Starting phenix.real_space_refine
on Thu Jun 12 18:46:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t7e_41091/06_2025/8t7e_41091_neut.cif"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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: 5
    Type Number    sf(0)   Gaussians
     P      37      5.49       5
     S      79      5.16       5
     C    8981      2.51       5
     N    2512      2.21       5
     O    2664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14273
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 908, 7158
          Classifications: {'peptide': 908}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 60, 'TRANS': 847}
          Chain breaks: 5
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 3188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3188
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 18, 'TRANS': 379}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 3166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3166
          Classifications: {'peptide': 400}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 18, 'TRANS': 381}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "P"
      Number of atoms: 394
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 18, 373
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
      Conformer: "B"
        Number of residues, atoms: 18, 373
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
          bond proxies already assigned to first conformer: 395
    Chain: "T"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 367
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DA P  27 " occ=0.50
      ... (40 atoms not shown)
      pdb=" C4 B DA P  27 " occ=0.50
  Time building chain proxies: 8.80, per 1000 atoms: 0.62
  Number of scatterers: 14273
  At special positions: 0
  Unit cell: (105.728, 102.424, 142.072, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      79     16.00
     P      37     15.00
     O    2664      8.00
     N    2512      7.00
     C    8981      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: 3.33
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3178

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 10 sheets defined
      34.9% alpha, 11.1% beta
      17 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 4.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 108
    Processing helix  chain 'A' and resid 134 through 140
    Processing helix  chain 'A' and resid 141 through 146
      removed outlier: 4.317A  pdb=" N   GLN A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 160
      removed outlier: 3.820A  pdb=" N   ALA A 154 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 306 through 316
      removed outlier: 3.568A  pdb=" N   SER A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 4.079A  pdb=" N   ASP A 349 " --> pdb=" O   TRP A 345 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER A 351 " --> pdb=" O   TRP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 388 through 418
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 420 through 431
      removed outlier: 4.154A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 448
      removed outlier: 3.526A  pdb=" N   ALA A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 469
      removed outlier: 3.880A  pdb=" N   MET A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 550
    Processing helix  chain 'A' and resid 570 through 575
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 793 through 809
      removed outlier: 5.254A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ASN A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 903
      removed outlier: 3.766A  pdb=" N   TRP A 897 " --> pdb=" O   SER A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 919
    Processing helix  chain 'A' and resid 932 through 940
      removed outlier: 4.367A  pdb=" N   THR A 938 " --> pdb=" O   LYS A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 944 through 955
      removed outlier: 4.308A  pdb=" N   ILE A 948 " --> pdb=" O   GLU A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 969
      removed outlier: 3.505A  pdb=" N   ALA A 962 " --> pdb=" O   GLY A 958 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE A 969 " --> pdb=" O   LEU A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 980
    Processing helix  chain 'A' and resid 982 through 989
      removed outlier: 3.747A  pdb=" N   TYR A 986 " --> pdb=" O   ALA A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1066
    Processing helix  chain 'A' and resid 1095 through 1115
    Processing helix  chain 'A' and resid 1145 through 1168
      removed outlier: 3.650A  pdb=" N   ASN A1157 " --> pdb=" O   LEU A1153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 77
      removed outlier: 3.819A  pdb=" N   GLN B  74 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.603A  pdb=" N   LYS B 176 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR B 177 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 173 through 177'
    Processing helix  chain 'B' and resid 185 through 192
    Processing helix  chain 'B' and resid 192 through 200
