Starting phenix.real_space_refine
on Fri Dec  8 15:36:43 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x10_32932/12_2023/7x10_32932_neut.pdb"
  }
  resolution = 2.93
  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      61      5.16       5
     C    5546      2.51       5
     N    1486      2.21       5
     O    1581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "E TYR   95": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8674
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1744
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 4, 'TRANS': 206}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "E"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    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
  Time building chain proxies: 4.76, per 1000 atoms: 0.55
  Number of scatterers: 8674
  At special positions: 0
  Unit cell: (90.2, 124.3, 132, 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      61     16.00
     O    1581      8.00
     N    1486      7.00
     C    5546      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 161 " - pdb=" SG  CYS E 231 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R1008 " - pdb=" SG  CYS R1080 " distance=2.03

  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: 3.03
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2056

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      35.6% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 39
      removed outlier: 3.948A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A  31 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ALA A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 66
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 4.000A  pdb=" N   TRP A 234 " --> pdb=" O   GLN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.537A  pdb=" N   ASN A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.778A  pdb=" N   PHE A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.752A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 322
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 350 through 371
      removed outlier: 3.742A  pdb=" N   ASN A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS A 363 " --> pdb=" O   PHE A 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.782A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.876A  pdb=" N   SER E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.601A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.072A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 925 through 930
      removed outlier: 3.866A  pdb=" N   ALA R 930 " --> pdb=" O   VAL R 927 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 940 through 956
      removed outlier: 3.990A  pdb=" N   LEU R 944 " --> pdb=" O   VAL R 940 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 958 through 967
    Processing helix  chain 'R' and resid 970 through 974
      removed outlier: 3.930A  pdb=" N   LEU R 973 " --> pdb=" O   PHE R 970 " (cutoff:3.500A)
      removed outlier: 3.946A  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 998
    Processing helix  chain 'R' and resid 1010 through 1038
      removed outlier: 4.732A  pdb=" N   HIS R1016 " --> pdb=" O   ALA R1012 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY R1030 " --> pdb=" O   MET R1026 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1047 through 1070
      Proline residue:  R1059  - end of helix
    Processing helix  chain 'R' and resid 1086 through 1091
      removed outlier: 4.403A  pdb=" N   ILE R1089 " --> pdb=" O   THR R1086 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1092 through 1117
      removed outlier: 3.735A  pdb=" N   HIS R1117 " --> pdb=" O   LYS R1113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1144 through 1154
      removed outlier: 4.002A  pdb=" N   LEU R1151 " --> pdb=" O   ALA R1147 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS R1152 " --> pdb=" O   ILE R1148 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU R1153 " --> pdb=" O   ALA R1149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1159 through 1164
      removed outlier: 3.738A  pdb=" N   LEU R1162 " --> pdb=" O   ALA R1159 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR R1164 " --> pdb=" O   GLY R1161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1166 through 1168
      No H-bonds generated for 'chain 'R' and resid 1166 through 1168'
    Processing helix  chain 'R' and resid 1169 through 1181
      removed outlier: 3.874A  pdb=" N   ALA R1173 " --> pdb=" O   THR R1169 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR R1177 " --> pdb=" O   ALA R1173 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER R1181 " --> pdb=" O   THR R1177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1182 through 1191
      removed outlier: 3.536A  pdb=" N   PHE R1188 " --> pdb=" O   GLY R1184 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1195 through 1204
