Starting phenix.real_space_refine
on Sat Aug 23 13:55:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qp5_18543/08_2025/8qp5_18543.map"
  }
  resolution = 4.4
  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=   0.003 sd=   0.019
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      33      5.16       5
     C    7836      2.51       5
     N    2209      2.21       5
     O    2476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12554
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4886
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 24, 'TRANS': 589}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 2674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2674
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 11, 'TRANS': 345}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 1036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1036
          Classifications: {'peptide': 171}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 280
          Unresolved non-hydrogen angles: 366
          Unresolved non-hydrogen dihedrals: 229
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 12, 'PHE:plan': 1, 'ASP:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 5, 'TRP:plan': 3, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 183
    Chain: "D"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1744
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 11, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 693
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "P"
      Number of atoms: 1521
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 299, 1516
          Classifications: {'peptide': 299}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 296}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 844
          Unresolved non-hydrogen angles: 1088
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 65
          Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 12, 'PHE:plan': 13, 'ASP:plan': 24, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 8, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 509
      Conformer: "B"
        Number of residues, atoms: 299, 1516
          Classifications: {'peptide': 299}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 296}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 844
          Unresolved non-hydrogen angles: 1088
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 65
          Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 12, 'PHE:plan': 13, 'ASP:plan': 24, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'HIS:plan': 8, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 509
          bond proxies already assigned to first conformer: 1513
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR P1150 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BTYR P1150 " occ=0.50
  Time building chain proxies: 2.72, per 1000 atoms: 0.22
  Number of scatterers: 12554
  At special positions: 0
  Unit cell: (135.42, 130.24, 128.76, 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      33     16.00
     O    2476      8.00
     N    2209      7.00
     C    7836      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: 0.84
  Conformation dependent library (CDL) restraints added in 624.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3164

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 19 sheets defined
      22.7% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.791A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.556A  pdb=" N   ILE A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.547A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.809A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.180A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 501
      removed outlier: 3.605A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU A 501 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 501'
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'B' and resid 136 through 139
    Processing helix  chain 'C' and resid 39 through 44
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.574A  pdb=" N   LEU C  80 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 114
      No H-bonds generated for 'chain 'C' and resid 112 through 114'
    Processing helix  chain 'C' and resid 115 through 125
    Processing helix  chain 'C' and resid 191 through 209
      removed outlier: 3.680A  pdb=" N   LEU C 209 " --> pdb=" O   ILE C 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 4.241A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.758A  pdb=" N   VAL D  71 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 3.584A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 129
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 192 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.736A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 228 through 243
      removed outlier: 3.990A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER D 243 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 45
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'P' and resid 1003 through 1022
      removed outlier: 3.562A  pdb=" N   ALA P1008 " --> pdb=" O   THR P1004 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1024 through 1029
      removed outlier: 3.759A  pdb=" N   MET P1029 " --> pdb=" O   LEU P1025 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1136 through 1139
      removed outlier: 3.693A  pdb=" N   LEU P1139 " --> pdb=" O   PHE P1136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 1136 through 1139'
    Processing helix  chain 'P' and resid 1185 through 1189
    Processing helix  chain 'P' and resid 1282 through 1287
      removed outlier: 3.853A  pdb=" N   TYR P1286 " --> pdb=" O   ALA P1282 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181
      removed outlier: 7.414A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274
      removed outlier: 7.198A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 355
      removed outlier: 4.057A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 781 through 783
      removed outlier: 6.267A  pdb=" N   ALA A 770 " --> pdb=" O   PRO A 790 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ILE A 772 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   ALA A 788 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU A 774 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   SER A 786 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 783
      removed outlier: 3.571A  pdb=" N   GLY A 742 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR A 467 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 671 through 674
      removed outlier: 4.549A  pdb=" N   ALA A 672 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 49
      removed outlier: 3.633A  pdb=" N   THR B  45 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.747A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.682A  pdb=" N   THR B 116 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.664A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.794A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 253 through 254
      removed outlier: 3.798A  pdb=" N   ALA B 260 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B 268 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ALA B 262 " --> pdb=" O   ASN B 266 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ASN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 299
      removed outlier: 3.661A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET B 306 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 136
      removed outlier: 3.741A  pdb=" N   ASP C 136 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 33
      removed outlier: 4.667A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 33
    Processing sheet with id=AB9, first strand: chain 'P' and resid 1040 through 1051
      removed outlier: 3.646A  pdb=" N   VAL P1103 " --> pdb=" O   HIS P1127 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASP P1209 " --> pdb=" O   GLU P1168 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'P' and resid 1182 through 1183

    625 hydrogen bonds defined for protein.
