Starting phenix.real_space_refine
on Wed Mar  4 00:20:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_26612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_26612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_26612.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_26612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7un3_26612/03_2026/7un3_26612.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.13, per 1000 atoms: 0.23
  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: 0.58
  Conformation dependent library (CDL) restraints added in 341.4 milliseconds
  

  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: 0.32
  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: 1.46

  Time building geometry restraints manager: 0.77 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:             2.530
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.960
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.010
-------------------------------------------------------------------------------
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= 0.142
  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 : 13.47
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.015   0.001   ARG A1088 
 TYR   0.021   0.002   TYR A1100 
 PHE   0.014   0.001   PHE A 622 
 TRP   0.009   0.001   TRP C 171 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9634)
  covalent geometry    : angle       0.61220 (13016)
  hydrogen bonds       : bond        0.12789 (  375)
  hydrogen bonds       : angle       6.47472 ( 1053)

*********************** 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  : 0.346 
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: 0.5816 (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: 0.6998 (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: 0.6001 (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: 0.0976
  time to fit residues: 34.0395
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  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.3980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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
A 581 ASN
A 582 ASN
B 188 HIS
** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 GLN
C 122 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.208728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.170032 restraints weight = 14949.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.172854 restraints weight = 8897.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.173942 restraints weight = 7346.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.175067 restraints weight = 5131.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.175724 restraints weight = 4589.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.2241

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= 0.170
  Angle     :  0.677   7.731  13016  Z= 0.352
  Chirality :  0.048   0.196   1441
  Planarity :  0.005   0.045   1665
  Dihedral  :  5.082  22.214   1246
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.08 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.25), residues: 1130
  helix:  0.97 (0.30), residues: 296
  sheet: -0.52 (0.34), residues: 239
  loop : -0.85 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1117 
 TYR   0.017   0.002   TYR B  96 
 PHE   0.026   0.002   PHE A1084 
 TRP   0.013   0.002   TRP A1145 
 HIS   0.008   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 9634)
  covalent geometry    : angle       0.67704 (13016)
  hydrogen bonds       : bond        0.04137 (  375)
  hydrogen bonds       : angle       5.34308 ( 1053)

*********************** 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
  213 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   21 ASP cc_start: 0.7205 (t70) cc_final: 0.6970 (t70)
REVERT: D   59 TYR cc_start: 0.7749 (m-80) cc_final: 0.7544 (m-80)
REVERT: A  190 LYS cc_start: 0.7297 (mmtt) cc_final: 0.7037 (tppt)
REVERT: A  199 MET cc_start: 0.7156 (mtp) cc_final: 0.6783 (mtp)
REVERT: A  552 MET cc_start: 0.6534 (ttt) cc_final: 0.6323 (ttp)
REVERT: A  974 MET cc_start: 0.6408 (ppp) cc_final: 0.5811 (ppp)
REVERT: A 1084 PHE cc_start: 0.6870 (m-80) cc_final: 0.6072 (m-80)
REVERT: A 1285 MET cc_start: 0.6462 (mmp) cc_final: 0.6073 (mmt)
REVERT: C  325 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6600 (mm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 204
  average time/residue: 0.0964
  time to fit residues: 27.2591
Evaluate side-chains
  171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  276 VAL
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 1258 LEU
Chi-restraints excluded: chain B residue  111 GLN
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 62 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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
A1024 GLN
B  90 GLN
** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS
C  90 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.208120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.169364 restraints weight = 14978.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.171217 restraints weight = 9037.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.172553 restraints weight = 7922.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.174088 restraints weight = 5359.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.174583 restraints weight = 4726.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9634  Z= 0.159
  Angle     :  0.644   7.410  13016  Z= 0.331
  Chirality :  0.046   0.202   1441
  Planarity :  0.005   0.052   1665
  Dihedral  :  4.944  19.251   1246
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.59 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.25), residues: 1130
  helix:  0.92 (0.29), residues: 297
  sheet: -0.50 (0.34), residues: 237
  loop : -0.84 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.012   0.002   TYR B  96 
 PHE   0.020   0.002   PHE B  95 
 TRP   0.017   0.002   TRP A 308 
 HIS   0.006   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9634)
  covalent geometry    : angle       0.64440 (13016)
  hydrogen bonds       : bond        0.03956 (  375)
  hydrogen bonds       : angle       5.16157 ( 1053)

