Starting phenix.real_space_refine
on Thu Feb 13 23:12:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7un3_26612/02_2025/7un3_26612.cif"
  }
  resolution = 3.5
  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=  -0.002 sd=   0.043
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      41      5.16       5
     C    6056      2.51       5
     N    1605      2.21       5
     O    1721      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9423
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 582
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "A"
      Number of atoms: 5196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5196
          Classifications: {'peptide': 649}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611}
          Chain breaks: 9
    Chain: "B"
      Number of atoms: 1838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1838
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 12, 'TRANS': 210}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1807
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 11, 'TRANS': 207}
          Chain breaks: 2
  Time building chain proxies: 5.73, per 1000 atoms: 0.61
  Number of scatterers: 9423
  At special positions: 0
  Unit cell: (83.325, 113.025, 141.075, 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      41     16.00
     O    1721      8.00
     N    1605      7.00
     C    6056      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      32.2% alpha, 28.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'D' and resid 22 through 35
      removed outlier: 3.589A  pdb=" N   VAL D  26 " --> pdb=" O   THR D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 56 through 60
    Processing helix  chain 'A' and resid 127 through 130
      removed outlier: 4.145A  pdb=" N   GLY A 130 " --> pdb=" O   TYR A 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 127 through 130'
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.523A  pdb=" N   LYS A 139 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 4.429A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 336
      removed outlier: 4.399A  pdb=" N   GLY A 334 " --> pdb=" O   GLU A 331 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG A 335 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 950 through 968
      removed outlier: 3.559A  pdb=" N   LYS A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1041 through 1045
    Processing helix  chain 'A' and resid 1060 through 1071
    Processing helix  chain 'A' and resid 1076 through 1080
      removed outlier: 3.531A  pdb=" N   ASN A1080 " --> pdb=" O   PRO A1077 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.806A  pdb=" N   ARG A1088 " --> pdb=" O   ASP A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1118
    Processing helix  chain 'A' and resid 1123 through 1133
    Processing helix  chain 'A' and resid 1134 through 1152
      removed outlier: 4.049A  pdb=" N   VAL A1139 " --> pdb=" O   GLY A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1283
      removed outlier: 3.708A  pdb=" N   GLN A1275 " --> pdb=" O   GLY A1271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 121
      removed outlier: 3.860A  pdb=" N   VAL B 108 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU B 109 " --> pdb=" O   LYS B 105 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 169 through 177
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 188 through 194
      removed outlier: 4.194A  pdb=" N   ILE B 192 " --> pdb=" O   HIS B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 302
    Processing helix  chain 'B' and resid 320 through 333
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.776A  pdb=" N   TYR B 341 " --> pdb=" O   ARG B 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 122
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 169 through 177
    Processing helix  chain 'C' and resid 178 through 183
      removed outlier: 3.826A  pdb=" N   ASP C 183 " --> pdb=" O   ASP C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 188
      No H-bonds generated for 'chain 'C' and resid 186 through 188'
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 296 through 302
      removed outlier: 4.150A  pdb=" N   PHE C 300 " --> pdb=" O   PHE C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 333
    Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16
      removed outlier: 4.102A  pdb=" N   SER D  65 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134
      removed outlier: 6.787A  pdb=" N   ARG A 123 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   SER A  67 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   LEU A 142 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 188