    1726 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 3877
        1.33 -     1.45: 1956
        1.45 -     1.57: 6897
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 12793
  Sorted by residual:
  bond pdb=" N   ILE C 131 "
       pdb=" CA  ILE C 131 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.24e-02 6.50e+03 8.19e+00
  bond pdb=" N   ASN C 110 "
       pdb=" CA  ASN C 110 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.18e-02 7.18e+03 8.10e+00
  bond pdb=" N   LEU C 106 "
       pdb=" CA  LEU C 106 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.23e-02 6.61e+03 6.60e+00
  bond pdb=" N   SER C 105 "
       pdb=" CA  SER C 105 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.34e-02 5.57e+03 6.47e+00
  bond pdb=" N   LYS C 127 "
       pdb=" CA  LYS C 127 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.79e+00
  ... (remaining 12788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 17159
        2.10 -     4.21: 258
        4.21 -     6.31: 17
        6.31 -     8.42: 3
        8.42 -    10.52: 3
  Bond angle restraints: 17440
  Sorted by residual:
  angle pdb=" C   THR A 479 "
        pdb=" N   VAL A 480 "
        pdb=" CA  VAL A 480 "
      ideal   model   delta    sigma   weight residual
     121.65  117.82    3.83 9.40e-01 1.13e+00 1.66e+01
  angle pdb=" N   LEU C 124 "
        pdb=" CA  LEU C 124 "
        pdb=" C   LEU C 124 "
      ideal   model   delta    sigma   weight residual
     113.01  108.67    4.34 1.20e+00 6.94e-01 1.31e+01
  angle pdb=" CB  MET D 227 "
        pdb=" CG  MET D 227 "
        pdb=" SD  MET D 227 "
      ideal   model   delta    sigma   weight residual
     112.70  123.10  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N   ASN C 128 "
        pdb=" CA  ASN C 128 "
        pdb=" C   ASN C 128 "
      ideal   model   delta    sigma   weight residual
     114.39  109.39    5.00 1.45e+00 4.76e-01 1.19e+01
  angle pdb=" CA  SER C 105 "
        pdb=" C   SER C 105 "
        pdb=" O   SER C 105 "
      ideal   model   delta    sigma   weight residual
     121.87  118.24    3.63 1.16e+00 7.43e-01 9.77e+00
  ... (remaining 17435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6855
       17.73 -    35.46: 542
       35.46 -    53.19: 82
       53.19 -    70.92: 18
       70.92 -    88.65: 4
  Dihedral angle restraints: 7501
    sinusoidal: 2526
      harmonic: 4975
  Sorted by residual:
  dihedral pdb=" CA  VAL A 480 "
           pdb=" C   VAL A 480 "
           pdb=" N   ASP A 481 "
           pdb=" CA  ASP A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.18   19.82     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLU A 717 "
           pdb=" C   GLU A 717 "
           pdb=" N   PHE A 718 "
           pdb=" CA  PHE A 718 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.24   19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ASN A 259 "
           pdb=" C   ASN A 259 "
           pdb=" N   ILE A 260 "
           pdb=" CA  ILE A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 7498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1336
       0.040 -    0.080: 444
       0.080 -    0.119: 151
       0.119 -    0.159: 15
       0.159 -    0.199: 5
  Chirality restraints: 1951
  Sorted by residual:
  chirality pdb=" CG  LEU D 167 "
            pdb=" CB  LEU D 167 "
            pdb=" CD1 LEU D 167 "
            pdb=" CD2 LEU D 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" CA  PHE A 586 "
            pdb=" N   PHE A 586 "
            pdb=" C   PHE A 586 "
            pdb=" CB  PHE A 586 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CA  ILE C 131 "
            pdb=" N   ILE C 131 "
            pdb=" C   ILE C 131 "
            pdb=" CB  ILE C 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.98e-01
  ... (remaining 1948 not shown)

  Planarity restraints: 2338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 492 "    0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ASN A 492 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 492 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 493 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 586 "   -0.017 2.00e-02 2.50e+03   1.39e-02 3.36e+00
        pdb=" CG  PHE A 586 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 586 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 586 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 586 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 586 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 586 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 136 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO D 137 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO D 137 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 137 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2335 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 292