*********************** 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
  203 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 174
  time to evaluate  : 0.354 
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: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6697 (ptm)
REVERT: D   49 GLN cc_start: 0.5528 (tp40) cc_final: 0.5271 (tp40)
REVERT: D   59 TYR cc_start: 0.7630 (m-80) cc_final: 0.7428 (m-80)
REVERT: A  190 LYS cc_start: 0.7408 (mmtt) cc_final: 0.7189 (tppt)
REVERT: A  271 LYS cc_start: 0.7486 (mmmt) cc_final: 0.7184 (mmtm)
REVERT: A 1084 PHE cc_start: 0.6588 (m-80) cc_final: 0.6349 (m-80)
REVERT: A 1285 MET cc_start: 0.6549 (mmp) cc_final: 0.6192 (mmt)
REVERT: B  117 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6973 (ttp80)
REVERT: B  118 PHE cc_start: 0.7229 (t80) cc_final: 0.6990 (t80)
REVERT: B  221 ASN cc_start: 0.7898 (p0) cc_final: 0.7602 (p0)
REVERT: B  332 GLU cc_start: 0.6579 (pt0) cc_final: 0.6325 (pt0)
REVERT: C  170 PHE cc_start: 0.3858 (t80) cc_final: 0.3475 (t80)
REVERT: C  171 TRP cc_start: 0.6294 (m-90) cc_final: 0.4679 (m-90)
  outliers start: 29
  outliers final: 15
  residues processed: 187
  average time/residue: 0.1002
  time to fit residues: 25.7493
Evaluate side-chains
  175 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
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  276 VAL
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  579 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  235 MET
Chi-restraints excluded: chain B residue  339 VAL
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 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0770
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 99 optimal weight:    0.2980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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
A 680 GLN
A1275 GLN
B 221 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.210528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.171749 restraints weight = 14982.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.174665 restraints weight = 8535.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.176078 restraints weight = 6884.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.176869 restraints weight = 4911.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.177948 restraints weight = 4471.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.3267

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= 0.126
  Angle     :  0.605   7.195  13016  Z= 0.312
  Chirality :  0.045   0.166   1441
  Planarity :  0.005   0.050   1665
  Dihedral  :  4.767  21.473   1246
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.02 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.25), residues: 1130
  helix:  1.08 (0.30), residues: 297
  sheet: -0.68 (0.33), residues: 243
  loop : -0.74 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 236 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.020   0.002   PHE B  95 
 TRP   0.012   0.001   TRP A1145 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9634)
  covalent geometry    : angle       0.60547 (13016)
  hydrogen bonds       : bond        0.03669 (  375)
  hydrogen bonds       : angle       4.98427 ( 1053)

