Starting phenix.real_space_refine
on Fri Dec  8 09:38:20 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy5_32884/12_2023/7wy5_32884_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy5_32884/12_2023/7wy5_32884.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/7wy5_32884/12_2023/7wy5_32884.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy5_32884/12_2023/7wy5_32884.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy5_32884/12_2023/7wy5_32884_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wy5_32884/12_2023/7wy5_32884_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=   0.021
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    5097      2.51       5
     N    1382      2.21       5
     O    1474      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  230": "OE1" <-> "OE2"
    Residue "A PHE  312": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  330": "OE1" <-> "OE2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "N PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   95": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  970": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE 1190": "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: 8009
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1877
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
    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: "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: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    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: 4.78, per 1000 atoms: 0.60
  Number of scatterers: 8009
  At special positions: 0
  Unit cell: (79.2, 100.1, 134.2, 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    1474      8.00
     N    1382      7.00
     C    5097      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R1008 " - pdb=" SG  CYS R1080 " 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: 2.82
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      38.0% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 3.797A  pdb=" N   ALA A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.764A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 239'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.620A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.748A  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 317
      removed outlier: 3.532A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.576A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.572A  pdb=" N   GLU A 390 " --> pdb=" O   MET A 386 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TYR A 391 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'G' and resid 7 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.737A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.505A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 940 through 956
      removed outlier: 3.877A  pdb=" N   LEU R 944 " --> pdb=" O   VAL R 940 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 958 through 970
      removed outlier: 3.695A  pdb=" N   ILE R 962 " --> pdb=" O   VAL R 958 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE R 970 " --> pdb=" O   THR R 966 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 971 through 974
      removed outlier: 3.657A  pdb=" N   GLN R 974 " --> pdb=" O   ARG R 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 971 through 974'
    Processing helix  chain 'R' and resid 975 through 999
      removed outlier: 3.725A  pdb=" N   ILE R 999 " --> pdb=" O   PHE R 995 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1010 through 1035
      removed outlier: 3.616A  pdb=" N   GLY R1030 " --> pdb=" O   MET R1026 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1047 through 1056
      removed outlier: 3.650A  pdb=" N   TYR R1056 " --> pdb=" O   TYR R1052 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1056 through 1070
      removed outlier: 3.923A  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 1118
      Proline residue:  R1095  - end of helix
      removed outlier: 4.436A  pdb=" N   ILE R1105 " --> pdb=" O   MET R1101 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR R1118 " --> pdb=" O   MET R1114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1144 through 1154
      removed outlier: 3.674A  pdb=" N   LEU R1151 " --> pdb=" O   ALA R1147 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   CYS R1152 " --> pdb=" O   ILE R1148 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU R1153 " --> pdb=" O   ALA R1149 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU R1154 " --> pdb=" O   LEU R1150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1155 through 1163
      removed outlier: 3.644A  pdb=" N   TRP R1158 " --> pdb=" O   GLY R1155 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA R1159 " --> pdb=" O   LEU R1156 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLY R1161 " --> pdb=" O   TRP R1158 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU R1162 " --> pdb=" O   ALA R1159 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   MET R1163 " --> pdb=" O   PHE R1160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1169 through 1181
      removed outlier: 4.170A  pdb=" N   ALA R1173 " --> pdb=" O   THR R1169 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER R1181 " --> pdb=" O   THR R1177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1182 through 1193
    Processing helix  chain 'R' and resid 1195 through 1207