      removed outlier: 3.758A  pdb=" N   LYS R1204 " --> pdb=" O   LYS R1200 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 3.807A  pdb=" N   SER A 243 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE A 343 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.871A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.943A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.881A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149
      removed outlier: 7.056A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.634A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.579A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.806A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.845A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.246A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144
    Processing sheet with id=AB3, first strand: chain 'E' and resid 148 through 150
      removed outlier: 3.517A  pdb=" N   VAL E 149 " --> pdb=" O   LYS E 246 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU E 248 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU E 180 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   LEU E 189 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1077 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: 2.37

  Time building geometry restraints manager: 3.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2093
        1.33 -     1.46: 2466
        1.46 -     1.59: 4205
        1.59 -     1.71: 0
        1.71 -     1.84: 92
  Bond restraints: 8856
  Sorted by residual:
  bond pdb=" CA  GLN E 113 "
       pdb=" C   GLN E 113 "
    ideal  model  delta    sigma   weight residual
    1.521  1.560 -0.039 1.29e-02 6.01e+03 9.08e+00
  bond pdb=" CA  GLY E  16 "
       pdb=" C   GLY E  16 "
    ideal  model  delta    sigma   weight residual
    1.524  1.474  0.050 1.67e-02 3.59e+03 9.06e+00
  bond pdb=" CA  SER E 186 "
       pdb=" CB  SER E 186 "
    ideal  model  delta    sigma   weight residual
    1.532  1.485  0.047 1.58e-02 4.01e+03 8.93e+00
  bond pdb=" C   LEU E 216 "
       pdb=" N   THR E 217 "
    ideal  model  delta    sigma   weight residual
    1.330  1.369 -0.039 1.32e-02 5.74e+03 8.90e+00
  bond pdb=" C   GLU E 236 "
       pdb=" O   GLU E 236 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.26e-02 6.30e+03 6.55e+00
  ... (remaining 8851 not shown)

  Histogram of bond angle deviations from ideal:
       98.70 -   105.77: 131
      105.77 -   112.84: 4695
      112.84 -   119.91: 2957
      119.91 -   126.97: 4092
      126.97 -   134.04: 101
  Bond angle restraints: 11976
  Sorted by residual:
  angle pdb=" N   ALA R1009 "
        pdb=" CA  ALA R1009 "
        pdb=" C   ALA R1009 "
      ideal   model   delta    sigma   weight residual
     113.51   99.88   13.63 1.52e+00 4.33e-01 8.04e+01
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     110.61  116.81   -6.20 1.25e+00 6.40e-01 2.46e+01
  angle pdb=" C   CYS R1008 "
        pdb=" N   ALA R1009 "
        pdb=" CA  ALA R1009 "
      ideal   model   delta    sigma   weight residual
     126.86  119.08    7.78 1.57e+00 4.06e-01 2.46e+01
  angle pdb=" C   GLU E 224 "
        pdb=" CA  GLU E 224 "
        pdb=" CB  GLU E 224 "
      ideal   model   delta    sigma   weight residual
     111.26  103.81    7.45 1.67e+00 3.59e-01 1.99e+01
  angle pdb=" C   PRO E  14 "
        pdb=" CA  PRO E  14 "
        pdb=" CB  PRO E  14 "
      ideal   model   delta    sigma   weight residual
     111.39  116.57   -5.18 1.28e+00 6.10e-01 1.64e+01
  ... (remaining 11971 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4811
       17.99 -    35.98: 367
       35.98 -    53.97: 47
       53.97 -    71.96: 8
       71.96 -    89.95: 4
  Dihedral angle restraints: 5237
    sinusoidal: 2058
      harmonic: 3179
  Sorted by residual:
  dihedral pdb=" C   CYS R1008 "
           pdb=" N   CYS R1008 "
           pdb=" CA  CYS R1008 "
           pdb=" CB  CYS R1008 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.77   10.17     0      2.50e+00 1.60e-01 1.65e+01
  dihedral pdb=" CB  CYS R1008 "
           pdb=" SG  CYS R1008 "
           pdb=" SG  CYS R1080 "
           pdb=" CB  CYS R1080 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.62   33.62     1      1.00e+01 1.00e-02 1.61e+01
  dihedral pdb=" CA  ASP R1085 "
           pdb=" C   ASP R1085 "
           pdb=" N   THR R1086 "
           pdb=" CA  THR R1086 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.12   19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5234 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1188
       0.075 -    0.150: 158
       0.150 -    0.225: 9
       0.225 -    0.299: 2
       0.299 -    0.374: 1
  Chirality restraints: 1358
  Sorted by residual:
  chirality pdb=" CA  CYS R1008 "
            pdb=" N   CYS R1008 "
            pdb=" C   CYS R1008 "
            pdb=" CB  CYS R1008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CA  SER R1073 "
            pdb=" N   SER R1073 "
            pdb=" C   SER R1073 "
            pdb=" CB  SER R1073 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ALA B 203 "
            pdb=" N   ALA B 203 "
            pdb=" C   ALA B 203 "