        2.67 -     3.23: 12474
        3.23 -     3.79: 19221
        3.79 -     4.34: 24775
        4.34 -     4.90: 40392
  Nonbonded interactions: 97154
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  60 "
            pdb=" OH  TYR E  75 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" O   ILE D 238 "
            pdb=" OG  SER D 242 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR A 608 "
            pdb=" OE1 GLU A 650 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OD1 ASN A 297 "
            pdb=" OG1 THR A 299 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OG1 THR E  39 "
            pdb=" OD1 ASN E  41 "
     model   vdw
     2.196 3.040
  ... (remaining 97149 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             1.640
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.470
  Find NCS groups from input model:        0.050
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
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   0.035  12793  Z= 0.174
  Angle     :  0.626  10.521  17440  Z= 0.346
  Chirality :  0.044   0.199   1951
  Planarity :  0.004   0.038   2338
  Dihedral  : 13.403  88.651   4337
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.69 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.49 (0.20), residues: 1729
  helix:  1.26 (0.28), residues: 310
  sheet: -0.76 (0.21), residues: 570
  loop : -2.04 (0.21), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  94 
 TYR   0.020   0.001   TYR A 230 
 PHE   0.031   0.001   PHE A 586 
 TRP   0.015   0.001   TRP B  93 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12793)
  covalent geometry    : angle       0.62586 (17440)
  hydrogen bonds       : bond        0.14475 (  619)
  hydrogen bonds       : angle       6.46554 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 0.397 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  191 ASP cc_start: 0.9102 (p0) cc_final: 0.8773 (p0)
REVERT: B   93 TRP cc_start: 0.4473 (p-90) cc_final: 0.4225 (p-90)
REVERT: B  123 TYR cc_start: 0.7907 (m-80) cc_final: 0.7540 (m-80)
REVERT: B  347 HIS cc_start: 0.7976 (m-70) cc_final: 0.7694 (m-70)
REVERT: D   74 ASP cc_start: 0.9310 (m-30) cc_final: 0.9068 (m-30)
REVERT: D  105 ILE cc_start: 0.9123 (mm) cc_final: 0.8822 (mm)
REVERT: D  232 GLU cc_start: 0.9130 (mp0) cc_final: 0.8887 (mp0)
REVERT: E   28 TYR cc_start: 0.8906 (t80) cc_final: 0.8254 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 195
  average time/residue: 0.0855
  time to fit residues: 25.3557
Evaluate side-chains
  155 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    0.0170
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:   40.0000
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    7.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 168 ASN
B 172 GLN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.102244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.069316 restraints weight = 44381.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.070253 restraints weight = 27147.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.069970 restraints weight = 18426.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.070428 restraints weight = 18629.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.070789 restraints weight = 16230.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12793  Z= 0.133
  Angle     :  0.558   8.792  17440  Z= 0.301
  Chirality :  0.043   0.179   1951
  Planarity :  0.004   0.038   2338
  Dihedral  :  4.483  21.013   1878
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.67 %
    Favored  : 93.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.20), residues: 1729
  helix:  1.05 (0.27), residues: 324
  sheet: -0.74 (0.21), residues: 576
  loop : -1.98 (0.21), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 321 
 TYR   0.016   0.001   TYR D 184 
 PHE   0.029   0.001   PHE A 586 
 TRP   0.014   0.001   TRP B 143 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (12793)
  covalent geometry    : angle       0.55760 (17440)
  hydrogen bonds       : bond        0.03857 (  619)
  hydrogen bonds       : angle       5.48093 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  191 ASP cc_start: 0.9182 (p0) cc_final: 0.8759 (p0)
REVERT: A  193 LEU cc_start: 0.9200 (mt) cc_final: 0.8964 (mt)
REVERT: A  369 MET cc_start: 0.9166 (mmt) cc_final: 0.8902 (mmt)
REVERT: B  111 LEU cc_start: 0.9024 (mp) cc_final: 0.8793 (mp)
REVERT: B  123 TYR cc_start: 0.7881 (m-80) cc_final: 0.7499 (m-80)
REVERT: B  346 LEU cc_start: 0.8404 (mp) cc_final: 0.7855 (tt)
REVERT: C   78 LYS cc_start: 0.8565 (mttp) cc_final: 0.8257 (mttm)
REVERT: D   74 ASP cc_start: 0.9321 (m-30) cc_final: 0.9076 (m-30)
REVERT: D  105 ILE cc_start: 0.9245 (mm) cc_final: 0.8794 (mm)
REVERT: D  109 MET cc_start: 0.8779 (mtp) cc_final: 0.8519 (mtp)
REVERT: D  219 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: D  232 GLU cc_start: 0.9007 (mp0) cc_final: 0.8744 (mp0)
