Starting phenix.real_space_refine
on Wed Feb 12 14:35:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_32884_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_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/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_32884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_32884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_32884_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wy5_32884/02_2025/7wy5_32884_neut.cif"
  }
  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. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.77, 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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.82
  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: 2.08

  Time building geometry restraints manager: 2.21 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:
        0.00 -     1.83: 10719
        1.83 -     3.66: 277
        3.66 -     5.48: 46
        5.48 -     7.31: 13
        7.31 -     9.14: 3
  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 3.040
  nonbonded pdb=" OG1 THR R 966 "
            pdb=" OH  TYR R1202 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OD1 ASP A 229 "
            pdb=" OG1 THR N 113 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.241 3.040
  ... (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
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.530
  Find NCS groups from input model:        0.060
  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:             0.000
  Load rotamer database and sin/cos tables:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.500
-------------------------------------------------------------------------------
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 to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6208 (mm-30)
REVERT: R  947 VAL cc_start: 0.8045 (t) cc_final: 0.7806 (m)
REVERT: R  954 LEU cc_start: 0.7756 (mt) cc_final: 0.7329 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 1.2395
  time to fit residues: 216.4901
Evaluate side-chains
  148 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 88 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:
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.141297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.121911 restraints weight = 11023.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.08
r_work: 0.3476 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8172  Z= 0.281
  Angle     :  0.645   9.562  11058  Z= 0.350
  Chirality :  0.044   0.166   1249
  Planarity :  0.004   0.054   1403
  Dihedral  :  5.104  26.301   1098
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  8.29 %
    Favored  : 90.32 %
  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:  0.14 (0.27), residues: 997
  helix:  1.31 (0.28), residues: 354
  sheet:  0.77 (0.35), residues: 223
  loop : -1.39 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.018   0.002   PHE B 241 
 TYR   0.028   0.002   TYR B  59 
 ARG   0.004   0.000   ARG B 214 

*********************** 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
  168 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7786 (mttm)
REVERT: A  299 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6872 (mm-30)
REVERT: B  270 ILE cc_start: 0.8520 (pt) cc_final: 0.8042 (mt)
REVERT: B  312 ASP cc_start: 0.7799 (t0) cc_final: 0.7551 (t0)
REVERT: R  947 VAL cc_start: 0.8188 (t) cc_final: 0.7985 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 160
  average time/residue: 1.2397
  time to fit residues: 210.3109
Evaluate side-chains
  154 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 147
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 91 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 34 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 55 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.144675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125293 restraints weight = 11302.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.08
r_work: 0.3514 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8172  Z= 0.160
  Angle     :  0.547  10.418  11058  Z= 0.294
  Chirality :  0.041   0.141   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.571  22.504   1098
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.29 %
    Favored  : 86.75 %
  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:  0.49 (0.27), residues: 997
  helix:  1.79 (0.29), residues: 353
  sheet:  0.83 (0.34), residues: 221
  loop : -1.26 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.016   0.001   TYR N  95 
 ARG   0.004   0.000   ARG A 389 

*********************** 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
  170 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  283 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7635 (mtm110)
REVERT: A  285 ILE cc_start: 0.8633 (mt) cc_final: 0.8420 (mp)
REVERT: A  300 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7220 (ttmp)
REVERT: B  270 ILE cc_start: 0.8484 (pt) cc_final: 0.8035 (mt)
REVERT: B  312 ASP cc_start: 0.7786 (t0) cc_final: 0.7433 (t0)
REVERT: R 1079 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7950 (m)
  outliers start: 17
  outliers final: 8
  residues processed: 162
  average time/residue: 1.1654
  time to fit residues: 200.6581
Evaluate side-chains
  153 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0060
   chunk 11 optimal weight:    0.0770
   chunk 91 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.4354

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.145375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125040 restraints weight = 10998.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.08
r_work: 0.3529 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8172  Z= 0.169
  Angle     :  0.546   9.482  11058  Z= 0.294
  Chirality :  0.042   0.138   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.475  22.931   1098
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.36 %
    Favored  : 84.45 %
  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:  0.52 (0.27), residues: 997
  helix:  1.68 (0.28), residues: 364
  sheet:  0.76 (0.34), residues: 223
  loop : -1.14 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE A 340 
 TYR   0.020   0.001   TYR A  37 
 ARG   0.004   0.000   ARG B 134 