      removed outlier: 6.624A  pdb=" N   ILE A 183 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU A 177 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   TYR A 185 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   VAL A 175 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   VAL A 166 " --> pdb=" O   MET A 558 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   MET A 558 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ASP A 168 " --> pdb=" O   ASP A 556 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL A 557 " --> pdb=" O   CYS A 566 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   CYS A 566 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   TRP A 559 " --> pdb=" O   VAL A 564 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL A 564 " --> pdb=" O   TRP A 559 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 194
      removed outlier: 6.187A  pdb=" N   ALA A 174 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269
      removed outlier: 6.187A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   LEU A 224 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   GLU A 297 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LEU A 222 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A 220 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASN A 218 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   GLU A 303 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   LEU A 216 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS A 305 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU A 210 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 280
      removed outlier: 5.524A  pdb=" N   TRP A 278 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   SER A 231 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU A 210 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LYS A 305 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   LEU A 216 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   GLU A 303 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASN A 218 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A 220 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LEU A 222 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   GLU A 297 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   LEU A 224 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 291 through 311
    current: chain 'A' and resid 337 through 338
    Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 641
      removed outlier: 5.333A  pdb=" N   LEU A 633 " --> pdb=" O   LYS A 623 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LYS A 623 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ASP A 639 " --> pdb=" O   CYS A 617 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   CYS A 617 " --> pdb=" O   ASP A 639 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER A 609 " --> pdb=" O   MET A 618 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LYS A 620 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   VAL A 607 " --> pdb=" O   LYS A 620 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   PHE A 622 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   GLY A 605 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 702
      removed outlier: 3.985A  pdb=" N   SER A 698 " --> pdb=" O   TRP A 694 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   GLU A 691 " --> pdb=" O   ALA A 682 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932
      removed outlier: 3.541A  pdb=" N   PHE A 978 " --> pdb=" O   LEU A 984 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   LEU A 984 " --> pdb=" O   PHE A 978 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203
      removed outlier: 3.635A  pdb=" N   PHE B 212 " --> pdb=" O   TYR B 233 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B 214 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LYS B 231 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY B 254 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 278
    Processing sheet with id=AB3, first strand: chain 'C' and resid 196 through 203
      removed outlier: 3.716A  pdb=" N   THR C 232 " --> pdb=" O   THR C 256 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ARG C 234 " --> pdb=" O   GLY C 254 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   GLY C 254 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 270 through 278

    379 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 2.85 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: 3043
        1.34 -     1.46: 1868
        1.46 -     1.58: 4661
        1.58 -     1.70: 0
        1.70 -     1.81: 62
  Bond restraints: 9634
  Sorted by residual:
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.08e+00
  bond pdb=" CG  LEU C  81 "
       pdb=" CD2 LEU C  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.50e+00
  bond pdb=" CB  TRP A 308 "
       pdb=" CG  TRP A 308 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 9.02e-01
  bond pdb=" CG  LYS C 231 "
       pdb=" CD  LYS C 231 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.95e-01
  bond pdb=" CE  LYS C 231 "
       pdb=" NZ  LYS C 231 "
    ideal  model  delta    sigma   weight residual
    1.489  1.461  0.028 3.00e-02 1.11e+03 8.66e-01
  ... (remaining 9629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 12657