    Processing helix  chain 'B' and resid 247 through 265
      removed outlier: 3.888A  pdb=" N   ASP B 253 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 342 through 354
    Processing helix  chain 'B' and resid 394 through 409
      removed outlier: 3.894A  pdb=" N   VAL B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 419
      No H-bonds generated for 'chain 'B' and resid 417 through 419'
    Processing helix  chain 'B' and resid 424 through 435
      removed outlier: 3.883A  pdb=" N   LEU B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.603A  pdb=" N   THR B 447 " --> pdb=" O   THR B 444 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU B 448 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 444 through 448'
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'C' and resid 68 through 76
    Processing helix  chain 'C' and resid 87 through 93
      removed outlier: 3.724A  pdb=" N   LEU C  91 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 119
    Processing helix  chain 'C' and resid 185 through 192
      removed outlier: 3.692A  pdb=" N   ALA C 189 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 200
    Processing helix  chain 'C' and resid 247 through 264
      removed outlier: 3.655A  pdb=" N   LEU C 260 " --> pdb=" O   LEU C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 342 through 354
    Processing helix  chain 'C' and resid 391 through 409
      removed outlier: 3.542A  pdb=" N   LEU C 395 " --> pdb=" O   PRO C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 450
      removed outlier: 3.897A  pdb=" N   LEU C 448 " --> pdb=" O   THR C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 478
    Processing helix  chain 'C' and resid 479 through 484
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186
      removed outlier: 3.536A  pdb=" N   VAL A 185 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA A 212 " --> pdb=" O   TRP A 223 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 213 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASP A 198 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436
      removed outlier: 3.703A  pdb=" N   LEU A 435 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 884 through 890
    Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127
      removed outlier: 6.209A  pdb=" N   PHE B 126 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 8.511A  pdb=" N   ILE B 211 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B 300 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LEU B 299 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LYS B 285 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326
    Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415
      removed outlier: 6.844A  pdb=" N   TRP B 414 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL B 383 " --> pdb=" O   TRP B 414 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LYS B 382 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   VAL B 441 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ALA B 384 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ASP B 386 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127
      removed outlier: 6.138A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.649A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ILE C 300 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   LEU C 299 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   TYR C 291 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326
    Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415
      removed outlier: 6.997A  pdb=" N   VAL C 383 " --> pdb=" O   TRP C 414 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ALA C 384 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      45 hydrogen bonds
      90 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 5.22

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4252
        1.34 -     1.46: 3109
        1.46 -     1.58: 7144
        1.58 -     1.70: 72
        1.70 -     1.82: 125
  Bond restraints: 14702
  Sorted by residual:
  bond pdb=" C   ILE A1069 "
       pdb=" N   PRO A1070 "
    ideal  model  delta    sigma   weight residual
    1.335  1.381 -0.046 8.70e-03 1.32e+04 2.75e+01
  bond pdb=" N   GLU B 394 "
       pdb=" CA  GLU B 394 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.30e-02 5.92e+03 6.63e+00
  bond pdb=" C3'  DT P  16 "
       pdb=" O3'  DT P  16 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.53e+00
  bond pdb=" N   GLY B 390 "
       pdb=" CA  GLY B 390 "
    ideal  model  delta    sigma   weight residual
    1.443  1.477 -0.035 1.37e-02 5.33e+03 6.48e+00
  bond pdb=" N   GLY B 388 "
       pdb=" CA  GLY B 388 "
    ideal  model  delta    sigma   weight residual
    1.446  1.479 -0.033 1.30e-02 5.92e+03 6.38e+00
  ... (remaining 14697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.21: 20016
        6.21 -    12.42: 65
       12.42 -    18.63: 4
       18.63 -    24.84: 1
       24.84 -    31.05: 4
  Bond angle restraints: 20090
  Sorted by residual:
  angle pdb=" O3'  DC P  25 "
        pdb=" P    DG P  26 "
        pdb=" OP2  DG P  26 "
      ideal   model   delta    sigma   weight residual