*********************** 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
  209 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.347 
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: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6723 (ptm)
REVERT: D   49 GLN cc_start: 0.5718 (tp40) cc_final: 0.5510 (tp40)
REVERT: A  271 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7226 (mmtm)
REVERT: A 1084 PHE cc_start: 0.6614 (m-80) cc_final: 0.6388 (m-80)
REVERT: A 1094 TYR cc_start: 0.8158 (t80) cc_final: 0.7952 (t80)
REVERT: A 1285 MET cc_start: 0.6673 (mmp) cc_final: 0.6362 (mmt)
REVERT: B   98 GLU cc_start: 0.8417 (tp30) cc_final: 0.7919 (tp30)
REVERT: B  110 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6858 (t80)
REVERT: B  117 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7004 (ttp80)
REVERT: B  118 PHE cc_start: 0.7191 (t80) cc_final: 0.6883 (t80)
REVERT: B  221 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7508 (p0)
REVERT: B  332 GLU cc_start: 0.6432 (pt0) cc_final: 0.6180 (pt0)
REVERT: C  170 PHE cc_start: 0.3922 (t80) cc_final: 0.3579 (t80)
REVERT: C  171 TRP cc_start: 0.6309 (m-90) cc_final: 0.4744 (m-90)
  outliers start: 34
  outliers final: 18
  residues processed: 196
  average time/residue: 0.1020
  time to fit residues: 27.6234
Evaluate side-chains
  180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  222 LEU
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  549 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain B residue   88 CYS
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  221 ASN
Chi-restraints excluded: chain B residue  248 ASP
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 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** B  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.210386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.171606 restraints weight = 15066.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.176609 restraints weight = 8937.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.177269 restraints weight = 6537.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.177410 restraints weight = 4714.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.178090 restraints weight = 4358.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9634  Z= 0.134
  Angle     :  0.616  11.914  13016  Z= 0.315
  Chirality :  0.046   0.319   1441
  Planarity :  0.005   0.045   1665
  Dihedral  :  4.686  23.534   1246
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.25), residues: 1130
  helix:  1.14 (0.30), residues: 295
  sheet: -0.69 (0.33), residues: 244
  loop : -0.71 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 236 
 TYR   0.012   0.001   TYR C 106 
 PHE   0.015   0.002   PHE A 292 
 TRP   0.012   0.001   TRP A1145 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9634)
  covalent geometry    : angle       0.61618 (13016)
  hydrogen bonds       : bond        0.03653 (  375)
  hydrogen bonds       : angle       4.90506 ( 1053)

*********************** 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
  202 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6405 (ptm)
REVERT: D   49 GLN cc_start: 0.5856 (tp40) cc_final: 0.5557 (tp40)
REVERT: D   54 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5680 (ttt180)
REVERT: A  271 LYS cc_start: 0.7488 (mmmt) cc_final: 0.7217 (mmtm)
REVERT: A  930 SER cc_start: 0.8335 (t) cc_final: 0.7858 (m)
REVERT: A  982 MET cc_start: 0.6007 (mmm) cc_final: 0.4901 (tmm)
REVERT: A 1090 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6965 (mm)
REVERT: A 1112 MET cc_start: 0.7087 (mmt) cc_final: 0.6859 (mmt)
REVERT: B   98 GLU cc_start: 0.8405 (tp30) cc_final: 0.7952 (tp30)
REVERT: B  110 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.7022 (t80)
REVERT: B  117 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6786 (ttp80)
REVERT: B  118 PHE cc_start: 0.7086 (t80) cc_final: 0.6845 (t80)
REVERT: B  221 ASN cc_start: 0.7865 (p0) cc_final: 0.7647 (p0)
REVERT: B  332 GLU cc_start: 0.6645 (pt0) cc_final: 0.6317 (pt0)
REVERT: C  170 PHE cc_start: 0.3871 (t80) cc_final: 0.3508 (t80)
REVERT: C  171 TRP cc_start: 0.6377 (m-90) cc_final: 0.4936 (m-90)
  outliers start: 35
  outliers final: 22
  residues processed: 186
  average time/residue: 0.0954
  time to fit residues: 25.1035
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  : 0.340 
-------------------------------------------------------------------------------
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  222 LEU
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  549 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1258 LEU
Chi-restraints excluded: chain A residue 1261 LEU
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  248 ASP
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  300 PHE
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 26 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 85 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
** B  85 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 = 0.4566 r_free = 0.4566 target = 0.201789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.161051 restraints weight = 15130.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.163553 restraints weight = 9232.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.164462 restraints weight = 8017.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.165434 restraints weight = 5548.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.168872 restraints weight = 4961.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9634  Z= 0.274
  Angle     :  0.738  10.610  13016  Z= 0.385
  Chirality :  0.049   0.207   1441
  Planarity :  0.006   0.053   1665
  Dihedral  :  5.282  20.105   1246
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.72 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.25), residues: 1130
  helix:  0.88 (0.30), residues: 300
  sheet: -0.87 (0.34), residues: 227
  loop : -1.00 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 236 
 TYR   0.023   0.002   TYR A 185 
 PHE   0.023   0.003   PHE C 300 
 TRP   0.013   0.002   TRP A 278 
 HIS   0.009   0.001   HIS A 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 9634)
  covalent geometry    : angle       0.73818 (13016)
  hydrogen bonds       : bond        0.04362 (  375)
  hydrogen bonds       : angle       5.25932 ( 1053)