        1.54 -     3.08: 284
        3.08 -     4.62: 62
        4.62 -     6.16: 12
        6.16 -     7.70: 1
  Bond angle restraints: 13016
  Sorted by residual:
  angle pdb=" CA  ARG A1128 "
        pdb=" CB  ARG A1128 "
        pdb=" CG  ARG A1128 "
      ideal   model   delta    sigma   weight residual
     114.10  121.80   -7.70 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CA  GLN B 111 "
        pdb=" C   GLN B 111 "
        pdb=" N   PRO B 112 "
      ideal   model   delta    sigma   weight residual
     118.44  122.78   -4.34 1.59e+00 3.96e-01 7.44e+00
  angle pdb=" CA  MET A1285 "
        pdb=" CB  MET A1285 "
        pdb=" CG  MET A1285 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.90e+00
  angle pdb=" CB  LYS A 136 "
        pdb=" CG  LYS A 136 "
        pdb=" CD  LYS A 136 "
      ideal   model   delta    sigma   weight residual
     111.30  117.14   -5.84 2.30e+00 1.89e-01 6.45e+00
  angle pdb=" N   ASN A1080 "
        pdb=" CA  ASN A1080 "
        pdb=" C   ASN A1080 "
      ideal   model   delta    sigma   weight residual
     111.56  115.06   -3.50 1.38e+00 5.25e-01 6.44e+00
  ... (remaining 13011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5274
       17.83 -    35.65: 446
       35.65 -    53.48: 75
       53.48 -    71.31: 12
       71.31 -    89.13: 8
  Dihedral angle restraints: 5815
    sinusoidal: 2431
      harmonic: 3384
  Sorted by residual:
  dihedral pdb=" CA  ARG B 333 "
           pdb=" C   ARG B 333 "
           pdb=" N   ILE B 334 "
           pdb=" CA  ILE B 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  PHE B 224 "
           pdb=" C   PHE B 224 "
           pdb=" N   THR B 225 "
           pdb=" CA  THR B 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.71  -17.29     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASN A 582 "
           pdb=" C   ASN A 582 "
           pdb=" N   GLU A 583 "
           pdb=" CA  GLU A 583 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 5812 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1036
       0.039 -    0.078: 252
       0.078 -    0.117: 122
       0.117 -    0.156: 29
       0.156 -    0.195: 2
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CB  ILE A1127 "
            pdb=" CA  ILE A1127 "
            pdb=" CG1 ILE A1127 "
            pdb=" CG2 ILE A1127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CA  GLN B 111 "
            pdb=" N   GLN B 111 "
            pdb=" C   GLN B 111 "
            pdb=" CB  GLN B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality pdb=" CA  ILE A1254 "
            pdb=" N   ILE A1254 "
            pdb=" C   ILE A1254 "
            pdb=" CB  ILE A1254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 1438 not shown)

  Planarity restraints: 1665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1256 "    0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO A1257 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A1257 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A1257 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 303 "    0.046 5.00e-02 4.00e+02   6.94e-02 7.71e+00
        pdb=" N   PRO C 304 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO C 304 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 304 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1012 "    0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO A1013 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A1013 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1013 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1662 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 104
        2.53 -     3.12: 7859
        3.12 -     3.71: 14619
        3.71 -     4.31: 20351
        4.31 -     4.90: 33811
  Nonbonded interactions: 76744
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 144 "
            pdb=" OG1 THR A 553 "
     model   vdw
     1.936 3.040
  nonbonded pdb=" NH1 ARG A 154 "
            pdb=" O   SER A 161 "
     model   vdw
     1.968 3.120
  nonbonded pdb=" OG  SER A1023 "
            pdb=" O   ASP A1035 "
     model   vdw
     2.003 3.040
  nonbonded pdb=" N   SER C 296 "
            pdb=" OD1 ASN C 299 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" NH1 ARG D  54 "
            pdb=" OD2 ASP D  58 "
     model   vdw
     2.119 3.120
  ... (remaining 76739 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 73 through 121 or resid 166 through 342))
  selection = (chain 'C' and (resid 73 through 121 or resid 166 through 306 or resid 319 throu \ 
gh 342))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.410
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.220
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6182
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9634  Z= 0.197
  Angle     :  0.612   7.699  13016  Z= 0.335
  Chirality :  0.044   0.195   1441
  Planarity :  0.005   0.071   1665
  Dihedral  : 13.626  89.132   3613
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.87 (0.25), residues: 1130
