Starting phenix.real_space_refine
on Fri Mar 14 02:59:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7un3_26612/03_2025/7un3_26612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7un3_26612/03_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_26612/03_2025/7un3_26612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2025/7un3_26612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2025/7un3_26612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_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-5624/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: 5.72, 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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.13
  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: 2.94

  Time building geometry restraints manager: 2.89 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.400
  Find NCS groups from input model:        0.200
  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:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.560
-------------------------------------------------------------------------------
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  : 1.059 
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: 0.2388
  time to fit residues: 82.3308
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  : 1.009 
-------------------------------------------------------------------------------
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 = 0.163050 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 = 9411.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167136 restraints weight = 7528.666|
|-----------------------------------------------------------------------------|
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  : 1.088 
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: 0.6485 (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: 0.2219
  time to fit residues: 63.7246
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  : 1.024 
-------------------------------------------------------------------------------
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:    0.2980
   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:    0.8980
   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:    0.0000
   overall best weight:    0.6388

-------------------------------------------------------------------------------
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 = 0.4609 r_free = 0.4609 target = 0.206459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.167085 restraints weight = 14816.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.169499 restraints weight = 8815.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.170819 restraints weight = 7319.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9634  Z= 0.215
  Angle     :  0.642   6.631  13016  Z= 0.332
  Chirality :  0.046   0.187   1441
  Planarity :  0.005   0.045   1665
  Dihedral  :  5.072  22.319   1246
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.16 %
    Favored  : 84.00 %
  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: -0.61 (0.25), residues: 1130
  helix:  0.90 (0.30), residues: 296
  sheet: -0.67 (0.35), residues: 229
  loop : -0.93 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 308 
 HIS   0.007   0.001   HIS B 328 
 PHE   0.014   0.002   PHE B 218 
 TYR   0.014   0.002   TYR B  96 
 ARG   0.004   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
  212 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 1.047 
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: 0.7303 (OUTLIER) cc_final: 0.6767 (ptm)
REVERT: D   49 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5606 (tp40)
REVERT: A  156 MET cc_start: 0.7413 (mtp) cc_final: 0.7186 (mtt)
REVERT: A  271 LYS cc_start: 0.7276 (mmmt) cc_final: 0.6917 (mmtm)
REVERT: A  707 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8398 (tp)
REVERT: A 1084 PHE cc_start: 0.6910 (m-80) cc_final: 0.6591 (m-80)
REVERT: A 1285 MET cc_start: 0.6543 (mmp) cc_final: 0.6302 (mmt)
REVERT: B  110 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6625 (t80)
REVERT: B  117 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7013 (ttp80)
REVERT: B  118 PHE cc_start: 0.7266 (t80) cc_final: 0.6929 (t80)
REVERT: B  221 ASN cc_start: 0.7997 (p0) cc_final: 0.7683 (p0)
REVERT: C  113 LEU cc_start: 0.8885 (mm) cc_final: 0.8665 (mm)
  outliers start: 30
  outliers final: 13
  residues processed: 196
  average time/residue: 0.2366
  time to fit residues: 64.2012
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
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 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:    0.0570
   chunk 58 optimal weight:    0.9990
   chunk 68 optimal weight:    8.9990
   chunk 90 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 47 optimal weight:   20.0000
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.9904

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.206549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.167073 restraints weight = 14908.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.169286 restraints weight = 8778.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.170284 restraints weight = 7272.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9634  Z= 0.251