REVERT: P 1271 ASN cc_start: 0.7843 (t0) cc_final: 0.7279 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 201
  average time/residue: 0.0850
  time to fit residues: 25.6277
Evaluate side-chains
  163 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 168 optimal weight:   30.0000
   chunk 126 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 140 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    4.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN
B 359 GLN
** D  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.100254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.066247 restraints weight = 45657.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.066893 restraints weight = 29295.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.067105 restraints weight = 20060.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.067537 restraints weight = 18956.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.067940 restraints weight = 16895.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12793  Z= 0.232
  Angle     :  0.621   8.607  17440  Z= 0.337
  Chirality :  0.044   0.178   1951
  Planarity :  0.004   0.049   2338
  Dihedral  :  4.826  23.758   1878
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.29 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.73 (0.20), residues: 1729
  helix:  0.73 (0.27), residues: 320
  sheet: -0.88 (0.21), residues: 579
  loop : -2.12 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 366 
 TYR   0.018   0.002   TYR D  67 
 PHE   0.024   0.002   PHE A 586 
 TRP   0.013   0.002   TRP B 143 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (12793)
  covalent geometry    : angle       0.62081 (17440)
  hydrogen bonds       : bond        0.04207 (  619)
  hydrogen bonds       : angle       5.71092 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9235 (mt) cc_final: 0.9012 (mt)
REVERT: A  369 MET cc_start: 0.9304 (mmt) cc_final: 0.8886 (mmt)
REVERT: B   93 TRP cc_start: 0.4637 (p-90) cc_final: 0.4279 (p-90)
REVERT: B  111 LEU cc_start: 0.9094 (mp) cc_final: 0.8877 (mp)
REVERT: B  123 TYR cc_start: 0.7944 (m-80) cc_final: 0.7405 (m-80)
REVERT: C   34 GLN cc_start: 0.8415 (pm20) cc_final: 0.8189 (pm20)
REVERT: D   74 ASP cc_start: 0.9338 (m-30) cc_final: 0.9106 (m-30)
REVERT: D  105 ILE cc_start: 0.9206 (mm) cc_final: 0.9002 (mm)
REVERT: D  109 MET cc_start: 0.8990 (mtp) cc_final: 0.8652 (mtp)
REVERT: D  219 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: P 1271 ASN cc_start: 0.7907 (t0) cc_final: 0.7209 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 203
  average time/residue: 0.0894
  time to fit residues: 27.0099
Evaluate side-chains
  160 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 132 optimal weight:    8.9990
   chunk 112 optimal weight:   20.0000
   chunk 155 optimal weight:   50.0000
   chunk 151 optimal weight:   20.0000
   chunk 79 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 136 optimal weight:    6.9990
   chunk 156 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 HIS
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 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 = 0.3637 r_free = 0.3637 target = 0.099661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.063860 restraints weight = 45183.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.066286 restraints weight = 27066.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.066913 restraints weight = 18065.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.067335 restraints weight = 14324.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.067480 restraints weight = 14800.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  12793  Z= 0.266
  Angle     :  0.655   9.955  17440  Z= 0.356
  Chirality :  0.045   0.179   1951
  Planarity :  0.005   0.038   2338
  Dihedral  :  5.103  24.387   1878
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  5.72 %
    Favored  : 94.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.91 (0.19), residues: 1729
  helix:  0.53 (0.27), residues: 317
  sheet: -0.94 (0.21), residues: 585
  loop : -2.25 (0.20), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 366 
 TYR   0.021   0.002   TYR D  67 
 PHE   0.028   0.002   PHE A 586 
 TRP   0.012   0.002   TRP A 376 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 (12793)
  covalent geometry    : angle       0.65534 (17440)
  hydrogen bonds       : bond        0.04311 (  619)
  hydrogen bonds       : angle       5.85219 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9226 (mt) cc_final: 0.9010 (mt)
REVERT: A  650 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8848 (mt-10)
REVERT: B   93 TRP cc_start: 0.4641 (p-90) cc_final: 0.4278 (p-90)
REVERT: B  123 TYR cc_start: 0.7929 (m-80) cc_final: 0.7262 (m-80)