     108.00   76.95   31.05 3.00e+00 1.11e-01 1.07e+02
  angle pdb=" OP1  DG P  26 "
        pdb=" P    DG P  26 "
        pdb=" O5'  DG P  26 "
      ideal   model   delta    sigma   weight residual
     109.00   78.32   30.68 3.00e+00 1.11e-01 1.05e+02
  angle pdb=" O3'  DC P  25 "
        pdb=" P    DG P  26 "
        pdb=" OP1  DG P  26 "
      ideal   model   delta    sigma   weight residual
     108.00   80.15   27.85 3.00e+00 1.11e-01 8.62e+01
  angle pdb=" OP1  DG P  26 "
        pdb=" P    DG P  26 "
        pdb=" OP2  DG P  26 "
      ideal   model   delta    sigma   weight residual
     120.00  145.39  -25.39 3.00e+00 1.11e-01 7.16e+01
  angle pdb=" N   PRO A 625 "
        pdb=" CA  PRO A 625 "
        pdb=" CB  PRO A 625 "
      ideal   model   delta    sigma   weight residual
     103.25  111.57   -8.32 1.05e+00 9.07e-01 6.28e+01
  ... (remaining 20085 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.84: 8288
       34.84 -    69.67: 344
       69.67 -   104.51: 23
      104.51 -   139.35: 2
      139.35 -   174.19: 4
  Dihedral angle restraints: 8661
    sinusoidal: 3743
      harmonic: 4918
  Sorted by residual:
  dihedral pdb=" CA  HIS B  77 "
           pdb=" C   HIS B  77 "
           pdb=" N   PHE B  78 "
           pdb=" CA  PHE B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  PRO A 241 "
           pdb=" C   PRO A 241 "
           pdb=" N   ALA A 242 "
           pdb=" CA  ALA A 242 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.81  -29.19     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  PRO A 745 "
           pdb=" C   PRO A 745 "
           pdb=" N   GLY A 746 "
           pdb=" CA  GLY A 746 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.92   28.08     0      5.00e+00 4.00e-02 3.15e+01
  ... (remaining 8658 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 2084
       0.120 -    0.240: 96
       0.240 -    0.360: 3
       0.360 -    0.480: 0
       0.480 -    0.600: 1
  Chirality restraints: 2184
  Sorted by residual:
  chirality pdb=" P    DG P  26 "
            pdb=" OP1  DG P  26 "
            pdb=" OP2  DG P  26 "
            pdb=" O5'  DG P  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    1.75    0.60 2.00e-01 2.50e+01 8.99e+00
  chirality pdb=" CA  ILE A 744 "
            pdb=" N   ILE A 744 "
            pdb=" C   ILE A 744 "
            pdb=" CB  ILE A 744 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  ILE A1185 "
            pdb=" CA  ILE A1185 "
            pdb=" CG1 ILE A1185 "
            pdb=" CG2 ILE A1185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 2181 not shown)

  Planarity restraints: 2452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 309 "   -0.663 9.50e-02 1.11e+02   2.97e-01 5.38e+01
        pdb=" NE  ARG A 309 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 309 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 309 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 309 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 389 "    0.543 9.50e-02 1.11e+02   2.44e-01 3.62e+01
        pdb=" NE  ARG B 389 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 389 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 389 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 389 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 139 "    0.053 5.00e-02 4.00e+02   7.97e-02 1.02e+01
        pdb=" N   PRO B 140 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 140 "    0.044 5.00e-02 4.00e+02
  ... (remaining 2449 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3615
        2.81 -     3.33: 12917
        3.33 -     3.86: 24734
        3.86 -     4.38: 28176
        4.38 -     4.90: 45888
  Nonbonded interactions: 115330
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 193 "
            pdb=" O   LEU C 322 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG  SER B 457 "
            pdb=" O   THR B 460 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   PRO B 244 "
            pdb=" OG  SER B 248 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   SER A 615 "
            pdb=" NZ  LYS A 751 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" O   GLU A 447 "
            pdb=" OG1 THR A 451 "
     model   vdw
     2.337 3.040
  ... (remaining 115325 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or (r \ 
esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219  \ 
or resid 229 through 283 or (resid 284 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 285 through 327 or (resid 328 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 329 through 355 or resid 368 through 48 \ 
5))
  selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ 
rough 485))
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.620
  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:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     37.630
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  14702  Z= 0.237
  Angle     :  1.092  31.048  20090  Z= 0.543
  Chirality :  0.056   0.600   2184
  Planarity :  0.011   0.297   2452
  Dihedral  : 18.219 174.187   5483