  Angle     :  0.635   9.401  13016  Z= 0.328
  Chirality :  0.046   0.171   1441
  Planarity :  0.005   0.046   1665
  Dihedral  :  5.008  20.385   1246
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.58 %
    Favored  : 82.20 %
  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:  0.78 (0.29), residues: 308
  sheet: -0.70 (0.35), residues: 227
  loop : -0.94 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.015   0.002   PHE B 218 
 TYR   0.014   0.002   TYR C 223 
 ARG   0.003   0.000   ARG B  77 

*********************** 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
  200 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 1.152 
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: 0.7286 (OUTLIER) cc_final: 0.6768 (ptm)
REVERT: D   39 ASP cc_start: 0.7239 (t0) cc_final: 0.7028 (p0)
REVERT: D   54 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5817 (ttt180)
REVERT: A  156 MET cc_start: 0.7419 (mtp) cc_final: 0.7180 (mtt)
REVERT: A  271 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6974 (mmtm)
REVERT: A 1084 PHE cc_start: 0.6860 (m-80) cc_final: 0.6476 (m-80)
REVERT: A 1285 MET cc_start: 0.6766 (mmp) cc_final: 0.6546 (mmt)
REVERT: B  110 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6828 (t80)
REVERT: B  117 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6892 (ttp80)
REVERT: B  118 PHE cc_start: 0.7144 (t80) cc_final: 0.6776 (t80)
REVERT: B  221 ASN cc_start: 0.8059 (p0) cc_final: 0.7705 (p0)
REVERT: B  236 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6767 (ttt-90)
REVERT: B  261 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7234 (p0)
REVERT: C  121 ILE cc_start: 0.2877 (mm) cc_final: 0.2563 (mm)
  outliers start: 34
  outliers final: 20
  residues processed: 187
  average time/residue: 0.2536
  time to fit residues: 67.5219
Evaluate side-chains
  182 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
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 1097 SER
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  235 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  339 VAL
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:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 18 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.3984

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.203993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.163423 restraints weight = 14762.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.166160 restraints weight = 8702.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.167142 restraints weight = 6762.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.3927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9634  Z= 0.298
  Angle     :  0.655  10.153  13016  Z= 0.336
  Chirality :  0.047   0.300   1441
  Planarity :  0.005   0.051   1665
  Dihedral  :  4.991  18.567   1246
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 15.34 %
    Favored  : 80.87 %
  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: -0.71 (0.25), residues: 1130
  helix:  0.84 (0.30), residues: 302
  sheet: -0.82 (0.34), residues: 231
  loop : -0.98 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.016   0.002   PHE C 170 
 TYR   0.012   0.002   TYR C 106 
 ARG   0.004   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
  213 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 1.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6340 (ptm)
REVERT: D   31 GLN cc_start: 0.6121 (tp40) cc_final: 0.5897 (tp40)
REVERT: D   39 ASP cc_start: 0.7404 (t0) cc_final: 0.7138 (p0)
REVERT: D   54 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.5901 (ttt180)
REVERT: A  156 MET cc_start: 0.7490 (mtp) cc_final: 0.7226 (mtt)
REVERT: A  260 PHE cc_start: 0.6812 (m-10) cc_final: 0.6603 (m-10)
REVERT: A  271 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6903 (mmtm)
REVERT: A 1013 PRO cc_start: 0.7691 (Cg_endo) cc_final: 0.7092 (Cg_exo)
REVERT: A 1090 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6949 (mm)
REVERT: A 1094 TYR cc_start: 0.8212 (t80) cc_final: 0.7926 (t80)
REVERT: B  117 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6828 (ttp80)
REVERT: B  118 PHE cc_start: 0.7170 (t80) cc_final: 0.6781 (t80)
REVERT: B  221 ASN cc_start: 0.7985 (p0) cc_final: 0.7611 (p0)
REVERT: B  236 ARG cc_start: 0.7267 (mtp180) cc_final: 0.6724 (ttt180)
REVERT: C   83 ASN cc_start: 0.8115 (m-40) cc_final: 0.7872 (m110)
REVERT: C  121 ILE cc_start: 0.2837 (mm) cc_final: 0.2438 (mm)
  outliers start: 40
  outliers final: 24
  residues processed: 197
  average time/residue: 0.2297
  time to fit residues: 64.6812
Evaluate side-chains
  181 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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  287 SER
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  684 VAL
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 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  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:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.0384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.204474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.163846 restraints weight = 14874.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.167190 restraints weight = 8536.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.168002 restraints weight = 6476.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9634  Z= 0.249
