Starting phenix.real_space_refine
on Fri Dec  8 09:54:16 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy8_32887/12_2023/7wy8_32887_neut.pdb"
  }
  resolution = 2.83
  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=   0.001 sd=   0.020
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5121      2.51       5
     N    1393      2.21       5
     O    1479      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  311": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  330": "OE1" <-> "OE2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8049
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2123
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 3, 'TRANS': 258}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1926
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331}
  Time building chain proxies: 4.51, per 1000 atoms: 0.56
  Number of scatterers: 8049
  At special positions: 0
  Unit cell: (80.3, 97.9, 133.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1479      8.00
     N    1393      7.00
     C    5121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R1008 " - pdb=" SG  CYS R1080 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 2.89
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1906

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      40.6% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'R' and resid 925 through 929
      removed outlier: 3.805A  pdb=" N   LEU R 928 " --> pdb=" O   PHE R 925 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 940 through 956
      removed outlier: 3.933A  pdb=" N   LEU R 944 " --> pdb=" O   VAL R 940 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 958 through 969
      removed outlier: 3.643A  pdb=" N   ILE R 962 " --> pdb=" O   VAL R 958 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 970 through 974
      removed outlier: 3.770A  pdb=" N   LEU R 973 " --> pdb=" O   PHE R 970 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN R 974 " --> pdb=" O   ARG R 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 970 through 974'
    Processing helix  chain 'R' and resid 975 through 999
      removed outlier: 3.578A  pdb=" N   ILE R 999 " --> pdb=" O   PHE R 995 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1008 through 1038
      removed outlier: 4.042A  pdb=" N   HIS R1016 " --> pdb=" O   ALA R1012 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET R1036 " --> pdb=" O   GLN R1032 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1047 through 1056
    Processing helix  chain 'R' and resid 1056 through 1070
      removed outlier: 3.574A  pdb=" N   ALA R1060 " --> pdb=" O   TYR R1056 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1086 through 1088
      No H-bonds generated for 'chain 'R' and resid 1086 through 1088'
    Processing helix  chain 'R' and resid 1089 through 1113
      Proline residue:  R1095  - end of helix
      removed outlier: 3.736A  pdb=" N   LEU R1098 " --> pdb=" O   GLY R1094 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1144 through 1152
    Processing helix  chain 'R' and resid 1155 through 1164
      removed outlier: 3.745A  pdb=" N   TRP R1158 " --> pdb=" O   GLY R1155 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA R1159 " --> pdb=" O   LEU R1156 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR R1164 " --> pdb=" O   GLY R1161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1169 through 1181
      removed outlier: 3.791A  pdb=" N   ALA R1173 " --> pdb=" O   THR R1169 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER R1181 " --> pdb=" O   THR R1177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1182 through 1193
      removed outlier: 3.625A  pdb=" N   PHE R1188 " --> pdb=" O   GLY R1184 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1195 through 1207
    Processing helix  chain 'C' and resid 9 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.779A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.508A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.824A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.735A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
      No H-bonds generated for 'chain 'A' and resid 252 through 264'
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.562A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.862A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.625A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.585A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.603A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 65
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.579A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.867A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.266A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.053A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.082A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.964A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.969A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.945A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.759A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.973A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1041 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: 2.30

  Time building geometry restraints manager: 3.16 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: 2622
        1.34 -     1.46: 1991
        1.46 -     1.58: 3526
        1.58 -     1.70: 0
        1.70 -     1.83: 80
  Bond restraints: 8219
  Sorted by residual:
  bond pdb=" C   LEU C  50 "
       pdb=" N   LEU C  51 "
    ideal  model  delta    sigma   weight residual
    1.332  1.277  0.055 1.35e-02 5.49e+03 1.68e+01
  bond pdb=" N   LYS R1113 "
       pdb=" CA  LYS R1113 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.22e-02 6.72e+03 5.24e+00
  bond pdb=" N   MET R1114 "
       pdb=" CA  MET R1114 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.025 1.28e-02 6.10e+03 3.95e+00
  bond pdb=" CA  PHE B 292 "
       pdb=" CB  PHE B 292 "
    ideal  model  delta    sigma   weight residual
    1.530  1.492  0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" CB  TRP D  36 "
       pdb=" CG  TRP D  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.450  0.048 3.10e-02 1.04e+03 2.43e+00
  ... (remaining 8214 not shown)