  helix:  0.62 (0.30), residues: 303
  sheet: -0.75 (0.32), residues: 254
  loop : -1.12 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 171 
 HIS   0.006   0.001   HIS B 328 
 PHE   0.014   0.001   PHE A 622 
 TYR   0.021   0.002   TYR A1100 
 ARG   0.015   0.001   ARG A1088 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   31 GLN cc_start: 0.5815 (tm-30) cc_final: 0.5500 (tm-30)
REVERT: A   58 ARG cc_start: 0.7121 (ptm160) cc_final: 0.6799 (ptm160)
REVERT: A  156 MET cc_start: 0.7240 (mtp) cc_final: 0.6997 (mtt)
REVERT: A  171 ILE cc_start: 0.7482 (mm) cc_final: 0.6787 (mm)
REVERT: A  190 LYS cc_start: 0.7344 (mmtt) cc_final: 0.7097 (tppt)
REVERT: A  577 HIS cc_start: 0.6000 (m-70) cc_final: 0.5772 (m-70)
REVERT: A 1084 PHE cc_start: 0.6401 (m-80) cc_final: 0.5451 (m-80)
REVERT: B  205 ASP cc_start: 0.7709 (m-30) cc_final: 0.7392 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.2282
  time to fit residues: 78.7584
Evaluate side-chains
  179 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    8.9990
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 170 ASN
A 581 ASN
B 188 HIS
C 122 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.202655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.163051 restraints weight = 14998.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.166465 restraints weight = 9411.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167136 restraints weight = 7528.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.080   9634  Z= 0.495
  Angle     :  0.790   7.676  13016  Z= 0.414
  Chirality :  0.051   0.211   1441
  Planarity :  0.006   0.054   1665
  Dihedral  :  5.512  24.667   1246
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.27 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.94 (0.25), residues: 1130
  helix:  0.63 (0.29), residues: 294
  sheet: -0.74 (0.34), residues: 235
  loop : -1.21 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 209 
 HIS   0.011   0.002   HIS B 328 
 PHE   0.025   0.003   PHE A1084 
 TYR   0.016   0.003   TYR B  96 
 ARG   0.015   0.001   ARG A 347 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   31 GLN cc_start: 0.6360 (tm-30) cc_final: 0.5969 (tm-30)
REVERT: A  156 MET cc_start: 0.7511 (mtp) cc_final: 0.7255 (mtt)
REVERT: A  190 LYS cc_start: 0.7368 (mmtt) cc_final: 0.7100 (tppt)
REVERT: A  271 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6955 (mmtm)
REVERT: A  552 MET cc_start: 0.6697 (ttt) cc_final: 0.6486 (ttp)
REVERT: A 1285 MET cc_start: 0.6639 (mmp) cc_final: 0.6212 (mmt)
REVERT: B  110 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6831 (t80)
REVERT: B  118 PHE cc_start: 0.7449 (t80) cc_final: 0.7088 (t80)
REVERT: B  236 ARG cc_start: 0.7301 (mtp180) cc_final: 0.7022 (mtp180)
REVERT: C  171 TRP cc_start: 0.6853 (m-90) cc_final: 0.6230 (m-90)
  outliers start: 26
  outliers final: 14
  residues processed: 209
  average time/residue: 0.2326
  time to fit residues: 66.8185
Evaluate side-chains
  175 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  133 GLN
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1106 ILE
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  258 CYS
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 88 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0070
   overall best weight:    0.7602

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 170 ASN
** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A 680 GLN
A1024 GLN
B 328 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.205551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.156297 restraints weight = 14742.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.161652 restraints weight = 7937.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.165472 restraints weight = 5308.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9634  Z= 0.231
  Angle     :  0.647   6.937  13016  Z= 0.335
  Chirality :  0.046   0.187   1441
  Planarity :  0.005   0.046   1665
  Dihedral  :  5.096  22.541   1246
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.16 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.64 (0.25), residues: 1130
  helix:  0.87 (0.30), residues: 296
  sheet: -0.69 (0.35), residues: 229
  loop : -0.95 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 308 
 HIS   0.008   0.001   HIS B 328 
 PHE   0.014   0.002   PHE B 300 
 TYR   0.013   0.002   TYR B  96 
 ARG   0.005   0.000   ARG A 154 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6770 (ptm)
REVERT: D   49 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.5459 (tp40)
REVERT: A  156 MET cc_start: 0.7381 (mtp) cc_final: 0.7136 (mtt)
REVERT: A  271 LYS cc_start: 0.7250 (mmmt) cc_final: 0.6901 (mmtm)
REVERT: A  707 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8444 (tp)
REVERT: A 1084 PHE cc_start: 0.6825 (m-80) cc_final: 0.6547 (m-80)
REVERT: A 1285 MET cc_start: 0.6841 (mmp) cc_final: 0.6486 (mmt)
REVERT: B  110 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6687 (t80)