  Angle     :  0.631   8.702  13016  Z= 0.326
  Chirality :  0.045   0.138   1441
  Planarity :  0.005   0.049   1665
  Dihedral  :  4.939  18.395   1246
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.86 %
    Favored  : 79.83 %
  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: -0.67 (0.25), residues: 1130
  helix:  1.02 (0.30), residues: 296
  sheet: -1.05 (0.34), residues: 223
  loop : -0.91 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 578 
 PHE   0.014   0.002   PHE B 218 
 TYR   0.010   0.001   TYR B 233 
 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
  204 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6298 (ptm)
REVERT: D   54 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.5929 (ttt180)
REVERT: A  156 MET cc_start: 0.7456 (mtp) cc_final: 0.7186 (mtt)
REVERT: A  171 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7212 (mm)
REVERT: A  271 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6924 (mmtm)
REVERT: A  553 THR cc_start: 0.8121 (p) cc_final: 0.7903 (p)
REVERT: A 1013 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7166 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7078 (m-80) cc_final: 0.6617 (m-80)
REVERT: A 1090 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6946 (mm)
REVERT: A 1094 TYR cc_start: 0.8298 (t80) cc_final: 0.8001 (t80)
REVERT: A 1285 MET cc_start: 0.5988 (mmm) cc_final: 0.5660 (mtt)
REVERT: B   85 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7832 (mm-40)
REVERT: B   98 GLU cc_start: 0.8502 (tp30) cc_final: 0.8049 (tp30)
REVERT: B  117 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6777 (ttp80)
REVERT: B  118 PHE cc_start: 0.7129 (t80) cc_final: 0.6861 (t80)
REVERT: B  221 ASN cc_start: 0.7971 (p0) cc_final: 0.7591 (p0)
REVERT: B  236 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6709 (ttt180)
REVERT: C   83 ASN cc_start: 0.8205 (m-40) cc_final: 0.7956 (m110)
REVERT: C  121 ILE cc_start: 0.2819 (mm) cc_final: 0.2342 (mm)
  outliers start: 35
  outliers final: 25
  residues processed: 187
  average time/residue: 0.2102
  time to fit residues: 54.8840
Evaluate side-chains
  193 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  171 ILE
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 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  256 THR
Chi-restraints excluded: chain C residue  300 PHE
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:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.206148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.166780 restraints weight = 14922.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.168966 restraints weight = 8877.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.170079 restraints weight = 7760.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9634  Z= 0.218
  Angle     :  0.623   8.644  13016  Z= 0.324
  Chirality :  0.045   0.139   1441
  Planarity :  0.005   0.047   1665
  Dihedral  :  4.844  18.297   1246
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.71 %
    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: -0.52 (0.25), residues: 1130
  helix:  1.20 (0.31), residues: 289
  sheet: -1.03 (0.34), residues: 227
  loop : -0.78 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.014   0.002   PHE B 218 
 TYR   0.012   0.001   TYR C 106 
 ARG   0.004   0.000   ARG A1107 

*********************** 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
  197 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6268 (ptm)
REVERT: D   31 GLN cc_start: 0.6230 (tp40) cc_final: 0.5931 (tp40)
REVERT: D   39 ASP cc_start: 0.7422 (t0) cc_final: 0.7154 (p0)
REVERT: D   54 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5937 (ttt180)
REVERT: A  156 MET cc_start: 0.7436 (mtp) cc_final: 0.7168 (mtt)
REVERT: A  171 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7265 (mm)
REVERT: A  260 PHE cc_start: 0.6732 (m-10) cc_final: 0.6530 (m-10)
REVERT: A  271 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6906 (mmtm)
REVERT: A  553 THR cc_start: 0.8117 (p) cc_final: 0.7879 (p)
REVERT: A  581 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8157 (t0)
REVERT: A  982 MET cc_start: 0.6108 (mmm) cc_final: 0.5054 (tmm)
REVERT: A 1013 PRO cc_start: 0.7814 (Cg_endo) cc_final: 0.7197 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7068 (m-80) cc_final: 0.6665 (m-80)
REVERT: A 1090 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6949 (mm)
REVERT: A 1094 TYR cc_start: 0.8286 (t80) cc_final: 0.8034 (t80)
REVERT: A 1285 MET cc_start: 0.6042 (mmm) cc_final: 0.5754 (mtt)
REVERT: B   85 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7820 (mm-40)
REVERT: B  117 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6756 (ttp80)
REVERT: B  118 PHE cc_start: 0.7075 (t80) cc_final: 0.6828 (t80)
REVERT: B  221 ASN cc_start: 0.7963 (p0) cc_final: 0.7589 (p0)
REVERT: B  236 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6733 (ttt180)
REVERT: C   83 ASN cc_start: 0.8153 (m-40) cc_final: 0.7923 (m110)
REVERT: C  121 ILE cc_start: 0.2877 (mm) cc_final: 0.2406 (mm)
  outliers start: 34
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2125
  time to fit residues: 54.9469
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  171 ILE