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.62 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.54 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.18), residues: 1680
  helix: -1.93 (0.17), residues: 589
  sheet: -0.58 (0.34), residues: 220
  loop : -2.35 (0.19), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 241 
 HIS   0.011   0.001   HIS C 454 
 PHE   0.025   0.002   PHE A 197 
 TYR   0.033   0.002   TYR A 150 
 ARG   0.009   0.001   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14702 (  507)
  hydrogen bonds       : angle       7.30120 ( 1440)
  covalent geometry    : bond        0.00455 (14702)
  covalent geometry    : angle       1.09155 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 298
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  454 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6726 (mm-30)
REVERT: A  457 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6571 (ptp-170)
REVERT: A  544 MET cc_start: 0.7305 (ppp) cc_final: 0.6993 (ppp)
REVERT: A  812 MET cc_start: 0.5800 (ppp) cc_final: 0.5520 (ptm)
REVERT: A  907 PHE cc_start: 0.7592 (t80) cc_final: 0.7344 (t80)
REVERT: A  970 ASN cc_start: 0.6988 (t0) cc_final: 0.6768 (t0)
REVERT: A 1079 ILE cc_start: 0.6772 (tt) cc_final: 0.6343 (tt)
REVERT: A 1170 LEU cc_start: 0.6554 (pt) cc_final: 0.6294 (pp)
REVERT: B   74 GLN cc_start: 0.7411 (mp10) cc_final: 0.7161 (mp10)
REVERT: C  325 ARG cc_start: 0.6100 (tpp-160) cc_final: 0.5768 (tpp-160)
REVERT: C  400 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7075 (tm-30)
  outliers start: 10
  outliers final: 2
  residues processed: 306
  average time/residue: 0.3211
  time to fit residues: 141.6530
Evaluate side-chains
  198 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  920 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9980
   chunk 71 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 134 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 155 optimal weight:    6.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 134 ASN
A 354 ASN
A 390 GLN
A 409 GLN
A 440 ASN
A 472 GLN
A 564 GLN
A 565 HIS
A 803 ASN
A 879 GLN
A 959 GLN
A 968 GLN
A 970 ASN
A1089 GLN
B  77 HIS
B  84 GLN
B  85 GLN
B 201 ASN
B 249 ASN
B 272 ASN
B 313 HIS
B 400 GLN
B 404 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 261 GLN
C 318 ASN
C 454 HIS

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.188520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.145952 restraints weight = 25050.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.92
r_work: 0.3795 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3802 r_free = 0.3802    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3803 r_free = 0.3803    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14702  Z= 0.172
  Angle     :  0.733  22.246  20090  Z= 0.367
  Chirality :  0.063   2.105   2184
  Planarity :  0.005   0.065   2452
  Dihedral  : 17.336 173.848   2232
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.74 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.71 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.20), residues: 1680
  helix: -0.48 (0.21), residues: 593
  sheet: -0.58 (0.35), residues: 215
  loop : -2.06 (0.20), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1118 
 HIS   0.011   0.001   HIS C 258 
 PHE   0.018   0.002   PHE B 266 
 TYR   0.017   0.002   TYR A 150 
 ARG   0.009   0.001   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  507)
  hydrogen bonds       : angle       5.31226 ( 1440)
  covalent geometry    : bond        0.00380 (14702)
  covalent geometry    : angle       0.73333 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 2.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TYR cc_start: 0.4138 (m-80) cc_final: 0.3927 (m-80)
REVERT: A  544 MET cc_start: 0.7820 (ppp) cc_final: 0.7573 (ppp)
REVERT: A  744 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8279 (mm)
REVERT: A  907 PHE cc_start: 0.8087 (t80) cc_final: 0.6934 (t80)
REVERT: A  955 TYR cc_start: 0.7470 (m-80) cc_final: 0.7214 (m-80)
REVERT: A 1093 MET cc_start: 0.5646 (tpt) cc_final: 0.4595 (ptp)
REVERT: C  219 PHE cc_start: 0.6667 (m-10) cc_final: 0.6461 (m-10)
REVERT: C  325 ARG cc_start: 0.6220 (tpp-160) cc_final: 0.5889 (tpp-160)
REVERT: C  400 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7576 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 232
  average time/residue: 0.3762
  time to fit residues: 129.2232
Evaluate side-chains
  211 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 197
  time to evaluate  : 1.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  920 THR
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  440 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 118 optimal weight:    0.2980
   chunk 154 optimal weight:    7.9990
   chunk 126 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 145 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 540 GLN
A 959 GLN
B 305 ASN
B 313 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.188998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.147653 restraints weight = 27018.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.38