            pdb=" CB  ALA B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1355 not shown)

  Planarity restraints: 1507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.044 5.00e-02 4.00e+02   6.83e-02 7.46e+00
        pdb=" N   PRO B 236 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 178 "   -0.021 2.00e-02 2.50e+03   1.49e-02 5.56e+00
        pdb=" CG  TRP E 178 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 178 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 178 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 178 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 178 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 178 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 151 "   -0.022 2.00e-02 2.50e+03   1.56e-02 4.25e+00
        pdb=" CG  PHE B 151 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 151 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 151 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 151 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 151 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 151 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1504 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 657
        2.73 -     3.28: 8069
        3.28 -     3.82: 12848
        3.82 -     4.36: 15022
        4.36 -     4.90: 27090
  Nonbonded interactions: 63686
  Sorted by model distance:
  nonbonded pdb=" O   ILE R 962 "
            pdb=" OG1 THR R 966 "
     model   vdw
     2.192 2.440
  nonbonded pdb=" O   THR R1177 "
            pdb=" OG  SER R1181 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.234 2.440
  nonbonded pdb=" OG1 THR R1076 "
            pdb=" O   VAL R1079 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ILE E 100 "
            pdb=" OG  SER E 105 "
     model   vdw
     2.248 2.440
  ... (remaining 63681 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:             1.300
  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:          3.900
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.680
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  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:11.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
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      :  0.005   0.059   8856  Z= 0.356
  Angle     :  0.799  13.631  11976  Z= 0.461
  Chirality :  0.051   0.374   1358
  Planarity :  0.005   0.068   1507
  Dihedral  : 12.695  89.948   3175
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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: -1.18 (0.26), residues: 1078
  helix:  0.67 (0.29), residues: 345
  sheet: -0.44 (0.31), residues: 266
  loop : -2.13 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.041   0.003   TRP E 178 
   HIS   0.011   0.002   HIS R1016 
   PHE   0.033   0.002   PHE B 151 
   TYR   0.020   0.002   TYR R1164 
   ARG   0.009   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.995 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 1.1180
  time to fit residues: 192.6468
Evaluate side-chains
  139 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.022 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4757
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0050
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
R1116 HIS
R1191 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.0923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8856  Z= 0.243
  Angle     :  0.614   9.298  11976  Z= 0.331
  Chirality :  0.044   0.138   1358
  Planarity :  0.004   0.047   1507
  Dihedral  :  5.170  31.638   1185
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.35 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.76 (0.26), residues: 1078
  helix:  1.27 (0.30), residues: 342
  sheet: -0.33 (0.30), residues: 272
  loop : -2.02 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP E 178 
   HIS   0.009   0.001   HIS R1016 
   PHE   0.023   0.002   PHE B 151 
   TYR   0.017   0.002   TYR R1112 
   ARG   0.005   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.904 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 155
  average time/residue: 1.1941
  time to fit residues: 197.5857
Evaluate side-chains
  152 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 0.939 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 1
  residues processed: 3
  average time/residue: 0.1107
  time to fit residues: 1.8944
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0870
   chunk 97 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 936 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8856  Z= 0.254
  Angle     :  0.603   9.605  11976  Z= 0.325
  Chirality :  0.043   0.144   1358
  Planarity :  0.004   0.046   1507
  Dihedral  :  5.023  29.515   1185
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.73 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.27), residues: 1078
  helix:  1.52 (0.30), residues: 343
  sheet: -0.23 (0.30), residues: 274
  loop : -1.91 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B  82 
   HIS   0.010   0.001   HIS R1016 
   PHE   0.026   0.002   PHE B 151 