*********************** 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
  166 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  285 ILE cc_start: 0.8661 (mt) cc_final: 0.8457 (mp)
REVERT: A  299 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6966 (mm-30)
REVERT: A  300 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7186 (ttmp)
REVERT: B  270 ILE cc_start: 0.8484 (pt) cc_final: 0.8041 (mt)
REVERT: B  312 ASP cc_start: 0.7891 (t0) cc_final: 0.7533 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 154
  average time/residue: 1.2188
  time to fit residues: 198.9376
Evaluate side-chains
  158 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain R residue  968 CYS
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 67 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B  75 GLN
B 268 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R1191 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.128135 restraints weight = 11103.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.07
r_work: 0.3569 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8172  Z= 0.124
  Angle     :  0.499   8.945  11058  Z= 0.267
  Chirality :  0.040   0.141   1249
  Planarity :  0.003   0.049   1403
  Dihedral  :  4.133  20.789   1098
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.29 %
    Favored  : 84.10 %
  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:  1.94 (0.29), residues: 363
  sheet:  0.90 (0.34), residues: 216
  loop : -1.02 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 340 
 TYR   0.019   0.001   TYR N  80 
 ARG   0.008   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
  163 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6984 (mm-30)
REVERT: B  270 ILE cc_start: 0.8383 (pt) cc_final: 0.7953 (mt)
REVERT: B  312 ASP cc_start: 0.7795 (t0) cc_final: 0.7498 (t0)
REVERT: B  318 LEU cc_start: 0.8361 (tt) cc_final: 0.8006 (tp)
REVERT: R 1172 MET cc_start: 0.6009 (mmm) cc_final: 0.5706 (mmm)
  outliers start: 14
  outliers final: 7
  residues processed: 156
  average time/residue: 1.1970
  time to fit residues: 198.0276
Evaluate side-chains
  149 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue  968 CYS
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0970
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.123279 restraints weight = 10919.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.08
r_work: 0.3509 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8172  Z= 0.228
  Angle     :  0.573   9.516  11058  Z= 0.308
  Chirality :  0.042   0.139   1249
  Planarity :  0.004   0.050   1403
  Dihedral  :  4.454  24.514   1098
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.55 %
    Favored  : 82.49 %
  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:  0.67 (0.27), residues: 997
  helix:  1.73 (0.28), residues: 365
  sheet:  0.97 (0.34), residues: 219
  loop : -1.06 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.023   0.002   PHE A 340 
 TYR   0.019   0.001   TYR N  95 
 ARG   0.006   0.000   ARG A 283 

*********************** 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
  167 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7068 (mm-30)
REVERT: A  300 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7139 (ttmp)
REVERT: B  270 ILE cc_start: 0.8490 (pt) cc_final: 0.8089 (mt)
REVERT: B  312 ASP cc_start: 0.7822 (t0) cc_final: 0.7510 (t0)
REVERT: B  314 ARG cc_start: 0.8481 (ttp-170) cc_final: 0.8227 (ttm170)
REVERT: N   43 LYS cc_start: 0.7788 (mmmm) cc_final: 0.7533 (mmmm)
  outliers start: 17
  outliers final: 11
  residues processed: 156
  average time/residue: 1.2773
  time to fit residues: 210.7830
Evaluate side-chains
  158 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain R residue  968 CYS
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 86 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 96 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.143218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.123048 restraints weight = 10932.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.06
r_work: 0.3501 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8172  Z= 0.236
  Angle     :  0.586   9.831  11058  Z= 0.315
  Chirality :  0.043   0.144   1249
  Planarity :  0.004   0.051   1403
  Dihedral  :  4.540  23.985   1098
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.24 %
    Favored  : 81.22 %
  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:  0.61 (0.27), residues: 997
  helix:  1.64 (0.28), residues: 365
  sheet:  1.01 (0.34), residues: 219
  loop : -1.10 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.002   PHE A 340 
 TYR   0.019   0.001   TYR N  95 
 ARG   0.005   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
  172 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: B  270 ILE cc_start: 0.8482 (pt) cc_final: 0.8033 (mt)
REVERT: B  312 ASP cc_start: 0.7849 (t0) cc_final: 0.7530 (t0)
REVERT: B  314 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.8234 (ttm170)
REVERT: N   43 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7517 (mmmm)
  outliers start: 22
  outliers final: 16
  residues processed: 159
  average time/residue: 1.1398
  time to fit residues: 193.3056
Evaluate side-chains
  161 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0170
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0570
   chunk 89 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0670
   overall best weight:    0.3274