r_work: 0.3770 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3777 r_free = 0.3777    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3777 r_free = 0.3777    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14702  Z= 0.133
  Angle     :  0.645  10.586  20090  Z= 0.327
  Chirality :  0.042   0.181   2184
  Planarity :  0.004   0.053   2452
  Dihedral  : 17.269 173.223   2231
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.14 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.96 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.20), residues: 1680
  helix:  0.14 (0.22), residues: 591
  sheet: -0.69 (0.33), residues: 214
  loop : -1.98 (0.20), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 312 
 HIS   0.008   0.001   HIS C 258 
 PHE   0.021   0.001   PHE A 961 
 TYR   0.017   0.001   TYR A 434 
 ARG   0.006   0.000   ARG A1187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  507)
  hydrogen bonds       : angle       4.91847 ( 1440)
  covalent geometry    : bond        0.00292 (14702)
  covalent geometry    : angle       0.64511 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 2.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  544 MET cc_start: 0.7840 (ppp) cc_final: 0.7496 (ppp)
REVERT: A  559 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5675 (mt)
REVERT: A  744 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8356 (mm)
REVERT: A  907 PHE cc_start: 0.8174 (t80) cc_final: 0.6909 (t80)
REVERT: A 1093 MET cc_start: 0.5620 (tpt) cc_final: 0.4776 (ptp)
REVERT: A 1116 MET cc_start: 0.6843 (mtm) cc_final: 0.6616 (mtt)
REVERT: A 1153 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7478 (tt)
REVERT: C  219 PHE cc_start: 0.6779 (m-10) cc_final: 0.6571 (m-10)
REVERT: C  281 GLU cc_start: 0.7747 (mp0) cc_final: 0.7413 (pp20)
REVERT: C  325 ARG cc_start: 0.6112 (tpp-160) cc_final: 0.5529 (tpp-160)
REVERT: C  400 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: C  466 MET cc_start: 0.7619 (ttm) cc_final: 0.7268 (ttt)
  outliers start: 33
  outliers final: 20
  residues processed: 238
  average time/residue: 0.4349
  time to fit residues: 152.8140
Evaluate side-chains
  226 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 5.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  920 THR
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1153 LEU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  440 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 169 optimal weight:   10.0000
   chunk 139 optimal weight:    9.9990
   chunk 131 optimal weight:    5.9990
   chunk 4 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   chunk 146 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 151 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 565 HIS
A 894 GLN
A 911 HIS
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 216 HIS
B 323 HIS
B 368 HIS
B 427 GLN
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 GLN
C 375 HIS
C 427 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.176156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.131429 restraints weight = 25666.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.93
r_work: 0.3603 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.096  14702  Z= 0.425
  Angle     :  0.936  16.238  20090  Z= 0.475
  Chirality :  0.052   0.218   2184
  Planarity :  0.007   0.093   2452
  Dihedral  : 17.483 174.461   2231
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.29 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.00 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.19), residues: 1680
  helix: -0.50 (0.20), residues: 606
  sheet: -0.95 (0.33), residues: 217
  loop : -2.26 (0.20), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 312 
 HIS   0.009   0.002   HIS C 258 
 PHE   0.035   0.003   PHE B 266 
 TYR   0.027   0.003   TYR A 434 
 ARG   0.008   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05571 (  507)
  hydrogen bonds       : angle       5.66195 ( 1440)
  covalent geometry    : bond        0.00960 (14702)
  covalent geometry    : angle       0.93614 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 211
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.6556 (mm) cc_final: 0.6236 (mm)
REVERT: A  356 LEU cc_start: 0.2185 (OUTLIER) cc_final: 0.1899 (tt)
REVERT: A  544 MET cc_start: 0.8173 (ppp) cc_final: 0.7828 (ppp)
REVERT: A  907 PHE cc_start: 0.8446 (t80) cc_final: 0.7128 (t80)
REVERT: A  955 TYR cc_start: 0.7878 (m-80) cc_final: 0.7519 (m-80)
REVERT: A  964 ARG cc_start: 0.6637 (mpt90) cc_final: 0.6375 (mpt180)
REVERT: A 1093 MET cc_start: 0.5663 (tpt) cc_final: 0.4803 (ptp)
REVERT: A 1214 GLN cc_start: 0.5866 (tm-30) cc_final: 0.5524 (tm-30)
REVERT: B  122 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7464 (tpp80)
REVERT: C  256 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7896 (tp)
REVERT: C  385 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4980 (mt)
REVERT: C  400 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: C  466 MET cc_start: 0.7936 (ttm) cc_final: 0.7423 (ttm)
REVERT: C  479 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7145 (pt)
  outliers start: 64
  outliers final: 40
  residues processed: 252
  average time/residue: 0.2701
  time to fit residues: 99.3462
Evaluate side-chains