  Histogram of bond angle deviations from ideal:
       99.65 -   106.52: 165
      106.52 -   113.39: 4411
      113.39 -   120.27: 3187
      120.27 -   127.14: 3279
      127.14 -   134.01: 81
  Bond angle restraints: 11123
  Sorted by residual:
  angle pdb=" N   VAL R 958 "
        pdb=" CA  VAL R 958 "
        pdb=" C   VAL R 958 "
      ideal   model   delta    sigma   weight residual
     112.12  107.19    4.93 8.40e-01 1.42e+00 3.45e+01
  angle pdb=" N   CYS B 204 "
        pdb=" CA  CYS B 204 "
        pdb=" C   CYS B 204 "
      ideal   model   delta    sigma   weight residual
     108.58  100.71    7.87 1.82e+00 3.02e-01 1.87e+01
  angle pdb=" N   MET R1114 "
        pdb=" CA  MET R1114 "
        pdb=" C   MET R1114 "
      ideal   model   delta    sigma   weight residual
     113.88  108.74    5.14 1.23e+00 6.61e-01 1.75e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     114.31  119.54   -5.23 1.29e+00 6.01e-01 1.64e+01
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     121.70  128.88   -7.18 1.80e+00 3.09e-01 1.59e+01
  ... (remaining 11118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 4472
       15.05 -    30.11: 296
       30.11 -    45.16: 57
       45.16 -    60.22: 30
       60.22 -    75.27: 10
  Dihedral angle restraints: 4865
    sinusoidal: 1915
      harmonic: 2950
  Sorted by residual:
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.64   42.36     1      1.00e+01 1.00e-02 2.51e+01
  dihedral pdb=" CA  PHE D 108 "
           pdb=" C   PHE D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.13   19.87     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  THR B  65 "
           pdb=" C   THR B  65 "
           pdb=" N   ASP B  66 "
           pdb=" CA  ASP B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.15   19.85     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 4862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1033
       0.064 -    0.129: 195
       0.129 -    0.193: 15
       0.193 -    0.257: 2
       0.257 -    0.322: 1
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CA  GLN B  75 "
            pdb=" N   GLN B  75 "
            pdb=" C   GLN B  75 "
            pdb=" CB  GLN B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  ASP B 163 "
            pdb=" N   ASP B 163 "
            pdb=" C   ASP B 163 "
            pdb=" CB  ASP B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  ASN R1166 "
            pdb=" N   ASN R1166 "
            pdb=" C   ASN R1166 "
            pdb=" CB  ASN R1166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 1414
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  40 "    0.050 5.00e-02 4.00e+02   7.69e-02 9.46e+00
        pdb=" N   PRO D  41 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO D  41 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO D  41 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN R1004 "   -0.037 5.00e-02 4.00e+02   5.72e-02 5.24e+00
        pdb=" N   PRO R1005 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO R1005 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R1005 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO B 236 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1411 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1193
        2.76 -     3.29: 7080
        3.29 -     3.83: 12083
        3.83 -     4.36: 14045
        4.36 -     4.90: 25419
  Nonbonded interactions: 59820
  Sorted by model distance:
  nonbonded pdb=" O   ASN R1166 "
            pdb=" OG1 THR R1169 "
     model   vdw
     2.220 2.440
  nonbonded pdb=" OG1 THR R 966 "
            pdb=" OH  TYR R1202 "
     model   vdw
     2.237 2.440
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.307 2.440
  nonbonded pdb=" O   PRO D 100 "
            pdb=" OG  SER B 227 "
     model   vdw
     2.330 2.440
  nonbonded pdb=" O   VAL D 110 "
            pdb=" NH1 ARG D 118 "
     model   vdw
     2.331 2.520
  ... (remaining 59815 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.930
  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:             0.000
  Extract box with map and model:          3.860
  Check model and map are aligned:         0.140
  Set scattering table:                    0.100
  Process input model:                     24.560
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
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      :  0.007   0.055   8219  Z= 0.439
  Angle     :  0.814   8.893  11123  Z= 0.489
  Chirality :  0.050   0.322   1246
  Planarity :  0.006   0.077   1414
  Dihedral  : 12.025  75.273   2953
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.25), residues: 1001
  helix:  0.49 (0.28), residues: 361
  sheet:  1.01 (0.36), residues: 209
  loop : -1.58 (0.25), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.003   TRP B  82 
   HIS   0.009   0.002   HIS A 357 
   PHE   0.034   0.003   PHE A 376 
   TYR   0.019   0.002   TYR R1034 
   ARG   0.006   0.001   ARG D  98 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.907 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 1.2205
  time to fit residues: 243.8530
Evaluate side-chains
  168 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1718
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0040
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
R1183 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B  75 GLN
B 155 ASN
B 239 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8219  Z= 0.180
  Angle     :  0.558   8.703  11123  Z= 0.308