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.146551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125974 restraints weight = 11110.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.11
r_work: 0.3543 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8172  Z= 0.151
  Angle     :  0.540   9.998  11058  Z= 0.287
  Chirality :  0.041   0.154   1249
  Planarity :  0.004   0.049   1403
  Dihedral  :  4.259  21.719   1098
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.51 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 997
  helix:  2.04 (0.29), residues: 357
  sheet:  1.02 (0.34), residues: 219
  loop : -0.96 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.019   0.001   PHE A 340 
 TYR   0.015   0.001   TYR N  95 
 ARG   0.010   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
  161 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7355 (mtm) cc_final: 0.7081 (mtp)
REVERT: A  299 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7090 (mm-30)
REVERT: B  270 ILE cc_start: 0.8439 (pt) cc_final: 0.8045 (mt)
REVERT: B  312 ASP cc_start: 0.7825 (t0) cc_final: 0.7545 (t0)
REVERT: B  314 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.8196 (ttm170)
REVERT: N   43 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7494 (mmmm)
REVERT: R 1114 MET cc_start: 0.6223 (tpp) cc_final: 0.5861 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 155
  average time/residue: 1.2463
  time to fit residues: 204.9736
Evaluate side-chains
  151 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain R residue 1082 LEU
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.143285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.122503 restraints weight = 11103.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.12
r_work: 0.3494 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1876

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= 0.262
  Angle     :  0.611  10.497  11058  Z= 0.326
  Chirality :  0.043   0.146   1249
  Planarity :  0.004   0.050   1403
  Dihedral  :  4.579  25.239   1098
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.55 %
    Favored  : 79.49 %
  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:  0.72 (0.27), residues: 997
  helix:  1.87 (0.29), residues: 356
  sheet:  1.03 (0.34), residues: 219
  loop : -1.08 (0.30), residues: 422

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   0.030   0.002   PHE A 340 
 TYR   0.021   0.002   TYR N  95 
 ARG   0.011   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
  167 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6981 (mm-30)
REVERT: B  270 ILE cc_start: 0.8503 (pt) cc_final: 0.8102 (mt)
REVERT: B  312 ASP cc_start: 0.7760 (t0) cc_final: 0.7482 (t0)
REVERT: B  314 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.8254 (ttm170)
REVERT: N   43 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7542 (mmmm)
  outliers start: 17
  outliers final: 12
  residues processed: 158
  average time/residue: 1.1647
  time to fit residues: 195.4448
Evaluate side-chains
  159 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   17 SER
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain R residue 1091 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0070
   chunk 87 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0980
   chunk 11 optimal weight:    0.3980
   chunk 3 optimal weight:    0.4980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.2998

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.146830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.126279 restraints weight = 10984.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.11
r_work: 0.3544 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8172  Z= 0.149
  Angle     :  0.546  12.198  11058  Z= 0.288
  Chirality :  0.041   0.164   1249
  Planarity :  0.004   0.049   1403
  Dihedral  :  4.233  21.245   1098
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 19.35 %
    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:  0.95 (0.27), residues: 997
  helix:  2.16 (0.29), residues: 354
  sheet:  1.06 (0.34), residues: 219
  loop : -0.97 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.022   0.001   PHE A 340 
 TYR   0.020   0.001   TYR A  37 
 ARG   0.010   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
  154 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A  299 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7066 (mm-30)
REVERT: B  270 ILE cc_start: 0.8410 (pt) cc_final: 0.8009 (mt)
REVERT: B  312 ASP cc_start: 0.7775 (t0) cc_final: 0.7524 (t0)
REVERT: B  314 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.8187 (ttm170)
REVERT: N   43 LYS cc_start: 0.7742 (mmmm) cc_final: 0.7497 (mmmm)
REVERT: R 1172 MET cc_start: 0.5789 (mmp) cc_final: 0.5274 (ptp)
  outliers start: 9
  outliers final: 8
  residues processed: 148
  average time/residue: 1.2439
  time to fit residues: 195.0615
Evaluate side-chains
  151 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain N residue   17 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 239 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.142458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.121719 restraints weight = 11020.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.10
r_work: 0.3486 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8172  Z= 0.291
  Angle     :  0.632  10.650  11058  Z= 0.337
  Chirality :  0.044   0.150   1249
  Planarity :  0.004   0.050   1403
  Dihedral  :  4.660  25.841   1098
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 19.47 %
    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:  0.68 (0.27), residues: 997
  helix:  1.72 (0.29), residues: 362
  sheet:  1.04 (0.33), residues: 223
  loop : -1.08 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.032   0.002   PHE A 340 
 TYR   0.021   0.002   TYR N  95 
 ARG   0.010   0.000   ARG A 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6278.44 seconds
wall clock time: 111 minutes 14.99 seconds (6674.99 seconds total)