238 ASN cc_start: 0.8126 (m-40) cc_final: 0.7363 (m110)
REVERT: F  251 LYS cc_start: 0.7322 (mptt) cc_final: 0.7019 (mmtp)
REVERT: F  271 MET cc_start: 0.6834 (mtt) cc_final: 0.6544 (mmp)
REVERT: F  277 ASP cc_start: 0.7747 (t70) cc_final: 0.7414 (t0)
REVERT: G 1042 TYR cc_start: 0.8047 (t80) cc_final: 0.7600 (t80)
  outliers start: 37
  outliers final: 25
  residues processed: 193
  average time/residue: 0.2171
  time to fit residues: 62.9060
Evaluate side-chains
  185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 2.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue 1023 GLN
Chi-restraints excluded: chain H residue  130 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 119 optimal weight:    0.5980
   chunk 98 optimal weight:   50.0000
   chunk 126 optimal weight:    3.9990
   chunk 133 optimal weight:    6.9990
   chunk 123 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
F 261 GLN
G1024 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.178454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131640 restraints weight = 16785.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.37
r_work: 0.3368 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11848  Z= 0.149
  Angle     :  0.567   7.499  16026  Z= 0.291
  Chirality :  0.040   0.155   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  6.856  79.996   1630
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 11.52 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1424
  helix:  1.79 (0.17), residues: 980
  sheet: -1.74 (0.45), residues: 88
  loop :  0.02 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 241 
 HIS   0.005   0.001   HIS A 308 
 PHE   0.022   0.001   PHE C 112 
 TYR   0.025   0.002   TYR F 272 
 ARG   0.004   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  718)
  hydrogen bonds       : angle       4.16421 ( 2148)
  metal coordination   : bond        0.00166 (    4)
  metal coordination   : angle       3.94895 (    6)
  covalent geometry    : bond        0.00350 (11844)
  covalent geometry    : angle       0.56148 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 172
  time to evaluate  : 2.040 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8175 (t0) cc_final: 0.7925 (m-30)
REVERT: A   89 LYS cc_start: 0.8834 (tptt) cc_final: 0.8462 (mtmt)
REVERT: A  118 MET cc_start: 0.2694 (mmt) cc_final: 0.1784 (mpp)
REVERT: A  121 MET cc_start: 0.2149 (mtt) cc_final: 0.1570 (ptt)
REVERT: A  126 MET cc_start: 0.6044 (ttt) cc_final: 0.5174 (tmm)
REVERT: A  157 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8454 (t)
REVERT: A  306 ASP cc_start: 0.7066 (t70) cc_final: 0.6809 (m-30)
REVERT: B   78 ASP cc_start: 0.8161 (t0) cc_final: 0.7916 (m-30)
REVERT: B  118 MET cc_start: 0.3013 (mmt) cc_final: 0.2220 (mpp)
REVERT: B  121 MET cc_start: 0.2111 (mtt) cc_final: 0.1538 (ptt)
REVERT: B  126 MET cc_start: 0.6032 (ttt) cc_final: 0.5190 (tmm)
REVERT: B  128 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6876 (pt0)
REVERT: B  306 ASP cc_start: 0.7005 (t70) cc_final: 0.6745 (m-30)
REVERT: C   36 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8592 (ttmt)
REVERT: C  238 ASN cc_start: 0.8080 (m-40) cc_final: 0.7373 (m110)
REVERT: C  277 ASP cc_start: 0.7808 (t0) cc_final: 0.7510 (t0)
REVERT: D 1024 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6405 (tp-100)
REVERT: D 1042 TYR cc_start: 0.7973 (t80) cc_final: 0.7416 (t80)
REVERT: F   36 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8555 (ttmt)
REVERT: F  238 ASN cc_start: 0.8234 (m-40) cc_final: 0.7448 (m110)
REVERT: F  251 LYS cc_start: 0.7282 (mptt) cc_final: 0.6963 (mmtp)
REVERT: F  271 MET cc_start: 0.6912 (mtt) cc_final: 0.6620 (mmp)
REVERT: F  277 ASP cc_start: 0.7863 (t70) cc_final: 0.7582 (t0)
REVERT: G 1042 TYR cc_start: 0.8039 (t80) cc_final: 0.7537 (t80)
  outliers start: 32
  outliers final: 28
  residues processed: 193
  average time/residue: 0.2123
  time to fit residues: 62.4293
Evaluate side-chains
  185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain G residue 1023 GLN