*********************** 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
  223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 180
  time to evaluate  : 0.363 
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: 0.7152 (OUTLIER) cc_final: 0.6435 (ptm)
REVERT: D   54 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.5927 (ttt180)
REVERT: A  271 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6844 (mmtm)
REVERT: A  581 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8452 (t0)
REVERT: A  930 SER cc_start: 0.8525 (t) cc_final: 0.7992 (m)
REVERT: A 1084 PHE cc_start: 0.7081 (m-80) cc_final: 0.6655 (m-80)
REVERT: A 1090 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6928 (mm)
REVERT: A 1285 MET cc_start: 0.6000 (mmm) cc_final: 0.5643 (mtt)
REVERT: B   85 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7685 (mm-40)
REVERT: B  117 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6805 (ttp80)
REVERT: B  118 PHE cc_start: 0.7322 (t80) cc_final: 0.6923 (t80)
REVERT: B  221 ASN cc_start: 0.8011 (p0) cc_final: 0.7741 (p0)
REVERT: B  306 VAL cc_start: 0.7333 (p) cc_final: 0.7048 (p)
REVERT: B  332 GLU cc_start: 0.6641 (pt0) cc_final: 0.6275 (pt0)
REVERT: C  113 LEU cc_start: 0.8885 (mm) cc_final: 0.8683 (mm)
REVERT: C  170 PHE cc_start: 0.4023 (t80) cc_final: 0.3303 (t80)
REVERT: C  323 ASP cc_start: 0.6827 (t70) cc_final: 0.6452 (t70)
  outliers start: 43
  outliers final: 28
  residues processed: 205
  average time/residue: 0.0913
  time to fit residues: 26.7064
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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  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  549 VAL
Chi-restraints excluded: chain A residue  570 SER
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1106 ILE
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain B residue  101 ASP
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  334 ILE
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 21 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 88 optimal weight:   30.0000
   chunk 26 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
A 582 ASN
** B  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.205480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.156450 restraints weight = 14845.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.161864 restraints weight = 7895.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.165663 restraints weight = 5239.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.168146 restraints weight = 4019.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.169424 restraints weight = 3395.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9634  Z= 0.146
  Angle     :  0.645  11.796  13016  Z= 0.333
  Chirality :  0.046   0.208   1441
  Planarity :  0.005   0.044   1665
  Dihedral  :  4.942  18.083   1246
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.18 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.25), residues: 1130
  helix:  0.95 (0.30), residues: 295
  sheet: -0.99 (0.34), residues: 229
  loop : -0.87 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 236 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.017   0.002   PHE A 292 
 TRP   0.031   0.002   TRP C 171 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9634)
  covalent geometry    : angle       0.64500 (13016)
  hydrogen bonds       : bond        0.03753 (  375)
  hydrogen bonds       : angle       5.03910 ( 1053)