REVERT: B  347 HIS cc_start: 0.8116 (m90) cc_final: 0.7770 (m-70)
REVERT: D   74 ASP cc_start: 0.9334 (m-30) cc_final: 0.9084 (m-30)
REVERT: D  232 GLU cc_start: 0.9029 (mp0) cc_final: 0.8802 (mp0)
REVERT: E   50 MET cc_start: 0.8134 (ptm) cc_final: 0.7748 (ptm)
REVERT: P 1271 ASN cc_start: 0.7964 (t0) cc_final: 0.7427 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 203
  average time/residue: 0.1114
  time to fit residues: 33.3895
Evaluate side-chains
  160 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 146 optimal weight:   30.0000
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:   40.0000
   chunk 35 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 154 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 57 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 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 = 0.3639 r_free = 0.3639 target = 0.099762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.063890 restraints weight = 45710.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.066248 restraints weight = 27047.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.066569 restraints weight = 19077.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.067260 restraints weight = 16525.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.067367 restraints weight = 14056.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12793  Z= 0.248
  Angle     :  0.645   9.600  17440  Z= 0.351
  Chirality :  0.045   0.224   1951
  Planarity :  0.005   0.041   2338
  Dihedral  :  5.112  24.290   1878
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.05 (0.19), residues: 1729
  helix:  0.36 (0.26), residues: 321
  sheet: -1.08 (0.21), residues: 570
  loop : -2.27 (0.20), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 233 
 TYR   0.022   0.002   TYR B 132 
 PHE   0.020   0.002   PHE P1296 
 TRP   0.012   0.002   TRP A 776 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (12793)
  covalent geometry    : angle       0.64546 (17440)
  hydrogen bonds       : bond        0.04300 (  619)
  hydrogen bonds       : angle       5.84894 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9244 (mt) cc_final: 0.9033 (mt)
REVERT: A  650 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8806 (mt-10)
REVERT: B  111 LEU cc_start: 0.9072 (mp) cc_final: 0.8727 (mp)
REVERT: B  123 TYR cc_start: 0.7872 (m-80) cc_final: 0.7174 (m-80)
REVERT: B  347 HIS cc_start: 0.8025 (m90) cc_final: 0.7702 (m-70)
REVERT: C   34 GLN cc_start: 0.8400 (pm20) cc_final: 0.8089 (pm20)
REVERT: D   74 ASP cc_start: 0.9364 (m-30) cc_final: 0.9129 (m-30)
REVERT: D  109 MET cc_start: 0.8983 (mtp) cc_final: 0.8703 (mtp)
REVERT: E   50 MET cc_start: 0.8075 (ptm) cc_final: 0.7702 (ptm)
REVERT: P 1271 ASN cc_start: 0.7962 (t0) cc_final: 0.7451 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 198
  average time/residue: 0.1126
  time to fit residues: 32.9076
Evaluate side-chains
  160 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 148 optimal weight:   50.0000
   chunk 12 optimal weight:    9.9990
   chunk 164 optimal weight:    9.9990
   chunk 162 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 170 optimal weight:   40.0000
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 138 optimal weight:    5.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 GLN
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.100579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.067754 restraints weight = 45412.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.068776 restraints weight = 27574.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.068941 restraints weight = 19364.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.069258 restraints weight = 19649.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.069501 restraints weight = 17182.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12793  Z= 0.197
  Angle     :  0.616   8.926  17440  Z= 0.333
  Chirality :  0.044   0.211   1951
  Planarity :  0.004   0.042   2338
  Dihedral  :  4.956  23.113   1878
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.03 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.91 (0.19), residues: 1729
  helix:  0.58 (0.27), residues: 321
  sheet: -0.99 (0.21), residues: 589
  loop : -2.26 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 321 
 TYR   0.018   0.002   TYR D  67 
 PHE   0.020   0.002   PHE A 586 
 TRP   0.012   0.002   TRP A 376 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (12793)
  covalent geometry    : angle       0.61563 (17440)
  hydrogen bonds       : bond        0.04038 (  619)
  hydrogen bonds       : angle       5.67396 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: B   93 TRP cc_start: 0.4654 (p-90) cc_final: 0.4248 (p-90)
REVERT: B  123 TYR cc_start: 0.7732 (m-80) cc_final: 0.7031 (m-80)
REVERT: B  221 MET cc_start: 0.7756 (ptm) cc_final: 0.7075 (ptm)