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.470A  pdb=" N   LEU A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.905A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 9.123A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.341A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.681A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.826A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.066A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.826A  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: 6.877A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.180A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.055A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.421A  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: 6.844A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.472A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.194A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    987 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: 2.20

  Time building geometry restraints manager: 3.10 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: 2498
        1.34 -     1.45: 1232
        1.45 -     1.57: 4362
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 8172
  Sorted by residual:
  bond pdb=" C   ASP B 291 "
       pdb=" N   PHE B 292 "
    ideal  model  delta    sigma   weight residual
    1.331  1.373 -0.043 1.35e-02 5.49e+03 1.00e+01
  bond pdb=" CA  ASP B 291 "
       pdb=" C   ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.525  1.493  0.032 1.38e-02 5.25e+03 5.38e+00
  bond pdb=" CA  ASP B 291 "
       pdb=" CB  ASP B 291 "
    ideal  model  delta    sigma   weight residual
    1.528  1.559 -0.031 1.37e-02 5.33e+03 5.10e+00
  bond pdb=" N   THR R1169 "
       pdb=" CA  THR R1169 "
    ideal  model  delta    sigma   weight residual
    1.458  1.438  0.020 9.00e-03 1.23e+04 4.84e+00
  bond pdb=" CA  THR R1169 "
       pdb=" C   THR R1169 "
    ideal  model  delta    sigma   weight residual
    1.525  1.547 -0.023 1.11e-02 8.12e+03 4.12e+00
  ... (remaining 8167 not shown)

  Histogram of bond angle deviations from ideal:
       98.24 -   105.40: 100
      105.40 -   112.56: 4165
      112.56 -   119.72: 2707
      119.72 -   126.88: 3992
      126.88 -   134.04: 94
  Bond angle restraints: 11058
  Sorted by residual:
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     110.41  117.51   -7.10 1.18e+00 7.18e-01 3.62e+01
  angle pdb=" N   ILE R1165 "
        pdb=" CA  ILE R1165 "
        pdb=" C   ILE R1165 "
      ideal   model   delta    sigma   weight residual
     111.62  116.00   -4.38 7.90e-01 1.60e+00 3.08e+01
  angle pdb=" N   TYR N  94 "
        pdb=" CA  TYR N  94 "
        pdb=" C   TYR N  94 "
      ideal   model   delta    sigma   weight residual
     108.90  115.18   -6.28 1.63e+00 3.76e-01 1.48e+01
  angle pdb=" N   MET R1163 "
        pdb=" CA  MET R1163 "
        pdb=" C   MET R1163 "
      ideal   model   delta    sigma   weight residual
     110.68  115.87   -5.19 1.39e+00 5.18e-01 1.40e+01
  angle pdb=" C   ILE R1165 "
        pdb=" CA  ILE R1165 "
        pdb=" CB  ILE R1165 "
      ideal   model   delta    sigma   weight residual
     111.05  107.76    3.29 8.90e-01 1.26e+00 1.37e+01
  ... (remaining 11053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4444
       17.66 -    35.33: 336
       35.33 -    52.99: 49
       52.99 -    70.65: 7
       70.65 -    88.31: 7
  Dihedral angle restraints: 4843
    sinusoidal: 1903
      harmonic: 2940
  Sorted by residual:
  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 -133.09   47.09     1      1.00e+01 1.00e-02 3.06e+01
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ILE R 997 "
           pdb=" C   ILE R 997 "
           pdb=" N   GLY R 998 "
           pdb=" CA  GLY R 998 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.75  -19.25     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 4840 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 992
       0.055 -    0.110: 213
       0.110 -    0.165: 36
       0.165 -    0.219: 1
       0.219 -    0.274: 7
  Chirality restraints: 1249
  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    2.24    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  MET R1163 "
            pdb=" N   MET R1163 "
            pdb=" C   MET R1163 "
            pdb=" CB  MET R1163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+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 1.37e+00
  ... (remaining 1246 not shown)

  Planarity restraints: 1403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.021 2.00e-02 2.50e+03   1.74e-02 6.06e+00
        pdb=" CG  TYR B  59 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO B 236 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "    0.032 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO G  60 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1400 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 47
        2.57 -     3.15: 6069
        3.15 -     3.73: 10982
        3.73 -     4.32: 15324
        4.32 -     4.90: 26433
  Nonbonded interactions: 58855
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R1076 "
            pdb=" O   VAL R1079 "
     model   vdw
     1.986 2.440
  nonbonded pdb=" OG1 THR R 966 "
            pdb=" OH  TYR R1202 "
     model   vdw
     2.175 2.440
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.183 2.520
  nonbonded pdb=" OD1 ASP A 229 "
            pdb=" OG1 THR N 113 "
     model   vdw
     2.233 2.440
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.241 2.440
  ... (remaining 58850 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:             0.710
  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:          3.800
  Check model and map are aligned:         0.130
  Set scattering table:                    0.070
  Process input model:                     24.520
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
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   0.043   8172  Z= 0.336
  Angle     :  0.746   9.138  11058  Z= 0.441
  Chirality :  0.049   0.274   1249
  Planarity :  0.004   0.056   1403
  Dihedral  : 12.829  88.312   2938