*********************** 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
  199 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.360 
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: 0.7146 (ptm) cc_final: 0.6378 (ptm)
REVERT: D   54 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.5841 (ttt180)
REVERT: D   60 ASN cc_start: 0.8928 (m-40) cc_final: 0.8697 (t0)
REVERT: A  171 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7096 (mm)
REVERT: A  239 LYS cc_start: 0.8046 (pttt) cc_final: 0.7757 (pttm)
REVERT: A  271 LYS cc_start: 0.7194 (mmmt) cc_final: 0.6884 (mmtm)
REVERT: A  930 SER cc_start: 0.8608 (t) cc_final: 0.8195 (m)
REVERT: A  982 MET cc_start: 0.6083 (mmm) cc_final: 0.4989 (tmm)
REVERT: A 1013 PRO cc_start: 0.7511 (Cg_endo) cc_final: 0.6933 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.6921 (m-80) cc_final: 0.6496 (m-80)
REVERT: A 1090 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6945 (mm)
REVERT: A 1285 MET cc_start: 0.6212 (mmm) cc_final: 0.5858 (mtt)
REVERT: B  118 PHE cc_start: 0.7127 (t80) cc_final: 0.6884 (t80)
REVERT: B  221 ASN cc_start: 0.7820 (p0) cc_final: 0.7574 (p0)
REVERT: B  236 ARG cc_start: 0.7056 (mtp180) cc_final: 0.6668 (ttt180)
REVERT: C   83 ASN cc_start: 0.8092 (m-40) cc_final: 0.7874 (m110)
REVERT: C   97 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7930 (mm-30)
REVERT: C  113 LEU cc_start: 0.8923 (mm) cc_final: 0.8696 (mm)
REVERT: C  323 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6175 (t70)
  outliers start: 34
  outliers final: 19
  residues processed: 187
  average time/residue: 0.0860
  time to fit residues: 23.3678
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
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  171 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  222 LEU
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  549 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  218 PHE
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  323 ASP
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 89 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0050
   chunk 76 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6794

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.204228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165088 restraints weight = 14975.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.167671 restraints weight = 8867.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.168693 restraints weight = 7548.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.170037 restraints weight = 5174.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.170715 restraints weight = 4546.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9634  Z= 0.136
  Angle     :  0.624  10.117  13016  Z= 0.323
  Chirality :  0.045   0.199   1441
  Planarity :  0.005   0.041   1665
  Dihedral  :  4.769  18.919   1246
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.99 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.25), residues: 1130
  helix:  0.91 (0.30), residues: 301
  sheet: -0.80 (0.34), residues: 227
  loop : -0.79 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 145 
 TYR   0.009   0.001   TYR B  96 
 PHE   0.016   0.002   PHE A 292 
 TRP   0.022   0.001   TRP C 171 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9634)
  covalent geometry    : angle       0.62440 (13016)
  hydrogen bonds       : bond        0.03611 (  375)
  hydrogen bonds       : angle       4.97284 ( 1053)