REVERT: B  347 HIS cc_start: 0.8013 (m90) cc_final: 0.7711 (m-70)
REVERT: C  195 GLN cc_start: 0.7448 (pp30) cc_final: 0.6938 (pp30)
REVERT: D   56 GLU cc_start: 0.9072 (pt0) cc_final: 0.8696 (tm-30)
REVERT: D   74 ASP cc_start: 0.9332 (m-30) cc_final: 0.9108 (m-30)
REVERT: D  109 MET cc_start: 0.8927 (mtp) cc_final: 0.8588 (mtp)
REVERT: D  219 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8160 (tm-30)
REVERT: E   50 MET cc_start: 0.7965 (ptm) cc_final: 0.7685 (ptm)
REVERT: P 1271 ASN cc_start: 0.7936 (t0) cc_final: 0.7468 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 203
  average time/residue: 0.1119
  time to fit residues: 33.4615
Evaluate side-chains
  162 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   chunk 113 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 155 optimal weight:   50.0000
   chunk 93 optimal weight:   30.0000
   chunk 72 optimal weight:   20.0000
   chunk 106 optimal weight:   50.0000
   chunk 107 optimal weight:    7.9990
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 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 = 0.3643 r_free = 0.3643 target = 0.100006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.065453 restraints weight = 45298.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.066586 restraints weight = 29517.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.067280 restraints weight = 18783.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.067600 restraints weight = 17683.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.067609 restraints weight = 15976.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12793  Z= 0.241
  Angle     :  0.656   9.296  17440  Z= 0.356
  Chirality :  0.046   0.242   1951
  Planarity :  0.005   0.050   2338
  Dihedral  :  5.121  24.418   1878
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.60 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -2.05 (0.19), residues: 1729
  helix:  0.44 (0.27), residues: 322
  sheet: -1.11 (0.21), residues: 590
  loop : -2.32 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  47 
 TYR   0.018   0.002   TYR D  67 
 PHE   0.023   0.002   PHE A 586 
 TRP   0.013   0.002   TRP A 776 
 HIS   0.004   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (12793)
  covalent geometry    : angle       0.65561 (17440)
  hydrogen bonds       : bond        0.04257 (  619)
  hydrogen bonds       : angle       5.81635 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.529 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  598 LYS cc_start: 0.8772 (tptt) cc_final: 0.8551 (tppt)
REVERT: B   93 TRP cc_start: 0.4629 (p-90) cc_final: 0.4253 (p-90)
REVERT: B  123 TYR cc_start: 0.7883 (m-80) cc_final: 0.7018 (m-80)
REVERT: B  221 MET cc_start: 0.7922 (ptm) cc_final: 0.7627 (ppp)
REVERT: B  347 HIS cc_start: 0.8058 (m90) cc_final: 0.7729 (m-70)
REVERT: C   34 GLN cc_start: 0.8612 (pm20) cc_final: 0.8412 (pm20)
REVERT: C  195 GLN cc_start: 0.7440 (pp30) cc_final: 0.6957 (pp30)
REVERT: D   56 GLU cc_start: 0.9139 (pt0) cc_final: 0.8909 (pt0)
REVERT: D   74 ASP cc_start: 0.9340 (m-30) cc_final: 0.9103 (m-30)
REVERT: D  109 MET cc_start: 0.9001 (mtp) cc_final: 0.8640 (mtp)
REVERT: D  219 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: D  232 GLU cc_start: 0.9017 (mp0) cc_final: 0.8552 (mp0)
REVERT: E   50 MET cc_start: 0.7919 (ptm) cc_final: 0.7673 (ptm)
REVERT: P 1271 ASN cc_start: 0.7986 (t0) cc_final: 0.7453 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 189
  average time/residue: 0.1002
  time to fit residues: 28.9972
Evaluate side-chains
  159 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 104 optimal weight:   20.0000
   chunk 128 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   chunk 99 optimal weight:    0.0020
   chunk 59 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0970
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.9790

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 GLN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 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 = 0.3696 r_free = 0.3696 target = 0.102906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.068661 restraints weight = 44087.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.070531 restraints weight = 26144.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.071347 restraints weight = 17368.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.071926 restraints weight = 13898.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.071937 restraints weight = 13280.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12793  Z= 0.113
  Angle     :  0.600  10.374  17440  Z= 0.316
  Chirality :  0.044   0.204   1951
  Planarity :  0.004   0.042   2338
  Dihedral  :  4.656  20.153   1878
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.56 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.69 (0.20), residues: 1729