Chi-restraints excluded: chain H residue  130 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0870
   overall best weight:    0.7562

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

Flipped N/Q/H residues before XYZ refinement:
F 261 GLN
G1024 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.178501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.134909 restraints weight = 16740.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.34
r_work: 0.3330 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11848  Z= 0.157
  Angle     :  0.599  13.518  16026  Z= 0.302
  Chirality :  0.040   0.161   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  6.760  78.118   1630
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.54 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.22), residues: 1424
  helix:  1.80 (0.17), residues: 980
  sheet: -1.80 (0.44), residues: 88
  loop : -0.01 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 241 
 HIS   0.005   0.001   HIS B 308 
 PHE   0.027   0.001   PHE C 255 
 TYR   0.017   0.002   TYR F 272 
 ARG   0.006   0.000   ARG F 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03877 (  718)
  hydrogen bonds       : angle       4.17803 ( 2148)
  metal coordination   : bond        0.00161 (    4)
  metal coordination   : angle       3.94148 (    6)
  covalent geometry    : bond        0.00374 (11844)
  covalent geometry    : angle       0.59458 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 ASP cc_start: 0.8176 (t0) cc_final: 0.7913 (m-30)
REVERT: A   89 LYS cc_start: 0.8806 (tptt) cc_final: 0.8425 (mtmt)
REVERT: A  118 MET cc_start: 0.2895 (mmt) cc_final: 0.1935 (mpp)
REVERT: A  121 MET cc_start: 0.2141 (mtt) cc_final: 0.1585 (ptt)
REVERT: A  126 MET cc_start: 0.6203 (ttt) cc_final: 0.5283 (tmm)
REVERT: A  157 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8493 (t)
REVERT: A  306 ASP cc_start: 0.7204 (t70) cc_final: 0.6900 (m-30)
REVERT: B   78 ASP cc_start: 0.8189 (t0) cc_final: 0.7942 (m-30)
REVERT: B  118 MET cc_start: 0.3091 (mmt) cc_final: 0.2294 (mpp)
REVERT: B  121 MET cc_start: 0.2113 (mtt) cc_final: 0.1550 (ptt)
REVERT: B  126 MET cc_start: 0.6162 (ttt) cc_final: 0.5318 (tmm)
REVERT: B  128 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6878 (pt0)
REVERT: B  306 ASP cc_start: 0.7265 (t70) cc_final: 0.6912 (m-30)
REVERT: C   36 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8620 (ttmt)
REVERT: C  238 ASN cc_start: 0.8102 (m-40) cc_final: 0.7422 (m110)
REVERT: C  277 ASP cc_start: 0.7716 (t0) cc_final: 0.7416 (t70)
REVERT: D 1024 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6370 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8048 (t80) cc_final: 0.7482 (t80)
REVERT: F   36 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8551 (ttmt)
REVERT: F  173 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7203 (tm-30)
REVERT: F  230 PRO cc_start: 0.7575 (Cg_exo) cc_final: 0.7085 (Cg_endo)
REVERT: F  238 ASN cc_start: 0.8175 (m-40) cc_final: 0.7417 (m110)
REVERT: F  251 LYS cc_start: 0.7323 (mptt) cc_final: 0.6982 (mmtp)
REVERT: F  271 MET cc_start: 0.6743 (mtt) cc_final: 0.6394 (mmp)
REVERT: G 1042 TYR cc_start: 0.8081 (t80) cc_final: 0.7682 (t80)
  outliers start: 35
  outliers final: 31
  residues processed: 184
  average time/residue: 0.2245
  time to fit residues: 62.1378
Evaluate side-chains
  185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain F residue  261 GLN
Chi-restraints excluded: chain G residue 1023 GLN
Chi-restraints excluded: chain H residue  130 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 135 optimal weight:   50.0000
   chunk 74 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 114 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 261 GLN
F 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.178817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133019 restraints weight = 16695.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.59