REVERT: B  117 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6866 (ttp80)
REVERT: B  118 PHE cc_start: 0.7257 (t80) cc_final: 0.6895 (t80)
REVERT: B  221 ASN cc_start: 0.7977 (p0) cc_final: 0.7680 (p0)
REVERT: C  113 LEU cc_start: 0.8915 (mm) cc_final: 0.8696 (mm)
REVERT: C  170 PHE cc_start: 0.4562 (t80) cc_final: 0.3901 (t80)
  outliers start: 31
  outliers final: 14
  residues processed: 195
  average time/residue: 0.2324
  time to fit residues: 62.9715
Evaluate side-chains
  184 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  133 GLN
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1106 ILE
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 68 optimal weight:    8.9990
   chunk 90 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 88 optimal weight:   30.0000
   chunk 84 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 581 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 HIS ** 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 = 0.4558 r_free = 0.4558 target = 0.201170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.160475 restraints weight = 14957.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.162054 restraints weight = 9159.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.163277 restraints weight = 8329.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9634  Z= 0.388
  Angle     :  0.706  10.782  13016  Z= 0.366
  Chirality :  0.048   0.163   1441
  Planarity :  0.005   0.057   1665
  Dihedral  :  5.304  21.983   1246
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 14.87 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.94 (0.25), residues: 1130
  helix:  0.57 (0.29), residues: 308
  sheet: -1.04 (0.34), residues: 233
  loop : -1.05 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 171 
 HIS   0.006   0.001   HIS A 155 
 PHE   0.017   0.002   PHE B 300 
 TYR   0.015   0.002   TYR A 355 
 ARG   0.004   0.001   ARG A 150 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 171
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6549 (ptm)
REVERT: D   39 ASP cc_start: 0.7320 (t0) cc_final: 0.7025 (p0)
REVERT: D   54 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5955 (ttt180)
REVERT: A  156 MET cc_start: 0.7546 (mtp) cc_final: 0.7267 (mtt)
REVERT: A  271 LYS cc_start: 0.7240 (mmmt) cc_final: 0.6891 (mmtm)
REVERT: A 1013 PRO cc_start: 0.7751 (Cg_endo) cc_final: 0.7159 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.6875 (m-80) cc_final: 0.6508 (m-80)
REVERT: A 1090 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6938 (mm)
REVERT: B  117 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6899 (ttp80)
REVERT: B  118 PHE cc_start: 0.7293 (t80) cc_final: 0.6846 (t80)
REVERT: B  221 ASN cc_start: 0.8048 (p0) cc_final: 0.7691 (p0)
REVERT: B  236 ARG cc_start: 0.7325 (mtp180) cc_final: 0.6745 (ttt180)
REVERT: B  261 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7411 (p0)
REVERT: C  113 LEU cc_start: 0.8951 (mm) cc_final: 0.8736 (mm)
REVERT: C  121 ILE cc_start: 0.2850 (mm) cc_final: 0.2506 (mm)
  outliers start: 44
  outliers final: 27
  residues processed: 194
  average time/residue: 0.2349
  time to fit residues: 64.0887
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  133 GLN
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
D  49 GLN
A 133 GLN
** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
A1275 GLN
B 259 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.203820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.154244 restraints weight = 14900.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.159453 restraints weight = 8096.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.163296 restraints weight = 5465.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9634  Z= 0.269
  Angle     :  0.647   7.258  13016  Z= 0.334
  Chirality :  0.046   0.195   1441
  Planarity :  0.005   0.056   1665
  Dihedral  :  5.057  21.305   1246
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 15.81 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.81 (0.25), residues: 1130
  helix:  0.76 (0.30), residues: 302
  sheet: -1.03 (0.34), residues: 227
  loop : -0.98 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.014   0.002   PHE B 218 
 TYR   0.012   0.002   TYR B 341 
 ARG   0.003   0.000   ARG A 150 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 176
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6441 (ptm)
REVERT: D   39 ASP cc_start: 0.7453 (t0) cc_final: 0.7147 (p0)
REVERT: D   54 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5861 (ttt180)
REVERT: D   60 ASN cc_start: 0.9036 (m-40) cc_final: 0.8756 (t0)
REVERT: A  156 MET cc_start: 0.7430 (mtp) cc_final: 0.7144 (mtt)
REVERT: A  271 LYS cc_start: 0.7125 (mmmt) cc_final: 0.6829 (mmtm)
REVERT: A  974 MET cc_start: 0.7028 (pmm) cc_final: 0.6484 (pmm)
REVERT: A 1013 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.6915 (Cg_exo)
REVERT: A 1090 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6885 (mm)
REVERT: A 1094 TYR cc_start: 0.8326 (t80) cc_final: 0.7989 (t80)