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  327 VAL
Chi-restraints excluded: chain A residue  581 ASN
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  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue   77 ARG
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:    0.6980
   chunk 88 optimal weight:   20.0000
   chunk 78 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4610 r_free = 0.4610 target = 0.206186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.166526 restraints weight = 15159.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.172274 restraints weight = 9273.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.172413 restraints weight = 6425.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.4524

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= 0.221
  Angle     :  0.615   9.479  13016  Z= 0.319
  Chirality :  0.045   0.143   1441
  Planarity :  0.005   0.045   1665
  Dihedral  :  4.765  18.048   1246
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  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: -0.55 (0.25), residues: 1130
  helix:  1.09 (0.30), residues: 295
  sheet: -1.04 (0.34), residues: 233
  loop : -0.77 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.016   0.002   PHE C 170 
 TYR   0.009   0.001   TYR C  96 
 ARG   0.004   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
  197 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 1.031 
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: 0.7117 (OUTLIER) cc_final: 0.6344 (ptm)
REVERT: D   39 ASP cc_start: 0.7421 (t0) cc_final: 0.6755 (p0)
REVERT: D   54 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5974 (ttt180)
REVERT: D   59 TYR cc_start: 0.7384 (m-80) cc_final: 0.7080 (m-80)
REVERT: A  156 MET cc_start: 0.7359 (mtp) cc_final: 0.7102 (mtt)
REVERT: A  171 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7294 (mm)
REVERT: A  271 LYS cc_start: 0.7235 (mmmt) cc_final: 0.6904 (mmtm)
REVERT: A  553 THR cc_start: 0.8100 (p) cc_final: 0.7867 (p)
REVERT: A  982 MET cc_start: 0.6121 (mmm) cc_final: 0.5052 (tmm)
REVERT: A 1013 PRO cc_start: 0.7858 (Cg_endo) cc_final: 0.7250 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7053 (m-80) cc_final: 0.6681 (m-80)
REVERT: A 1090 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6971 (mm)
REVERT: A 1094 TYR cc_start: 0.8304 (t80) cc_final: 0.8080 (t80)
REVERT: B   85 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7814 (mm-40)
REVERT: B  117 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6785 (ttp80)
REVERT: B  118 PHE cc_start: 0.7027 (t80) cc_final: 0.6738 (t80)
REVERT: B  221 ASN cc_start: 0.7919 (p0) cc_final: 0.7570 (p0)
REVERT: B  236 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6688 (ttt180)
REVERT: C   83 ASN cc_start: 0.8158 (m-40) cc_final: 0.7914 (m110)
REVERT: C  121 ILE cc_start: 0.2770 (mm) cc_final: 0.2237 (mm)
  outliers start: 36
  outliers final: 24
  residues processed: 182
  average time/residue: 0.2094
  time to fit residues: 53.8924
Evaluate side-chains
  186 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
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  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  171 ILE
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  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  288 VAL
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 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:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0060
   chunk 61 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
A 226 ASN
A 581 ASN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.204684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.165953 restraints weight = 14789.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.171606 restraints weight = 8919.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.171988 restraints weight = 5945.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9634  Z= 0.201
  Angle     :  0.633  13.078  13016  Z= 0.329
  Chirality :  0.045   0.150   1441
  Planarity :  0.004   0.043   1665
  Dihedral  :  4.714  22.555   1246
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.99 %
    Favored  : 79.36 %
  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: -0.51 (0.25), residues: 1130
  helix:  1.17 (0.31), residues: 295
  sheet: -1.06 (0.33), residues: 234
  loop : -0.76 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP C 171 
 HIS   0.003   0.001   HIS A 155 
 PHE   0.017   0.002   PHE A1265 
 TYR   0.011   0.001   TYR C 106 
 ARG   0.005   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
  193 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 165
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7070 (ptm) cc_final: 0.6311 (ptm)
REVERT: D   54 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5978 (ttt180)
REVERT: A  156 MET cc_start: 0.7233 (mtp) cc_final: 0.6998 (mtt)
REVERT: A  171 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7391 (mm)
REVERT: A  271 LYS cc_start: 0.7213 (mmmt) cc_final: 0.6948 (mmtm)
REVERT: A  553 THR cc_start: 0.8021 (p) cc_final: 0.7796 (p)
REVERT: A  982 MET cc_start: 0.6133 (mmm) cc_final: 0.5122 (tmm)
REVERT: A 1013 PRO cc_start: 0.7966 (Cg_endo) cc_final: 0.7381 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7029 (m-80) cc_final: 0.6741 (m-80)