  helix:  1.01 (0.27), residues: 319
  sheet: -0.93 (0.21), residues: 580
  loop : -2.13 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 233 
 TYR   0.017   0.001   TYR D 184 
 PHE   0.017   0.001   PHE A 586 
 TRP   0.017   0.002   TRP B 143 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (12793)
  covalent geometry    : angle       0.59963 (17440)
  hydrogen bonds       : bond        0.03546 (  619)
  hydrogen bonds       : angle       5.26783 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.530 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  245 VAL cc_start: 0.8996 (m) cc_final: 0.8708 (t)
REVERT: A  369 MET cc_start: 0.9174 (mmt) cc_final: 0.8878 (mmt)
REVERT: A  650 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8804 (mt-10)
REVERT: A  780 LEU cc_start: 0.9271 (mm) cc_final: 0.8985 (mt)
REVERT: B  123 TYR cc_start: 0.7851 (m-80) cc_final: 0.6960 (m-80)
REVERT: B  132 TYR cc_start: 0.8240 (m-80) cc_final: 0.7837 (m-80)
REVERT: B  221 MET cc_start: 0.7893 (ptm) cc_final: 0.7614 (ppp)
REVERT: B  347 HIS cc_start: 0.8103 (m90) cc_final: 0.7795 (m-70)
REVERT: C  195 GLN cc_start: 0.7512 (pp30) cc_final: 0.7081 (pp30)
REVERT: D   56 GLU cc_start: 0.9113 (pt0) cc_final: 0.8728 (tm-30)
REVERT: D   74 ASP cc_start: 0.9304 (m-30) cc_final: 0.9063 (m-30)
REVERT: D  105 ILE cc_start: 0.9159 (mm) cc_final: 0.8682 (mm)
REVERT: D  109 MET cc_start: 0.8976 (mtp) cc_final: 0.8644 (mtp)
REVERT: D  219 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: D  232 GLU cc_start: 0.8954 (mp0) cc_final: 0.8735 (mp0)
REVERT: D  236 LYS cc_start: 0.9293 (ptmt) cc_final: 0.8913 (ptmm)
REVERT: P 1271 ASN cc_start: 0.7798 (t0) cc_final: 0.7294 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 210
  average time/residue: 0.1079
  time to fit residues: 33.8313
Evaluate side-chains
  169 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 116 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 84 optimal weight:   20.0000
   chunk 87 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 165 optimal weight:   40.0000
   chunk 105 optimal weight:   50.0000
   chunk 40 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 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 = 0.3660 r_free = 0.3660 target = 0.100864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.065352 restraints weight = 44626.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.067921 restraints weight = 26128.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.068114 restraints weight = 17965.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.068502 restraints weight = 15798.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.068607 restraints weight = 14069.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12793  Z= 0.203
  Angle     :  0.640  10.981  17440  Z= 0.343
  Chirality :  0.045   0.191   1951
  Planarity :  0.005   0.044   2338
  Dihedral  :  4.865  23.446   1878
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.43 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.91 (0.19), residues: 1729
  helix:  0.68 (0.27), residues: 325
  sheet: -1.11 (0.21), residues: 573
  loop : -2.21 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  47 
 TYR   0.018   0.002   TYR A 468 
 PHE   0.024   0.002   PHE A 586 
 TRP   0.020   0.002   TRP B  93 
 HIS   0.003   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12793)
  covalent geometry    : angle       0.63952 (17440)
  hydrogen bonds       : bond        0.03983 (  619)
  hydrogen bonds       : angle       5.45837 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 0.547 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  650 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8769 (mt-10)
REVERT: A  717 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7831 (tt0)
REVERT: B   90 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7542 (ptmm)
REVERT: B  123 TYR cc_start: 0.7770 (m-80) cc_final: 0.6871 (m-80)
REVERT: B  221 MET cc_start: 0.7892 (ptm) cc_final: 0.7076 (ptm)
REVERT: B  347 HIS cc_start: 0.8090 (m90) cc_final: 0.7798 (m-70)
REVERT: C  195 GLN cc_start: 0.7500 (pp30) cc_final: 0.7038 (pp30)
REVERT: D   56 GLU cc_start: 0.9129 (pt0) cc_final: 0.8884 (pt0)
REVERT: D   74 ASP cc_start: 0.9320 (m-30) cc_final: 0.9073 (m-30)
REVERT: D  109 MET cc_start: 0.8958 (mtp) cc_final: 0.8527 (mtp)
REVERT: D  219 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: D  232 GLU cc_start: 0.8953 (mp0) cc_final: 0.8719 (mp0)
REVERT: E   50 MET cc_start: 0.8171 (ptm) cc_final: 0.7683 (ptm)
REVERT: P 1271 ASN cc_start: 0.7924 (t0) cc_final: 0.7436 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 195
  average time/residue: 0.1028
  time to fit residues: 30.2090
Evaluate side-chains
  161 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 140 optimal weight:   10.0000
   chunk 105 optimal weight:   50.0000
   chunk 156 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9980