  229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 184
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  122 ARG
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  427 GLN
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 144 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 136 optimal weight:    9.9990
   chunk 87 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 112 optimal weight:    0.8980
   chunk 169 optimal weight:   10.0000
   chunk 153 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 565 HIS
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
B 124 GLN
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 375 HIS
C 427 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.182614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.138703 restraints weight = 25784.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.97
r_work: 0.3698 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14702  Z= 0.150
  Angle     :  0.704  12.202  20090  Z= 0.357
  Chirality :  0.044   0.220   2184
  Planarity :  0.005   0.052   2452
  Dihedral  : 17.374 175.661   2230
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.86 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.15 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.20), residues: 1680
  helix:  0.09 (0.22), residues: 602
  sheet: -0.93 (0.33), residues: 212
  loop : -2.07 (0.21), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 312 
 HIS   0.005   0.001   HIS A 138 
 PHE   0.016   0.002   PHE B 403 
 TYR   0.021   0.001   TYR A 150 
 ARG   0.005   0.001   ARG A 972 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  507)
  hydrogen bonds       : angle       5.12455 ( 1440)
  covalent geometry    : bond        0.00331 (14702)
  covalent geometry    : angle       0.70407 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 219
  time to evaluate  : 1.656 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 LEU cc_start: 0.6812 (mm) cc_final: 0.6464 (mm)
REVERT: A  345 TRP cc_start: 0.6199 (m-90) cc_final: 0.4392 (t-100)
REVERT: A  420 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7426 (m-70)
REVERT: A  454 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7001 (mm-30)
REVERT: A  544 MET cc_start: 0.7971 (ppp) cc_final: 0.7653 (ppp)
REVERT: A  558 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6540 (pp)
REVERT: A  559 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5565 (mt)
REVERT: A  812 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6815 (ptm)
REVERT: A  907 PHE cc_start: 0.8403 (t80) cc_final: 0.7070 (t80)
REVERT: A  955 TYR cc_start: 0.7760 (m-80) cc_final: 0.7500 (m-80)
REVERT: A  964 ARG cc_start: 0.6504 (mpt90) cc_final: 0.6213 (mpt180)
REVERT: A 1057 MET cc_start: 0.6792 (ppp) cc_final: 0.6418 (ppp)
REVERT: A 1093 MET cc_start: 0.5492 (tpt) cc_final: 0.4827 (ptp)
REVERT: A 1094 THR cc_start: 0.6800 (p) cc_final: 0.6485 (t)
REVERT: A 1214 GLN cc_start: 0.6051 (tm-30) cc_final: 0.5701 (tm-30)
REVERT: B  261 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6800 (tp40)
REVERT: C  256 LEU cc_start: 0.7913 (tt) cc_final: 0.7707 (tp)
REVERT: C  400 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: C  466 MET cc_start: 0.7854 (ttm) cc_final: 0.7591 (ttm)
REVERT: C  479 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6795 (pt)
  outliers start: 54
  outliers final: 28
  residues processed: 257
  average time/residue: 0.3193
  time to fit residues: 125.3248
Evaluate side-chains
  237 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  420 HIS
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  837 TYR
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1125 ILE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 149 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 427 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.183024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.139193 restraints weight = 26072.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 2.98
r_work: 0.3705 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14702  Z= 0.154
  Angle     :  0.692  12.906  20090  Z= 0.349
  Chirality :  0.044   0.196   2184
  Planarity :  0.005   0.074   2452
  Dihedral  : 17.250 174.567   2230
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.15 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.61 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.20), residues: 1680
  helix:  0.29 (0.22), residues: 609
  sheet: -0.94 (0.33), residues: 219
  loop : -2.04 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 312 
 HIS   0.005   0.001   HIS A 138 
 PHE   0.024   0.002   PHE A 961 
 TYR   0.021   0.001   TYR A 434 
 ARG   0.009   0.000   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  507)
  hydrogen bonds       : angle       4.95259 ( 1440)
  covalent geometry    : bond        0.00343 (14702)
  covalent geometry    : angle       0.69235 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 212
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TYR cc_start: 0.3122 (m-80) cc_final: 0.2832 (m-80)
REVERT: A  211 LEU cc_start: 0.6372 (mm) cc_final: 0.6102 (mm)
REVERT: A  304 LEU cc_start: 0.6970 (mm) cc_final: 0.6481 (mm)