*********************** 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
  200 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6375 (ptm)
REVERT: D   54 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6065 (ttt180)
REVERT: D   60 ASN cc_start: 0.8845 (m-40) cc_final: 0.8627 (t0)
REVERT: A  171 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7174 (mm)
REVERT: A  185 TYR cc_start: 0.7161 (t80) cc_final: 0.6716 (t80)
REVERT: A  239 LYS cc_start: 0.8106 (pttt) cc_final: 0.7878 (pttm)
REVERT: A  271 LYS cc_start: 0.7254 (mmmt) cc_final: 0.6955 (mmtm)
REVERT: A  930 SER cc_start: 0.8616 (t) cc_final: 0.8285 (m)
REVERT: A  982 MET cc_start: 0.6104 (mmm) cc_final: 0.5047 (tmm)
REVERT: A 1013 PRO cc_start: 0.7825 (Cg_endo) cc_final: 0.7218 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.6987 (m-80) cc_final: 0.6627 (m-80)
REVERT: A 1090 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6998 (mm)
REVERT: A 1095 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7439 (mm-30)
REVERT: B  117 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6616 (ttp80)
REVERT: B  118 PHE cc_start: 0.6981 (t80) cc_final: 0.6746 (t80)
REVERT: B  221 ASN cc_start: 0.7884 (p0) cc_final: 0.7599 (p0)
REVERT: B  235 MET cc_start: 0.5640 (mtp) cc_final: 0.5422 (mtp)
REVERT: B  236 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6715 (ttt180)
REVERT: C   83 ASN cc_start: 0.8081 (m-40) cc_final: 0.7857 (m110)
REVERT: C  106 TYR cc_start: 0.8480 (m-80) cc_final: 0.8257 (m-80)
REVERT: C  323 ASP cc_start: 0.6523 (OUTLIER) cc_final: 0.6102 (t70)
  outliers start: 34
  outliers final: 22
  residues processed: 186
  average time/residue: 0.0908
  time to fit residues: 24.1263
Evaluate side-chains
  187 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  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  288 VAL
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  323 ASP
Chi-restraints excluded: chain C residue  330 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4599 r_free = 0.4599 target = 0.205068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.155710 restraints weight = 14867.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.160982 restraints weight = 8054.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.164659 restraints weight = 5415.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.166635 restraints weight = 4183.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.168524 restraints weight = 3593.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9634  Z= 0.173
  Angle     :  0.670  10.274  13016  Z= 0.345
  Chirality :  0.046   0.290   1441
  Planarity :  0.005   0.044   1665
  Dihedral  :  4.824  19.331   1246
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.09 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.25), residues: 1130
  helix:  0.80 (0.30), residues: 301
  sheet: -0.95 (0.33), residues: 234
  loop : -0.84 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 236 
 TYR   0.011   0.001   TYR C 106 
 PHE   0.021   0.002   PHE C 298 
 TRP   0.018   0.001   TRP C 171 
 HIS   0.005   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 9634)
  covalent geometry    : angle       0.67023 (13016)
  hydrogen bonds       : bond        0.03806 (  375)
  hydrogen bonds       : angle       5.06083 ( 1053)

*********************** 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
  194 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.361 
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: 0.7158 (OUTLIER) cc_final: 0.6428 (ptm)
REVERT: D   54 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6014 (ttt180)
REVERT: D   60 ASN cc_start: 0.8978 (m-40) cc_final: 0.8731 (t0)
REVERT: A   76 PHE cc_start: 0.7209 (m-10) cc_final: 0.6941 (m-10)
REVERT: A  171 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7134 (mm)
REVERT: A  239 LYS cc_start: 0.8044 (pttt) cc_final: 0.7828 (pttm)
REVERT: A  271 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6905 (mmtm)
REVERT: A  581 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8319 (t0)
REVERT: A  930 SER cc_start: 0.8703 (t) cc_final: 0.8362 (m)
REVERT: A  982 MET cc_start: 0.6225 (mmm) cc_final: 0.5096 (tmm)
REVERT: A 1013 PRO cc_start: 0.7767 (Cg_endo) cc_final: 0.7202 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.6915 (m-80) cc_final: 0.6617 (m-80)
REVERT: A 1090 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6978 (mm)
REVERT: A 1114 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6819 (tm-30)
REVERT: B  117 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6555 (ttp80)
REVERT: B  118 PHE cc_start: 0.7025 (t80) cc_final: 0.6763 (t80)
REVERT: B  221 ASN cc_start: 0.7788 (p0) cc_final: 0.7507 (p0)
REVERT: B  236 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6536 (ttt180)
REVERT: C  323 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6155 (t70)
  outliers start: 33
  outliers final: 23
  residues processed: 180
  average time/residue: 0.0809
  time to fit residues: 21.4237
Evaluate side-chains
  188 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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  171 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain B residue  101 ASP
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  288 VAL
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  253 MET
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  323 ASP
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 66 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0770
   chunk 110 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0870
   chunk 5 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.4322