REVERT: A 1090 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6958 (mm)
REVERT: A 1095 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7567 (mm-30)
REVERT: A 1114 GLN cc_start: 0.7314 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: B   85 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7855 (mm-40)
REVERT: B  118 PHE cc_start: 0.6926 (t80) cc_final: 0.6725 (t80)
REVERT: B  221 ASN cc_start: 0.7885 (p0) cc_final: 0.7550 (p0)
REVERT: B  236 ARG cc_start: 0.7275 (mtp180) cc_final: 0.6764 (ttt180)
REVERT: C  106 TYR cc_start: 0.8434 (m-80) cc_final: 0.8189 (m-80)
REVERT: C  121 ILE cc_start: 0.2852 (mm) cc_final: 0.2259 (mm)
  outliers start: 28
  outliers final: 21
  residues processed: 180
  average time/residue: 0.2029
  time to fit residues: 51.8778
Evaluate side-chains
  182 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
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  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  581 ASN
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  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  192 ILE
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:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.204291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.165137 restraints weight = 15001.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.168173 restraints weight = 9023.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.169205 restraints weight = 7282.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.4862

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= 0.211
  Angle     :  0.642  10.185  13016  Z= 0.333
  Chirality :  0.045   0.145   1441
  Planarity :  0.005   0.043   1665
  Dihedral  :  4.677  21.088   1246
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.37 %
    Favored  : 78.88 %
  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: -0.51 (0.25), residues: 1130
  helix:  1.13 (0.30), residues: 295
  sheet: -1.01 (0.33), residues: 234
  loop : -0.75 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.018   0.002   PHE C 170 
 TYR   0.013   0.001   TYR A 185 
 ARG   0.004   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
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6465 (ptm)
REVERT: D   54 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6297 (ttt180)
REVERT: A  156 MET cc_start: 0.7272 (mtp) cc_final: 0.7042 (mtt)
REVERT: A  171 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7435 (mm)
REVERT: A  271 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6946 (mmtm)
REVERT: A  553 THR cc_start: 0.8037 (p) cc_final: 0.7787 (p)
REVERT: A  982 MET cc_start: 0.6174 (mmm) cc_final: 0.5161 (tmm)
REVERT: A 1013 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7420 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.7055 (m-80) cc_final: 0.6774 (m-80)
REVERT: A 1090 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6937 (mm)
REVERT: A 1095 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7562 (mm-30)
REVERT: A 1114 GLN cc_start: 0.7294 (tm-30) cc_final: 0.7013 (tm-30)
REVERT: B   85 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7882 (mm-40)
REVERT: B  118 PHE cc_start: 0.6942 (t80) cc_final: 0.6692 (t80)
REVERT: B  221 ASN cc_start: 0.7972 (p0) cc_final: 0.7632 (p0)
REVERT: B  236 ARG cc_start: 0.7276 (mtp180) cc_final: 0.6772 (ttt180)
REVERT: C  121 ILE cc_start: 0.3020 (mm) cc_final: 0.2491 (mm)
  outliers start: 29
  outliers final: 23
  residues processed: 175
  average time/residue: 0.1918
  time to fit residues: 48.4719
Evaluate side-chains
  182 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
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  134 HIS
Chi-restraints excluded: chain A residue  151 ASP
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 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  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  192 ILE
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:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0270
   chunk 103 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** C 111 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 = 0.4582 r_free = 0.4582 target = 0.203401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.163317 restraints weight = 14996.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.165445 restraints weight = 9241.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.166667 restraints weight = 7770.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9634  Z= 0.301
  Angle     :  0.685   9.911  13016  Z= 0.358
  Chirality :  0.047   0.185   1441
  Planarity :  0.005   0.049   1665
  Dihedral  :  4.888  20.578   1246
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.84 %
    Favored  : 78.22 %
  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: -0.72 (0.25), residues: 1130
  helix:  0.98 (0.30), residues: 296
  sheet: -1.21 (0.32), residues: 245
  loop : -0.85 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.002   TRP C 171 
 HIS   0.008   0.001   HIS C 100 
 PHE   0.029   0.002   PHE C 170 
 TYR   0.019   0.002   TYR A1094 
 ARG   0.006   0.001   ARG A1107 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3695.08 seconds
wall clock time: 66 minutes 16.57 seconds (3976.57 seconds total)