REVERT: B  117 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6725 (ttp80)
REVERT: B  118 PHE cc_start: 0.7163 (t80) cc_final: 0.6759 (t80)
REVERT: B  221 ASN cc_start: 0.7911 (p0) cc_final: 0.7548 (p0)
REVERT: B  236 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6727 (ttt180)
REVERT: C   83 ASN cc_start: 0.8085 (m-40) cc_final: 0.7871 (m110)
REVERT: C  113 LEU cc_start: 0.8968 (mm) cc_final: 0.8730 (mm)
REVERT: C  121 ILE cc_start: 0.2752 (mm) cc_final: 0.2417 (mm)
REVERT: C  180 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6094 (mm)
  outliers start: 45
  outliers final: 28
  residues processed: 203
  average time/residue: 0.2136
  time to fit residues: 61.2754
Evaluate side-chains
  199 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  133 GLN
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 72 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 133 GLN
A 581 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.202487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.152797 restraints weight = 14872.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.158111 restraints weight = 8043.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.161726 restraints weight = 5388.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9634  Z= 0.317
  Angle     :  0.675   9.613  13016  Z= 0.348
  Chirality :  0.047   0.147   1441
  Planarity :  0.005   0.056   1665
  Dihedral  :  5.143  19.794   1246
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.23 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.86 (0.25), residues: 1130
  helix:  0.73 (0.30), residues: 308
  sheet: -1.06 (0.33), residues: 232
  loop : -1.03 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.016   0.002   PHE A 292 
 TYR   0.012   0.002   TYR A 355 
 ARG   0.003   0.000   ARG A 150 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 168
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6445 (ptm)
REVERT: D   54 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6114 (ttp-170)
REVERT: D   60 ASN cc_start: 0.9092 (m-40) cc_final: 0.8781 (t0)
REVERT: A  156 MET cc_start: 0.7361 (mtp) cc_final: 0.7082 (mtt)
REVERT: A  271 LYS cc_start: 0.7115 (mmmt) cc_final: 0.6828 (mmtm)
REVERT: A  982 MET cc_start: 0.6145 (mmm) cc_final: 0.5117 (tmm)
REVERT: A 1013 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7040 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7081 (m-80) cc_final: 0.6603 (m-80)
REVERT: A 1090 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6897 (mm)
REVERT: A 1094 TYR cc_start: 0.8312 (t80) cc_final: 0.8002 (t80)
REVERT: B  117 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6708 (ttp80)
REVERT: B  118 PHE cc_start: 0.7165 (t80) cc_final: 0.6824 (t80)
REVERT: B  221 ASN cc_start: 0.7962 (p0) cc_final: 0.7580 (p0)
REVERT: B  236 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6697 (ttt180)
REVERT: C   83 ASN cc_start: 0.8127 (m-40) cc_final: 0.7905 (m110)
REVERT: C  113 LEU cc_start: 0.9000 (mm) cc_final: 0.8764 (mm)
REVERT: C  180 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6124 (mm)
  outliers start: 42
  outliers final: 27
  residues processed: 190
  average time/residue: 0.2124
  time to fit residues: 56.2219
Evaluate side-chains
  189 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.204232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.164749 restraints weight = 14820.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.170034 restraints weight = 8771.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.170157 restraints weight = 6335.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9634  Z= 0.209
  Angle     :  0.629   9.173  13016  Z= 0.326
  Chirality :  0.045   0.146   1441
  Planarity :  0.005   0.050   1665
  Dihedral  :  4.925  20.879   1246
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.52 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.58 (0.25), residues: 1130
  helix:  1.03 (0.30), residues: 295
  sheet: -0.92 (0.35), residues: 217
  loop : -0.85 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP C 171 
 HIS   0.003   0.001   HIS A 155 
 PHE   0.014   0.002   PHE B 247 
 TYR   0.013   0.001   TYR C 106 
 ARG   0.003   0.000   ARG B 104 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6256 (ptm)
REVERT: D   54 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6102 (ttt180)
REVERT: D   60 ASN cc_start: 0.8995 (m-40) cc_final: 0.8696 (t0)
REVERT: A  156 MET cc_start: 0.7207 (mtp) cc_final: 0.6954 (mtt)
REVERT: A  185 TYR cc_start: 0.7216 (t80) cc_final: 0.6735 (t80)
REVERT: A  239 LYS cc_start: 0.8175 (pttt) cc_final: 0.7814 (pttm)
REVERT: A  260 PHE cc_start: 0.6713 (m-10) cc_final: 0.6506 (m-10)
REVERT: A  271 LYS cc_start: 0.7260 (mmmt) cc_final: 0.6919 (mmtm)
REVERT: A 1013 PRO cc_start: 0.7827 (Cg_endo) cc_final: 0.7215 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7089 (m-80) cc_final: 0.6691 (m-80)
REVERT: A 1094 TYR cc_start: 0.8278 (t80) cc_final: 0.8019 (t80)
REVERT: B  117 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6839 (ttp80)