   TYR   0.021   0.002   TYR R1112 
   ARG   0.005   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.933 
Fit side-chains
  outliers start: 21
  outliers final: 12
  residues processed: 160
  average time/residue: 1.1883
  time to fit residues: 202.5898
Evaluate side-chains
  160 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.900 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 4
  residues processed: 9
  average time/residue: 0.1351
  time to fit residues: 3.2722
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 73 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 104 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
B 268 ASN
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 936 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8856  Z= 0.273
  Angle     :  0.605   9.486  11976  Z= 0.326
  Chirality :  0.044   0.155   1358
  Planarity :  0.004   0.046   1507
  Dihedral  :  5.020  29.757   1185
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.11 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.26), residues: 1078
  helix:  1.54 (0.30), residues: 345
  sheet: -0.23 (0.30), residues: 274
  loop : -1.88 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B  82 
   HIS   0.009   0.001   HIS R1016 
   PHE   0.028   0.002   PHE B 151 
   TYR   0.021   0.002   TYR R1112 
   ARG   0.005   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 1.047 
Fit side-chains
  outliers start: 24
  outliers final: 16
  residues processed: 166
  average time/residue: 1.1750
  time to fit residues: 208.4422
Evaluate side-chains
  168 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 1.001 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 7
  residues processed: 9
  average time/residue: 0.2453
  time to fit residues: 4.3256
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 77 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0030
   chunk 89 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0670
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.4928

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8856  Z= 0.191
  Angle     :  0.556   9.591  11976  Z= 0.300
  Chirality :  0.042   0.159   1358
  Planarity :  0.004   0.044   1507
  Dihedral  :  4.758  27.851   1185
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.85 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.27), residues: 1078
  helix:  1.72 (0.30), residues: 344
  sheet: -0.26 (0.30), residues: 281
  loop : -1.79 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.007   0.001   HIS R1016 
   PHE   0.024   0.002   PHE R 989 
   TYR   0.010   0.001   TYR R1074 
   ARG   0.005   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.965 
Fit side-chains
  outliers start: 23
  outliers final: 17
  residues processed: 166
  average time/residue: 1.1967
  time to fit residues: 211.9707
Evaluate side-chains
  168 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.956 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 9
  residues processed: 8
  average time/residue: 0.4149
  time to fit residues: 5.2499
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 94 optimal weight:    0.0670
   chunk 20 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 936 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8856  Z= 0.185
  Angle     :  0.552   9.729  11976  Z= 0.296
  Chirality :  0.042   0.177   1358
  Planarity :  0.004   0.043   1507
  Dihedral  :  4.645  26.523   1185
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.32 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.27), residues: 1078
  helix:  1.76 (0.30), residues: 344
  sheet: -0.14 (0.30), residues: 281
  loop : -1.73 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B  82 
   HIS   0.007   0.001   HIS R1016 
   PHE   0.026   0.002   PHE R 989 
   TYR   0.010   0.001   TYR E 192 
   ARG   0.006   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.921 
Fit side-chains
  outliers start: 25
  outliers final: 16
  residues processed: 161
  average time/residue: 1.2433
  time to fit residues: 213.3995
Evaluate side-chains
  161 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.950 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 10
  residues processed: 6
  average time/residue: 0.1374
  time to fit residues: 2.7291
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8856  Z= 0.236
  Angle     :  0.583   9.747  11976  Z= 0.312
  Chirality :  0.043   0.169   1358
  Planarity :  0.004   0.044   1507
  Dihedral  :  4.770  27.852   1185
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.96 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.27), residues: 1078
  helix:  1.71 (0.30), residues: 344
  sheet: -0.22 (0.30), residues: 281
  loop : -1.73 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.007   0.001   HIS R1016 
   PHE   0.027   0.002   PHE R 989 
   TYR   0.013   0.001   TYR E 192 
   ARG   0.005   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 1.044 
Fit side-chains
  outliers start: 26
  outliers final: 17
  residues processed: 166
  average time/residue: 1.1455