r_work: 0.3339 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11848  Z= 0.152
  Angle     :  0.614  17.068  16026  Z= 0.305
  Chirality :  0.040   0.157   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  6.708  76.825   1630
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.15 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.22), residues: 1424
  helix:  1.80 (0.17), residues: 980
  sheet: -1.85 (0.44), residues: 88
  loop : -0.02 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 241 
 HIS   0.004   0.001   HIS F  43 
 PHE   0.027   0.001   PHE C 255 
 TYR   0.016   0.002   TYR A 250 
 ARG   0.004   0.000   ARG C 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03873 (  718)
  hydrogen bonds       : angle       4.17096 ( 2148)
  metal coordination   : bond        0.00151 (    4)
  metal coordination   : angle       3.88984 (    6)
  covalent geometry    : bond        0.00363 (11844)
  covalent geometry    : angle       0.60926 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 1.681 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.8146 (t0) cc_final: 0.7874 (m-30)
REVERT: A   89 LYS cc_start: 0.8784 (tptt) cc_final: 0.8405 (mtmt)
REVERT: A  118 MET cc_start: 0.2830 (mmt) cc_final: 0.1881 (mpp)
REVERT: A  121 MET cc_start: 0.2211 (mtt) cc_final: 0.1638 (ptt)
REVERT: A  126 MET cc_start: 0.6246 (ttt) cc_final: 0.5323 (tmm)
REVERT: A  157 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8481 (t)
REVERT: A  306 ASP cc_start: 0.7167 (t70) cc_final: 0.6951 (m-30)
REVERT: B   78 ASP cc_start: 0.8123 (t0) cc_final: 0.7860 (m-30)
REVERT: B  118 MET cc_start: 0.2951 (mmt) cc_final: 0.2041 (mpp)
REVERT: B  121 MET cc_start: 0.2149 (mtt) cc_final: 0.1651 (ptt)
REVERT: B  126 MET cc_start: 0.6234 (ttt) cc_final: 0.5382 (tmm)
REVERT: B  128 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6839 (pt0)
REVERT: B  306 ASP cc_start: 0.7282 (t70) cc_final: 0.6929 (m-30)
REVERT: C   36 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8582 (ttmt)
REVERT: C  230 PRO cc_start: 0.7549 (Cg_exo) cc_final: 0.7142 (Cg_endo)
REVERT: C  238 ASN cc_start: 0.8113 (m-40) cc_final: 0.7395 (m110)
REVERT: C  277 ASP cc_start: 0.7634 (t0) cc_final: 0.7368 (t0)
REVERT: D 1024 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6385 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8039 (t80) cc_final: 0.7508 (t80)
REVERT: F   36 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8543 (ttmt)
REVERT: F  230 PRO cc_start: 0.7537 (Cg_exo) cc_final: 0.7096 (Cg_endo)
REVERT: F  238 ASN cc_start: 0.8185 (m-40) cc_final: 0.7376 (m110)
REVERT: F  251 LYS cc_start: 0.7327 (mptt) cc_final: 0.6993 (mmtp)
REVERT: G 1042 TYR cc_start: 0.8086 (t80) cc_final: 0.7574 (t80)
  outliers start: 37
  outliers final: 32
  residues processed: 178
  average time/residue: 0.2665
  time to fit residues: 72.5006
Evaluate side-chains
  180 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 1.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  237 LEU
Chi-restraints excluded: chain F residue  261 GLN
Chi-restraints excluded: chain H residue  130 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 135 optimal weight:   50.0000
   chunk 96 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 261 GLN
F 261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.177763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.131781 restraints weight = 16530.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.95
r_work: 0.3311 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11848  Z= 0.189
  Angle     :  0.636  18.992  16026  Z= 0.317
  Chirality :  0.041   0.179   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  6.743  78.375   1630
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.15 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.22), residues: 1424
  helix:  1.74 (0.17), residues: 978
  sheet: -1.90 (0.44), residues: 88
  loop : -0.06 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 241 
 HIS   0.005   0.001   HIS A 308 