REVERT: A  345 TRP cc_start: 0.6175 (m-90) cc_final: 0.4410 (t-100)
REVERT: A  420 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7414 (m-70)
REVERT: A  615 SER cc_start: 0.4906 (OUTLIER) cc_final: 0.2971 (m)
REVERT: A  812 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6853 (ptm)
REVERT: A  907 PHE cc_start: 0.8409 (t80) cc_final: 0.7201 (t80)
REVERT: A  955 TYR cc_start: 0.7794 (m-80) cc_final: 0.7588 (m-80)
REVERT: A  964 ARG cc_start: 0.6486 (mpt90) cc_final: 0.6192 (mpt180)
REVERT: A 1057 MET cc_start: 0.6769 (ppp) cc_final: 0.6532 (ppp)
REVERT: A 1093 MET cc_start: 0.5315 (tpt) cc_final: 0.4741 (ptp)
REVERT: A 1108 TYR cc_start: 0.7757 (t80) cc_final: 0.7329 (t80)
REVERT: A 1116 MET cc_start: 0.6702 (mtm) cc_final: 0.6190 (mtp)
REVERT: A 1175 GLN cc_start: 0.8068 (tp40) cc_final: 0.7805 (tp40)
REVERT: A 1214 GLN cc_start: 0.6060 (tm-30) cc_final: 0.5696 (tm-30)
REVERT: B  261 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6901 (tp40)
REVERT: C  256 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7632 (tp)
REVERT: C  281 GLU cc_start: 0.7525 (mp0) cc_final: 0.7228 (pp20)
REVERT: C  400 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7648 (tm-30)
REVERT: C  466 MET cc_start: 0.7834 (ttm) cc_final: 0.7519 (ttm)
REVERT: C  479 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6729 (pt)
  outliers start: 48
  outliers final: 28
  residues processed: 247
  average time/residue: 0.2577
  time to fit residues: 94.2099
Evaluate side-chains
  234 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 200
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  420 HIS
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1119 LEU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  261 GLN
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 167 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 162 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
B 409 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 427 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 = 0.4409 r_free = 0.4409 target = 0.182532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.138619 restraints weight = 26735.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 3.02
r_work: 0.3696 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3704 r_free = 0.3704    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14702  Z= 0.161
  Angle     :  0.697  12.927  20090  Z= 0.350
  Chirality :  0.044   0.196   2184
  Planarity :  0.005   0.050   2452
  Dihedral  : 17.193 174.863   2230
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.27 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.37 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.21), residues: 1680
  helix:  0.31 (0.22), residues: 610
  sheet: -0.90 (0.33), residues: 219
  loop : -2.03 (0.21), residues: 851

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 312 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.016   0.001   PHE A 139 
 TYR   0.035   0.002   TYR A1108 
 ARG   0.009   0.000   ARG A 597 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  507)
  hydrogen bonds       : angle       4.92602 ( 1440)
  covalent geometry    : bond        0.00362 (14702)
  covalent geometry    : angle       0.69683 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 208
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.6323 (mm) cc_final: 0.6098 (mm)
REVERT: A  279 ARG cc_start: 0.5679 (OUTLIER) cc_final: 0.5450 (tpm170)
REVERT: A  304 LEU cc_start: 0.7000 (mm) cc_final: 0.6437 (mm)
REVERT: A  345 TRP cc_start: 0.6187 (m-90) cc_final: 0.4414 (t-100)
REVERT: A  623 LEU cc_start: 0.6050 (mt) cc_final: 0.5682 (mt)
REVERT: A  797 MET cc_start: 0.8081 (mtt) cc_final: 0.7868 (mtm)
REVERT: A  812 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7004 (ptm)
REVERT: A  907 PHE cc_start: 0.8449 (t80) cc_final: 0.7279 (t80)
REVERT: A  964 ARG cc_start: 0.6483 (mpt90) cc_final: 0.6179 (mpt180)
REVERT: A 1093 MET cc_start: 0.5284 (tpt) cc_final: 0.4796 (ptt)
REVERT: A 1094 THR cc_start: 0.6818 (p) cc_final: 0.6462 (t)
REVERT: A 1116 MET cc_start: 0.6791 (mtm) cc_final: 0.6379 (mtp)
REVERT: A 1214 GLN cc_start: 0.6089 (tm-30) cc_final: 0.5727 (tm-30)
REVERT: B   75 ARG cc_start: 0.7092 (ttp-170) cc_final: 0.6845 (mtp180)
REVERT: C  256 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7668 (tp)
REVERT: C  281 GLU cc_start: 0.7508 (mp0) cc_final: 0.7227 (pp20)
REVERT: C  400 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: C  466 MET cc_start: 0.7793 (ttm) cc_final: 0.7541 (ttm)
REVERT: C  479 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6742 (pt)
  outliers start: 48
  outliers final: 34
  residues processed: 240
  average time/residue: 0.2529
  time to fit residues: 89.6099
Evaluate side-chains
  239 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 201
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  279 ARG
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  615 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  431 LYS
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 115 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 125 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