REVERT: B  118 PHE cc_start: 0.7044 (t80) cc_final: 0.6753 (t80)
REVERT: B  221 ASN cc_start: 0.7923 (p0) cc_final: 0.7538 (p0)
REVERT: B  236 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6655 (ttt180)
REVERT: C   83 ASN cc_start: 0.8219 (m-40) cc_final: 0.7953 (m110)
REVERT: C  113 LEU cc_start: 0.8951 (mm) cc_final: 0.8692 (mm)
REVERT: C  121 ILE cc_start: 0.2616 (mm) cc_final: 0.2293 (mm)
  outliers start: 36
  outliers final: 26
  residues processed: 190
  average time/residue: 0.2150
  time to fit residues: 58.0611
Evaluate side-chains
  191 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 88 optimal weight:   30.0000
   chunk 78 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** B 259 GLN ** 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 = 0.4589 r_free = 0.4589 target = 0.204154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.164164 restraints weight = 14992.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.170100 restraints weight = 9008.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.170090 restraints weight = 6252.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6716
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9634  Z= 0.259
  Angle     :  0.666  11.627  13016  Z= 0.347
  Chirality :  0.046   0.146   1441
  Planarity :  0.005   0.049   1665
  Dihedral  :  4.944  22.501   1246
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.37 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.65 (0.25), residues: 1130
  helix:  0.99 (0.30), residues: 301
  sheet: -1.09 (0.33), residues: 229
  loop : -0.86 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.016   0.002   PHE A1265 
 TYR   0.010   0.001   TYR C  96 
 ARG   0.003   0.000   ARG B 104 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6278 (ptm)
REVERT: D   39 ASP cc_start: 0.7364 (t0) cc_final: 0.6963 (p0)
REVERT: D   54 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6226 (ttt180)
REVERT: D   60 ASN cc_start: 0.9006 (m-40) cc_final: 0.8737 (t0)
REVERT: A  156 MET cc_start: 0.7256 (mtp) cc_final: 0.6999 (mtt)
REVERT: A  239 LYS cc_start: 0.8190 (pttt) cc_final: 0.7830 (pttm)
REVERT: A  271 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6861 (mmtm)
REVERT: A  982 MET cc_start: 0.6018 (mmm) cc_final: 0.5087 (tmm)
REVERT: A 1013 PRO cc_start: 0.8014 (Cg_endo) cc_final: 0.7441 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7127 (m-80) cc_final: 0.6789 (m-80)
REVERT: A 1090 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6978 (mm)
REVERT: A 1094 TYR cc_start: 0.8301 (t80) cc_final: 0.8022 (t80)
REVERT: B  117 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6832 (ttp80)
REVERT: B  118 PHE cc_start: 0.7041 (t80) cc_final: 0.6773 (t80)
REVERT: B  221 ASN cc_start: 0.7939 (p0) cc_final: 0.7549 (p0)
REVERT: B  236 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6639 (ttt180)
REVERT: C   83 ASN cc_start: 0.8129 (m-40) cc_final: 0.7882 (m110)
REVERT: C  113 LEU cc_start: 0.8922 (mm) cc_final: 0.8644 (mm)
REVERT: C  121 ILE cc_start: 0.2721 (mm) cc_final: 0.2388 (mm)
  outliers start: 37
  outliers final: 25
  residues processed: 179
  average time/residue: 0.2015
  time to fit residues: 51.7790
Evaluate side-chains
  179 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 14 optimal weight:    0.5980
   chunk 108 optimal weight:    0.0980
   chunk 71 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 ASN
** B 259 GLN ** 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 = 0.4594 r_free = 0.4594 target = 0.204588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.165159 restraints weight = 14769.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.169945 restraints weight = 8645.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.170543 restraints weight = 6254.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9634  Z= 0.242
  Angle     :  0.657   9.315  13016  Z= 0.340
  Chirality :  0.046   0.147   1441
  Planarity :  0.005   0.048   1665
  Dihedral  :  4.878  22.860   1246
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.03 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.63 (0.25), residues: 1130
  helix:  1.16 (0.31), residues: 295
  sheet: -1.15 (0.33), residues: 230
  loop : -0.88 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A  83 
 PHE   0.020   0.002   PHE B 247 
 TYR   0.011   0.001   TYR B 341 
 ARG   0.004   0.000   ARG C  77 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6172 (ptm)
REVERT: D   54 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6317 (ttt180)
REVERT: D   60 ASN cc_start: 0.9003 (m-40) cc_final: 0.8736 (t0)
REVERT: A  156 MET cc_start: 0.7229 (mtp) cc_final: 0.6989 (mtt)
REVERT: A  271 LYS cc_start: 0.7148 (mmmt) cc_final: 0.6849 (mmtm)
REVERT: A 1013 PRO cc_start: 0.8020 (Cg_endo) cc_final: 0.7440 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7025 (m-80) cc_final: 0.6809 (m-80)
REVERT: A 1090 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6933 (mm)
REVERT: A 1094 TYR cc_start: 0.8312 (t80) cc_final: 0.8065 (t80)