 PHE   0.026   0.002   PHE C 255 
 TYR   0.018   0.002   TYR F 272 
 ARG   0.004   0.000   ARG C 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  718)
  hydrogen bonds       : angle       4.20544 ( 2148)
  metal coordination   : bond        0.00176 (    4)
  metal coordination   : angle       4.01770 (    6)
  covalent geometry    : bond        0.00459 (11844)
  covalent geometry    : angle       0.63171 (16020)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 1.094 
Fit side-chains
REVERT: A   78 ASP cc_start: 0.7899 (t0) cc_final: 0.7609 (m-30)
REVERT: A   89 LYS cc_start: 0.8655 (tptt) cc_final: 0.8408 (mtmt)
REVERT: A  118 MET cc_start: 0.2701 (mmt) cc_final: 0.1882 (mpp)
REVERT: A  121 MET cc_start: 0.2147 (mtt) cc_final: 0.1682 (ptt)
REVERT: A  126 MET cc_start: 0.6177 (ttt) cc_final: 0.5444 (tmm)
REVERT: B   78 ASP cc_start: 0.7892 (t0) cc_final: 0.7609 (m-30)
REVERT: B  118 MET cc_start: 0.2863 (mmt) cc_final: 0.2038 (mpp)
REVERT: B  121 MET cc_start: 0.2104 (mtt) cc_final: 0.1670 (ptt)
REVERT: B  126 MET cc_start: 0.6230 (ttt) cc_final: 0.5520 (tmm)
REVERT: B  128 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6767 (pt0)
REVERT: B  179 ARG cc_start: 0.7270 (mtm110) cc_final: 0.6841 (ttt-90)
REVERT: B  306 ASP cc_start: 0.7073 (t70) cc_final: 0.6821 (m-30)
REVERT: C  230 PRO cc_start: 0.7520 (Cg_exo) cc_final: 0.7107 (Cg_endo)
REVERT: C  238 ASN cc_start: 0.8006 (m-40) cc_final: 0.7339 (m110)
REVERT: C  277 ASP cc_start: 0.7216 (t0) cc_final: 0.7013 (t0)
REVERT: D 1024 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6395 (tp-100)
REVERT: D 1042 TYR cc_start: 0.8035 (t80) cc_final: 0.7509 (t80)
REVERT: F   36 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8517 (ttmt)
REVERT: F  230 PRO cc_start: 0.7529 (Cg_exo) cc_final: 0.7126 (Cg_endo)
REVERT: F  238 ASN cc_start: 0.8147 (m-40) cc_final: 0.7383 (m110)
REVERT: F  251 LYS cc_start: 0.7393 (mptt) cc_final: 0.7077 (mmtp)
  outliers start: 32
  outliers final: 31
  residues processed: 170
  average time/residue: 0.2886
  time to fit residues: 75.0753
Evaluate side-chains
  182 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 1.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  331 GLN
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  331 GLN
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue 1024 GLN
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain F residue   60 THR
Chi-restraints excluded: chain F residue   81 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  194 MET
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain H residue  130 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 133 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 135 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.177759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.133791 restraints weight = 16603.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.86
r_work: 0.3344 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093  11848  Z= 0.197
  Angle     :  0.866  59.199  16026  Z= 0.481
  Chirality :  0.041   0.390   1766
  Planarity :  0.005   0.062   2072
  Dihedral  :  6.746  78.347   1630
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.23 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.22), residues: 1424
  helix:  1.75 (0.17), residues: 978
  sheet: -1.91 (0.44), residues: 88
  loop : -0.06 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 241 
 HIS   0.004   0.001   HIS A 308 
 PHE   0.021   0.001   PHE C 255 
 TYR   0.017   0.002   TYR A 250 
 ARG   0.004   0.000   ARG C 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  718)
  hydrogen bonds       : angle       4.20366 ( 2148)
  metal coordination   : bond        0.00180 (    4)
  metal coordination   : angle       4.00982 (    6)
  covalent geometry    : bond        0.00455 (11844)
  covalent geometry    : angle       0.86305 (16020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7178.29 seconds
wall clock time: 128 minutes 19.87 seconds (7699.87 seconds total)