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN
B 328 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.202487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.152333 restraints weight = 14964.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.157630 restraints weight = 8064.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.161293 restraints weight = 5418.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.163737 restraints weight = 4196.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.164926 restraints weight = 3565.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9634  Z= 0.197
  Angle     :  0.697  11.793  13016  Z= 0.362
  Chirality :  0.047   0.241   1441
  Planarity :  0.005   0.076   1665
  Dihedral  :  4.967  20.821   1246
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.94 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.25), residues: 1130
  helix:  0.70 (0.29), residues: 301
  sheet: -1.07 (0.33), residues: 230
  loop : -0.90 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 236 
 TYR   0.015   0.002   TYR C 223 
 PHE   0.018   0.002   PHE A 574 
 TRP   0.019   0.002   TRP C 171 
 HIS   0.005   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 9634)
  covalent geometry    : angle       0.69722 (13016)
  hydrogen bonds       : bond        0.03876 (  375)
  hydrogen bonds       : angle       5.13785 ( 1053)

********************** 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
  186 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.360 
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: 0.7140 (OUTLIER) cc_final: 0.6406 (ptm)
REVERT: D   54 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6001 (ttt180)
REVERT: D   60 ASN cc_start: 0.9061 (m-40) cc_final: 0.8790 (t0)
REVERT: A  171 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7143 (mm)
REVERT: A  271 LYS cc_start: 0.7033 (mmmt) cc_final: 0.6755 (mmtm)
REVERT: A  930 SER cc_start: 0.8653 (t) cc_final: 0.8314 (m)
REVERT: A 1013 PRO cc_start: 0.7893 (Cg_endo) cc_final: 0.7337 (Cg_exo)
REVERT: A 1084 PHE cc_start: 0.6899 (m-80) cc_final: 0.6506 (m-80)
REVERT: A 1090 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6952 (mm)
REVERT: A 1114 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6795 (tm-30)
REVERT: B   85 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7633 (mm-40)
REVERT: B  117 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6586 (ttp80)
REVERT: B  118 PHE cc_start: 0.7043 (t80) cc_final: 0.6761 (t80)
REVERT: B  221 ASN cc_start: 0.7832 (p0) cc_final: 0.7504 (p0)
REVERT: B  236 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6537 (ttt180)
REVERT: C  106 TYR cc_start: 0.8657 (m-80) cc_final: 0.8428 (m-80)
REVERT: C  323 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6262 (t70)
  outliers start: 29
  outliers final: 23
  residues processed: 175
  average time/residue: 0.0844
  time to fit residues: 21.3878
Evaluate side-chains
  180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   54 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue  134 HIS
Chi-restraints excluded: chain A residue  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  310 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  607 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue 1090 LEU
Chi-restraints excluded: chain 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  288 VAL
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  253 MET
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  323 ASP
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 56 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 110 optimal weight:   20.0000
   chunk 10 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 77 optimal weight:    0.5980
   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 581 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.204548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.164115 restraints weight = 14899.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.166870 restraints weight = 8721.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.168030 restraints weight = 7025.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.168816 restraints weight = 5069.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.170107 restraints weight = 4581.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9634  Z= 0.152
  Angle     :  0.676  10.222  13016  Z= 0.348
  Chirality :  0.046   0.239   1441
  Planarity :  0.005   0.065   1665
  Dihedral  :  4.852  20.418   1246
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.22 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.25), residues: 1130
  helix:  0.69 (0.30), residues: 300
  sheet: -1.06 (0.33), residues: 235
  loop : -0.87 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 236 
 TYR   0.012   0.001   TYR C  96 
 PHE   0.019   0.002   PHE B 247 
 TRP   0.017   0.001   TRP C 171 
 HIS   0.005   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9634)
  covalent geometry    : angle       0.67589 (13016)
  hydrogen bonds       : bond        0.03747 (  375)
  hydrogen bonds       : angle       5.04937 ( 1053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1812.14 seconds
wall clock time: 31 minutes 58.70 seconds (1918.70 seconds total)