  time to fit residues: 203.2577
Evaluate side-chains
  165 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 10
  residues processed: 7
  average time/residue: 0.1164
  time to fit residues: 2.6273
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0010
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0020
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0170
   chunk 94 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.1832

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

Flipped N/Q/H residues before XYZ refinement:
A 324 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 936 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8856  Z= 0.129
  Angle     :  0.529  11.284  11976  Z= 0.278
  Chirality :  0.041   0.187   1358
  Planarity :  0.003   0.040   1507
  Dihedral  :  4.316  22.669   1185
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.27 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.27), residues: 1078
  helix:  1.87 (0.30), residues: 345
  sheet:  0.08 (0.31), residues: 278
  loop : -1.75 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.001   TRP B  82 
   HIS   0.003   0.000   HIS R1016 
   PHE   0.027   0.001   PHE R 989 
   TYR   0.008   0.001   TYR E 102 
   ARG   0.007   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 1.004 
Fit side-chains
  outliers start: 23
  outliers final: 14
  residues processed: 169
  average time/residue: 1.1855
  time to fit residues: 214.1806
Evaluate side-chains
  162 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.957 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 10
  residues processed: 4
  average time/residue: 0.3821
  time to fit residues: 3.2860
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    0.2980
   chunk 76 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 96 optimal weight:    0.5980
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 974 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8856  Z= 0.198
  Angle     :  0.564   9.996  11976  Z= 0.301
  Chirality :  0.042   0.176   1358
  Planarity :  0.004   0.041   1507
  Dihedral  :  4.451  23.036   1185
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 22.07 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.27), residues: 1078
  helix:  1.81 (0.30), residues: 345
  sheet: -0.00 (0.30), residues: 280
  loop : -1.63 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.006   0.001   HIS R1016 
   PHE   0.029   0.002   PHE R 989 
   TYR   0.011   0.001   TYR E 192 
   ARG   0.008   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.959 
Fit side-chains
  outliers start: 17
  outliers final: 13
  residues processed: 163
  average time/residue: 1.1580
  time to fit residues: 201.8627
Evaluate side-chains
  164 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.955 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.1419
  time to fit residues: 2.0151
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
R 974 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8856  Z= 0.279
  Angle     :  0.639  12.827  11976  Z= 0.339
  Chirality :  0.043   0.171   1358
  Planarity :  0.004   0.041   1507
  Dihedral  :  4.793  26.308   1185
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 22.28 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.27), residues: 1078
  helix:  1.60 (0.30), residues: 346
  sheet: -0.02 (0.30), residues: 277
  loop : -1.70 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.008   0.001   HIS R1016 
   PHE   0.029   0.002   PHE R 989 
   TYR   0.018   0.002   TYR R1164 
   ARG   0.009   0.000   ARG A 356 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.957 
Fit side-chains
  outliers start: 15
  outliers final: 12
  residues processed: 165
  average time/residue: 1.1738
  time to fit residues: 207.0054
Evaluate side-chains
  158 residues out of total 947 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.932 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 10
  residues processed: 2
  average time/residue: 0.1981
  time to fit residues: 1.8427
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 974 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.154232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.130807 restraints weight = 12611.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.34
r_work: 0.3617 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8856  Z= 0.236
  Angle     :  0.624  13.131  11976  Z= 0.332
  Chirality :  0.043   0.180   1358
  Planarity :  0.004   0.041   1507
  Dihedral  :  4.750  26.293   1185
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 22.49 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.27), residues: 1078
  helix:  1.61 (0.29), residues: 345
  sheet: -0.12 (0.30), residues: 280
  loop : -1.71 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.009   0.001   HIS R1016 
   PHE   0.029   0.002   PHE R 989 
   TYR   0.018   0.002   TYR B 289 
   ARG   0.009   0.000   ARG A 356 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3793.08 seconds
wall clock time: 67 minutes 49.01 seconds (4069.01 seconds total)