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 997
  helix:  0.77 (0.28), residues: 361
  sheet:  0.91 (0.35), residues: 217
  loop : -1.68 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.034   0.003   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.020   0.002   PHE B 151 
   TYR   0.043   0.002   TYR B  59 
   ARG   0.008   0.000   ARG B 214 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.876 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 1.2109
  time to fit residues: 211.6311
Evaluate side-chains
  148 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.817 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3408
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 50 optimal weight:    0.2980
   chunk 39 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B  75 GLN
B 268 ASN
G  44 HIS
R 981 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8172  Z= 0.203
  Angle     :  0.582   8.778  11058  Z= 0.316
  Chirality :  0.043   0.158   1249
  Planarity :  0.004   0.053   1403
  Dihedral  :  4.878  23.764   1098
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  8.64 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.27), residues: 997
  helix:  1.41 (0.28), residues: 360
  sheet:  0.81 (0.35), residues: 221
  loop : -1.38 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.016   0.002   PHE A 212 
   TYR   0.022   0.002   TYR B  59 
   ARG   0.005   0.000   ARG N  72 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.881 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 154
  average time/residue: 1.2286
  time to fit residues: 200.7994
Evaluate side-chains
  149 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.867 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 2
  residues processed: 5
  average time/residue: 0.1063
  time to fit residues: 2.0518
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 30 optimal weight:    0.3980
   chunk 71 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
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      :  0.003   0.029   8172  Z= 0.211
  Angle     :  0.578  10.050  11058  Z= 0.310
  Chirality :  0.042   0.152   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.695  24.158   1098
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.06 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.27), residues: 997
  helix:  1.60 (0.29), residues: 360
  sheet:  0.73 (0.34), residues: 223
  loop : -1.33 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.015   0.002   PHE B 241 
   TYR   0.018   0.001   TYR N  95 
   ARG   0.010   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 11
  residues processed: 160
  average time/residue: 1.0774
  time to fit residues: 183.7895
Evaluate side-chains
  157 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 4
  residues processed: 7
  average time/residue: 0.5103
  time to fit residues: 5.1881
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 924 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8172  Z= 0.277
  Angle     :  0.621   9.020  11058  Z= 0.333
  Chirality :  0.044   0.162   1249
  Planarity :  0.004   0.054   1403
  Dihedral  :  4.830  25.232   1098
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.33 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.27), residues: 997
  helix:  1.48 (0.28), residues: 361
  sheet:  0.90 (0.34), residues: 219
  loop : -1.42 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.020   0.002   PHE A 340 
   TYR   0.021   0.002   TYR A  37 
   ARG   0.009   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 0.867 
Fit side-chains
  outliers start: 23
  outliers final: 14
  residues processed: 161
  average time/residue: 1.1975
  time to fit residues: 204.4933
Evaluate side-chains
  158 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.883 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 7
  residues processed: 7
  average time/residue: 0.2810
  time to fit residues: 3.6848
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0370
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8172  Z= 0.249
  Angle     :  0.599   8.715  11058  Z= 0.321
  Chirality :  0.043   0.160   1249
  Planarity :  0.004   0.052   1403
  Dihedral  :  4.736  25.052   1098
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.09 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 997
  helix:  1.45 (0.28), residues: 368
  sheet:  0.89 (0.34), residues: 219
  loop : -1.39 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.019   0.002   PHE A 340 
   TYR   0.020   0.002   TYR N  80 
   ARG   0.006   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.912 
Fit side-chains
  outliers start: 24
  outliers final: 18
  residues processed: 158
  average time/residue: 1.2118
  time to fit residues: 203.2107
Evaluate side-chains
  160 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.902 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 9
  residues processed: 10
  average time/residue: 0.2293
  time to fit residues: 4.2147
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    0.0370
   chunk 18 optimal weight:    0.4980
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 94 optimal weight:    0.3980
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8172  Z= 0.163
  Angle     :  0.551  10.011  11058  Z= 0.294
  Chirality :  0.041   0.143   1249
  Planarity :  0.004   0.050   1403
  Dihedral  :  4.446  22.347   1098
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.01 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 997
  helix:  1.75 (0.28), residues: 366
  sheet:  0.87 (0.33), residues: 219
  loop : -1.32 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.018   0.001   PHE A 340 
   TYR   0.018   0.001   TYR A  37 
   ARG   0.005   0.000   ARG B 214 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.912 
Fit side-chains
  outliers start: 17