  Chirality :  0.042   0.159   1246
  Planarity :  0.005   0.070   1414
  Dihedral  :  4.707  21.906   1106
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.09 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1001
  helix:  1.68 (0.29), residues: 352
  sheet:  1.10 (0.36), residues: 207
  loop : -1.45 (0.25), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.015   0.002   PHE B 241 
   TYR   0.013   0.001   TYR D  95 
   ARG   0.006   0.000   ARG A 283 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.887 
Fit side-chains
  outliers start: 18
  outliers final: 11
  residues processed: 176
  average time/residue: 1.3359
  time to fit residues: 247.7136
Evaluate side-chains
  176 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 165
  time to evaluate  : 0.881 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 6
  residues processed: 6
  average time/residue: 0.5565
  time to fit residues: 4.9442
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0770
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8219  Z= 0.234
  Angle     :  0.571   7.835  11123  Z= 0.311
  Chirality :  0.042   0.155   1246
  Planarity :  0.004   0.055   1414
  Dihedral  :  4.586  22.471   1106
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 10.36 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 1001
  helix:  1.94 (0.29), residues: 352
  sheet:  1.29 (0.36), residues: 200
  loop : -1.44 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.020   0.002   PHE A 376 
   TYR   0.015   0.002   TYR D  95 
   ARG   0.008   0.000   ARG A 283 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 26
  outliers final: 20
  residues processed: 172
  average time/residue: 1.2663
  time to fit residues: 229.9470
Evaluate side-chains
  179 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.872 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 8
  residues processed: 12
  average time/residue: 0.5496
  time to fit residues: 8.5532
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   8219  Z= 0.381
  Angle     :  0.664   8.626  11123  Z= 0.359
  Chirality :  0.045   0.176   1246
  Planarity :  0.005   0.056   1414
  Dihedral  :  4.901  25.031   1106
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 11.28 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1001
  helix:  1.84 (0.29), residues: 351
  sheet:  1.07 (0.36), residues: 204
  loop : -1.45 (0.25), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.008   0.001   HIS C  44 
   PHE   0.025   0.003   PHE B 151 
   TYR   0.019   0.002   TYR D  95 
   ARG   0.005   0.000   ARG A 232 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 1.111 
Fit side-chains
  outliers start: 33
  outliers final: 28
  residues processed: 191
  average time/residue: 1.4280
  time to fit residues: 287.6152
Evaluate side-chains
  201 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.909 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 10
  residues processed: 18
  average time/residue: 0.4754
  time to fit residues: 10.9913
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0170
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 81 optimal weight:    0.5980
   chunk 66 optimal weight:   10.0000
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8219  Z= 0.202
  Angle     :  0.538   7.257  11123  Z= 0.294
  Chirality :  0.041   0.146   1246
  Planarity :  0.004   0.052   1414
  Dihedral  :  4.481  21.368   1106
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.00 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1001
  helix:  2.10 (0.29), residues: 353
  sheet:  1.28 (0.37), residues: 199
  loop : -1.44 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.003   0.001   HIS C  44 
   PHE   0.016   0.002   PHE B 151 
   TYR   0.015   0.001   TYR D  95 
   ARG   0.002   0.000   ARG A 373 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.827 
Fit side-chains
  outliers start: 26
  outliers final: 20
  residues processed: 177
  average time/residue: 1.3044
  time to fit residues: 243.6510
Evaluate side-chains
  187 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.889 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 10
  residues processed: 11
  average time/residue: 0.4419
  time to fit residues: 6.8296
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8219  Z= 0.279
  Angle     :  0.584   7.557  11123  Z= 0.318
  Chirality :  0.042   0.155   1246
  Planarity :  0.004   0.051   1414
  Dihedral  :  4.593  22.954   1106
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 13.00 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1001
  helix:  2.09 (0.28), residues: 353
  sheet:  1.30 (0.37), residues: 199
  loop : -1.43 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.005   0.001   HIS C  44 
   PHE   0.019   0.002   PHE B 151 
   TYR   0.016   0.002   TYR D  95 
   ARG   0.003   0.000   ARG A 232 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 177
  time to evaluate  : 1.776 
Fit side-chains
  outliers start: 36
  outliers final: 27
  residues processed: 193
  average time/residue: 1.2463
  time to fit residues: 254.4414
Evaluate side-chains
  202 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.889 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 12
  residues processed: 15
  average time/residue: 0.5474
  time to fit residues: 10.4012
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0060
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0060
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.4412