   chunk 144 optimal weight:    0.0020
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1006 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.069245 restraints weight = 44938.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.069957 restraints weight = 28078.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.070514 restraints weight = 18832.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.070884 restraints weight = 17579.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.070985 restraints weight = 15738.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12793  Z= 0.128
  Angle     :  0.609  11.719  17440  Z= 0.320
  Chirality :  0.044   0.189   1951
  Planarity :  0.004   0.043   2338
  Dihedral  :  4.676  19.869   1878
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.35 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.70 (0.20), residues: 1729
  helix:  0.97 (0.27), residues: 323
  sheet: -0.91 (0.21), residues: 580
  loop : -2.17 (0.21), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  47 
 TYR   0.026   0.001   TYR B 132 
 PHE   0.020   0.001   PHE A 586 
 TRP   0.030   0.002   TRP A 546 
 HIS   0.006   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12793)
  covalent geometry    : angle       0.60913 (17440)
  hydrogen bonds       : bond        0.03541 (  619)
  hydrogen bonds       : angle       5.22963 ( 1726)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 199
  time to evaluate  : 0.499 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  245 VAL cc_start: 0.8991 (m) cc_final: 0.8714 (t)
REVERT: A  369 MET cc_start: 0.9021 (mmt) cc_final: 0.8716 (mmt)
REVERT: A  546 TRP cc_start: 0.7835 (m100) cc_final: 0.7495 (m100)
REVERT: A  650 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8787 (mt-10)
REVERT: A  717 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7823 (tt0)
REVERT: B   90 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7620 (ptmm)
REVERT: B   93 TRP cc_start: 0.4706 (p-90) cc_final: 0.4479 (p-90)
REVERT: B  123 TYR cc_start: 0.7715 (m-80) cc_final: 0.6834 (m-80)
REVERT: B  183 TRP cc_start: 0.7816 (p90) cc_final: 0.7326 (p90)
REVERT: B  221 MET cc_start: 0.7843 (ptm) cc_final: 0.7342 (ptm)
REVERT: B  347 HIS cc_start: 0.8085 (m90) cc_final: 0.7797 (m-70)
REVERT: C  195 GLN cc_start: 0.7512 (pp30) cc_final: 0.7086 (pp30)
REVERT: D   56 GLU cc_start: 0.9156 (pt0) cc_final: 0.8724 (tm-30)
REVERT: D   74 ASP cc_start: 0.9308 (m-30) cc_final: 0.9083 (m-30)
REVERT: D  105 ILE cc_start: 0.9201 (mm) cc_final: 0.8910 (mm)
REVERT: D  109 MET cc_start: 0.8931 (mtp) cc_final: 0.8530 (mtp)
REVERT: D  219 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: D  232 GLU cc_start: 0.8931 (mp0) cc_final: 0.8716 (mp0)
REVERT: E   50 MET cc_start: 0.8144 (ptm) cc_final: 0.7684 (ptm)
REVERT: P 1271 ASN cc_start: 0.7848 (t0) cc_final: 0.7360 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 201
  average time/residue: 0.1032
  time to fit residues: 31.5785
Evaluate side-chains
  168 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 109 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 63 optimal weight:   20.0000
   chunk 61 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0270
   chunk 120 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.1042

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 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 = 0.3686 r_free = 0.3686 target = 0.102308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.066828 restraints weight = 44226.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.068915 restraints weight = 24501.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.070333 restraints weight = 16677.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.071173 restraints weight = 13020.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.071760 restraints weight = 11240.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12793  Z= 0.137
  Angle     :  0.609  11.248  17440  Z= 0.320
  Chirality :  0.044   0.187   1951
  Planarity :  0.004   0.044   2338
  Dihedral  :  4.664  21.472   1878
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.43 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -1.69 (0.20), residues: 1729
  helix:  1.01 (0.28), residues: 323
  sheet: -0.93 (0.21), residues: 587
  loop : -2.17 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  47 
 TYR   0.019   0.002   TYR B 132 
 PHE   0.021   0.001   PHE A 586 
 TRP   0.031   0.002   TRP A 546 
 HIS   0.003   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12793)
  covalent geometry    : angle       0.60860 (17440)
  hydrogen bonds       : bond        0.03536 (  619)
  hydrogen bonds       : angle       5.18251 ( 1726)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2356.71 seconds
wall clock time: 41 minutes 28.68 seconds (2488.68 seconds total)