  outliers final: 13
  residues processed: 159
  average time/residue: 1.1548
  time to fit residues: 195.2975
Evaluate side-chains
  161 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.906 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 7
  residues processed: 6
  average time/residue: 0.3560
  time to fit residues: 3.7251
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0050
   chunk 59 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8172  Z= 0.283
  Angle     :  0.619   9.872  11058  Z= 0.332
  Chirality :  0.043   0.157   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.736  25.965   1098
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.17 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 997
  helix:  1.50 (0.28), residues: 368
  sheet:  0.90 (0.33), residues: 219
  loop : -1.36 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.023   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.025   0.002   PHE A 340 
   TYR   0.021   0.002   TYR N  95 
   ARG   0.009   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 15
  residues processed: 158
  average time/residue: 1.2851
  time to fit residues: 215.0051
Evaluate side-chains
  160 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.850 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 8
  residues processed: 7
  average time/residue: 0.1370
  time to fit residues: 2.5966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8172  Z= 0.232
  Angle     :  0.586   9.122  11058  Z= 0.316
  Chirality :  0.042   0.151   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.633  23.839   1098
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.09 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.27), residues: 997
  helix:  1.61 (0.28), residues: 368
  sheet:  0.91 (0.33), residues: 219
  loop : -1.34 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.021   0.002   PHE A 340 
   TYR   0.019   0.001   TYR N  95 
   ARG   0.008   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 14
  residues processed: 157
  average time/residue: 1.2192
  time to fit residues: 202.7558
Evaluate side-chains
  160 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.812 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 8
  residues processed: 6
  average time/residue: 0.5538
  time to fit residues: 4.8307
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0670
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0870
   chunk 87 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0980
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
B  75 GLN
R1191 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8172  Z= 0.145
  Angle     :  0.540  12.399  11058  Z= 0.284
  Chirality :  0.040   0.154   1249
  Planarity :  0.004   0.049   1403
  Dihedral  :  4.236  21.618   1098
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.78 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 997
  helix:  1.92 (0.29), residues: 366
  sheet:  0.97 (0.33), residues: 216
  loop : -1.24 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.019   0.001   PHE A 340 
   TYR   0.021   0.001   TYR N  80 
   ARG   0.008   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.867 
Fit side-chains
  outliers start: 14
  outliers final: 7
  residues processed: 158
  average time/residue: 1.1256
  time to fit residues: 189.5449
Evaluate side-chains
  152 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 1.000 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.0912
  time to fit residues: 1.7680
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0020
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8172  Z= 0.179
  Angle     :  0.564  13.484  11058  Z= 0.296
  Chirality :  0.041   0.146   1249
  Planarity :  0.004   0.050   1403
  Dihedral  :  4.319  22.965   1098
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.82 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.27), residues: 997
  helix:  1.85 (0.29), residues: 370
  sheet:  0.99 (0.34), residues: 214
  loop : -1.14 (0.30), residues: 413

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   0.028   0.001   PHE A 340 
   TYR   0.017   0.001   TYR N  95 
   ARG   0.008   0.000   ARG A 283 

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.889 
Fit side-chains
  outliers start: 11
  outliers final: 8
  residues processed: 155
  average time/residue: 1.2380
  time to fit residues: 203.8503
Evaluate side-chains
  156 residues out of total 868 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.913 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 5
  residues processed: 3
  average time/residue: 0.1689
  time to fit residues: 2.0006
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 71 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0970
   chunk 79 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0670
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.3516

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.146026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.126755 restraints weight = 11068.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.06
r_work: 0.3543 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8172  Z= 0.158
  Angle     :  0.560  12.779  11058  Z= 0.291
  Chirality :  0.041   0.149   1249
  Planarity :  0.004   0.049   1403
  Dihedral  :  4.211  21.940   1098
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 20.05 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 997
  helix:  1.99 (0.29), residues: 366
  sheet:  0.93 (0.34), residues: 216
  loop : -1.11 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.024   0.001   PHE A 340 
   TYR   0.016   0.001   TYR N  95 
   ARG   0.011   0.000   ARG A 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3613.39 seconds
wall clock time: 64 minutes 37.71 seconds (3877.71 seconds total)