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8219  Z= 0.174
  Angle     :  0.518   6.874  11123  Z= 0.283
  Chirality :  0.041   0.146   1246
  Planarity :  0.004   0.050   1414
  Dihedral  :  4.300  20.208   1106
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.15 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1001
  helix:  2.34 (0.28), residues: 352
  sheet:  1.39 (0.37), residues: 197
  loop : -1.37 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.015   0.001   PHE B 241 
   TYR   0.020   0.001   TYR B 289 
   ARG   0.002   0.000   ARG A 373 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.901 
Fit side-chains
  outliers start: 28
  outliers final: 19
  residues processed: 184
  average time/residue: 1.2214
  time to fit residues: 237.9337
Evaluate side-chains
  183 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.950 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 12
  residues processed: 7
  average time/residue: 0.5199
  time to fit residues: 5.3395
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0670
   chunk 91 optimal weight:    0.5980
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
R1032 GLN
A  35 GLN
A  50 ASN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8219  Z= 0.157
  Angle     :  0.507   7.625  11123  Z= 0.276
  Chirality :  0.040   0.160   1246
  Planarity :  0.004   0.050   1414
  Dihedral  :  4.144  18.951   1106
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.84 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  1.01 (0.27), residues: 1001
  helix:  2.50 (0.28), residues: 351
  sheet:  1.36 (0.37), residues: 199
  loop : -1.23 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.014   0.001   PHE B 241 
   TYR   0.013   0.001   TYR B 289 
   ARG   0.003   0.000   ARG A 232 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.892 
Fit side-chains
  outliers start: 24
  outliers final: 20
  residues processed: 181
  average time/residue: 1.2218
  time to fit residues: 234.1078
Evaluate side-chains
  186 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.902 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 13
  residues processed: 7
  average time/residue: 0.3978
  time to fit residues: 4.4884
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   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  35 GLN
A 213 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8219  Z= 0.259
  Angle     :  0.580  10.199  11123  Z= 0.314
  Chirality :  0.042   0.163   1246
  Planarity :  0.004   0.051   1414
  Dihedral  :  4.398  21.258   1106
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.30 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1001
  helix:  2.41 (0.28), residues: 349
  sheet:  1.32 (0.37), residues: 199
  loop : -1.28 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A  41 
   PHE   0.017   0.002   PHE B 151 
   TYR   0.018   0.002   TYR B 289 
   ARG   0.004   0.000   ARG B 219 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.834 
Fit side-chains
  outliers start: 26
  outliers final: 23
  residues processed: 186
  average time/residue: 1.2786
  time to fit residues: 252.0259
Evaluate side-chains
  194 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.893 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 12
  residues processed: 11
  average time/residue: 0.3709
  time to fit residues: 6.0870
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 60 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 83 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8219  Z= 0.210
  Angle     :  0.550  10.418  11123  Z= 0.297
  Chirality :  0.041   0.160   1246
  Planarity :  0.004   0.051   1414
  Dihedral  :  4.289  20.204   1106
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.00 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.27), residues: 1001
  helix:  2.49 (0.28), residues: 349
  sheet:  1.41 (0.37), residues: 197
  loop : -1.27 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.016   0.002   PHE D  68 
   TYR   0.015   0.001   TYR B 289 
   ARG   0.003   0.000   ARG A 373 

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

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

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2002 Ramachandran restraints generated.
    1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.813 
Fit side-chains
  outliers start: 20
  outliers final: 17
  residues processed: 182
  average time/residue: 1.2576
  time to fit residues: 242.0363
Evaluate side-chains
  183 residues out of total 869 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.913 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 13
  residues processed: 4
  average time/residue: 0.1294
  time to fit residues: 2.0510
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 69 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
A 292 ASN
D  31 ASN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.152600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.130536 restraints weight = 11031.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.97
r_work: 0.3594 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8219  Z= 0.175
  Angle     :  0.524  10.109  11123  Z= 0.283
  Chirality :  0.041   0.166   1246
  Planarity :  0.004   0.051   1414
  Dihedral  :  4.140  18.823   1106
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.11 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  1.11 (0.27), residues: 1001
  helix:  2.61 (0.28), residues: 350
  sheet:  1.45 (0.37), residues: 197
  loop : -1.20 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.016   0.002   PHE D  68 
   TYR   0.013   0.001   TYR B 289 
   ARG   0.003   0.000   ARG A 373 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4138.04 seconds
wall clock time: 73 minutes 43.83 seconds (4423.83 seconds total)