REVERT: A 1114 GLN cc_start: 0.7295 (tm-30) cc_final: 0.6986 (tm-30)
REVERT: B  117 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6703 (ttp80)
REVERT: B  118 PHE cc_start: 0.6995 (t80) cc_final: 0.6738 (t80)
REVERT: B  221 ASN cc_start: 0.7933 (p0) cc_final: 0.7534 (p0)
REVERT: B  236 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6622 (ttt180)
REVERT: C   83 ASN cc_start: 0.8286 (m-40) cc_final: 0.7971 (m110)
REVERT: C  113 LEU cc_start: 0.8960 (mm) cc_final: 0.8665 (mm)
REVERT: C  121 ILE cc_start: 0.2870 (mm) cc_final: 0.2409 (mm)
  outliers start: 33
  outliers final: 27
  residues processed: 175
  average time/residue: 0.2036
  time to fit residues: 51.4033
Evaluate side-chains
  185 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    0.1980
   chunk 49 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0070
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0770
   chunk 36 optimal weight:    0.0040
   overall best weight:    0.1968

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 581 ASN
** A1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  85 GLN ** 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 = 0.4631 r_free = 0.4631 target = 0.208280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.169280 restraints weight = 14967.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.171288 restraints weight = 8236.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.172783 restraints weight = 6889.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9634  Z= 0.176
  Angle     :  0.644   9.479  13016  Z= 0.332
  Chirality :  0.045   0.201   1441
  Planarity :  0.005   0.043   1665
  Dihedral  :  4.734  22.630   1246
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.60 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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: -0.54 (0.25), residues: 1130
  helix:  1.21 (0.31), residues: 290
  sheet: -1.05 (0.34), residues: 220
  loop : -0.83 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.002   TRP C 171 
 HIS   0.003   0.000   HIS A 155 
 PHE   0.022   0.001   PHE B 247 
 TYR   0.009   0.001   TYR C 106 
 ARG   0.003   0.000   ARG A1107 

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7033 (ptm) cc_final: 0.6216 (ptm)
REVERT: D   39 ASP cc_start: 0.7522 (t0) cc_final: 0.7096 (t0)
REVERT: D   54 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6316 (ttt180)
REVERT: D   60 ASN cc_start: 0.8994 (m-40) cc_final: 0.8747 (t0)
REVERT: A  156 MET cc_start: 0.7196 (mtp) cc_final: 0.6989 (mtt)
REVERT: A  271 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6934 (mmtm)
REVERT: A  982 MET cc_start: 0.6215 (mmm) cc_final: 0.5209 (tpt)
REVERT: A 1013 PRO cc_start: 0.7936 (Cg_endo) cc_final: 0.7362 (Cg_exo)
REVERT: A 1090 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6947 (mm)
REVERT: A 1095 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7649 (mm-30)
REVERT: A 1114 GLN cc_start: 0.7247 (tm-30) cc_final: 0.7007 (tm-30)
REVERT: B  117 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6565 (ttp80)
REVERT: B  221 ASN cc_start: 0.7942 (p0) cc_final: 0.7565 (p0)
REVERT: B  236 ARG cc_start: 0.7203 (mtp180) cc_final: 0.6631 (ttt180)
REVERT: C   83 ASN cc_start: 0.8251 (m-40) cc_final: 0.7943 (m110)
REVERT: C  106 TYR cc_start: 0.8473 (m-80) cc_final: 0.8114 (m-80)
REVERT: C  113 LEU cc_start: 0.8989 (mm) cc_final: 0.8681 (mm)
REVERT: C  121 ILE cc_start: 0.2651 (mm) cc_final: 0.2336 (mm)
  outliers start: 28
  outliers final: 20
  residues processed: 181
  average time/residue: 0.2064
  time to fit residues: 53.1917
Evaluate side-chains
  177 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  288 VAL
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 22 optimal weight:    0.1980
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 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 = 0.4580 r_free = 0.4580 target = 0.203416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.162911 restraints weight = 14881.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.165711 restraints weight = 8851.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.166794 restraints weight = 7294.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9634  Z= 0.302
  Angle     :  0.694   8.754  13016  Z= 0.359
  Chirality :  0.047   0.317   1441
  Planarity :  0.005   0.047   1665
  Dihedral  :  4.934  22.521   1246
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.64 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    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 (0.25), residues: 1130
  helix:  1.01 (0.30), residues: 295
  sheet: -1.11 (0.33), residues: 230
  loop : -0.88 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.085   0.003   TRP C 171 
 HIS   0.008   0.001   HIS C 100 
 PHE   0.028   0.002   PHE B 118 
 TYR   0.014   0.002   TYR C 233 
 ARG   0.005   0.000   ARG A1107 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3351.21 seconds
wall clock time: 60 minutes 53.77 seconds (3653.77 seconds total)