B 132 HIS
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
C 187 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.178631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.134342 restraints weight = 25469.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.92
r_work: 0.3643 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  14702  Z= 0.258
  Angle     :  0.778  13.166  20090  Z= 0.394
  Chirality :  0.047   0.214   2184
  Planarity :  0.005   0.052   2452
  Dihedral  : 17.253 175.405   2230
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.99 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.58 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.20), residues: 1680
  helix:  0.02 (0.21), residues: 610
  sheet: -0.87 (0.34), residues: 214
  loop : -2.20 (0.21), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 312 
 HIS   0.019   0.001   HIS C 258 
 PHE   0.030   0.002   PHE A 961 
 TYR   0.024   0.002   TYR B 432 
 ARG   0.009   0.001   ARG B 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04439 (  507)
  hydrogen bonds       : angle       5.18383 ( 1440)
  covalent geometry    : bond        0.00589 (14702)
  covalent geometry    : angle       0.77816 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 196
  time to evaluate  : 1.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7007 (pp30) cc_final: 0.6752 (pp30)
REVERT: A  211 LEU cc_start: 0.6376 (mm) cc_final: 0.6125 (mm)
REVERT: A  275 ARG cc_start: 0.7919 (tmt170) cc_final: 0.7194 (tmt170)
REVERT: A  279 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5540 (tpm170)
REVERT: A  304 LEU cc_start: 0.7200 (mm) cc_final: 0.6421 (mm)
REVERT: A  454 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: A  797 MET cc_start: 0.8111 (mtt) cc_final: 0.7906 (mtm)
REVERT: A  812 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6814 (ptm)
REVERT: A  907 PHE cc_start: 0.8515 (t80) cc_final: 0.7477 (t80)
REVERT: A  964 ARG cc_start: 0.6563 (mpt90) cc_final: 0.6250 (mpt180)
REVERT: A 1093 MET cc_start: 0.5233 (tpt) cc_final: 0.4648 (ptt)
REVERT: A 1094 THR cc_start: 0.6914 (p) cc_final: 0.6522 (t)
REVERT: A 1214 GLN cc_start: 0.6055 (tm-30) cc_final: 0.5671 (tm-30)
REVERT: B   75 ARG cc_start: 0.7171 (ttp-170) cc_final: 0.6908 (mtp180)
REVERT: C  203 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7319 (ptt180)
REVERT: C  256 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7865 (tp)
REVERT: C  400 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: C  479 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6918 (pt)
  outliers start: 51
  outliers final: 35
  residues processed: 229
  average time/residue: 0.2573
  time to fit residues: 88.4442
Evaluate side-chains
  226 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 187
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  279 ARG
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  420 HIS
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  256 LEU
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 114 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 108 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 163 optimal weight:    0.5980
   chunk 67 optimal weight:    8.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
B 409 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 HIS
C 318 ASN
** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.183010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.139280 restraints weight = 25837.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.97
r_work: 0.3708 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14702  Z= 0.140
  Angle     :  0.708  11.491  20090  Z= 0.353
  Chirality :  0.044   0.178   2184
  Planarity :  0.004   0.050   2452
  Dihedral  : 17.164 175.285   2230
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.04 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 22.83 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.21), residues: 1680
  helix:  0.29 (0.22), residues: 602
  sheet: -0.74 (0.34), residues: 214
  loop : -2.04 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 312 
 HIS   0.012   0.001   HIS C 258 
 PHE   0.027   0.001   PHE A 961 
 TYR   0.035   0.001   TYR A1108 
 ARG   0.008   0.001   ARG A 597 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  507)
  hydrogen bonds       : angle       4.91307 ( 1440)
  covalent geometry    : bond        0.00312 (14702)
  covalent geometry    : angle       0.70810 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 203
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6897 (pp30) cc_final: 0.6682 (pp30)
REVERT: A  275 ARG cc_start: 0.7651 (tmt170) cc_final: 0.7424 (tpt-90)
REVERT: A  279 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5360 (tpm170)
REVERT: A  304 LEU cc_start: 0.6994 (mm) cc_final: 0.6369 (mm)
REVERT: A  345 TRP cc_start: 0.6144 (m-90) cc_final: 0.4388 (t-100)
REVERT: A  812 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6988 (ptm)
REVERT: A  907 PHE cc_start: 0.8445 (t80) cc_final: 0.7396 (t80)
REVERT: A  964 ARG cc_start: 0.6445 (mpt90) cc_final: 0.6122 (mpt180)
REVERT: A 1093 MET cc_start: 0.5284 (tpt) cc_final: 0.4848 (ptt)
REVERT: A 1094 THR cc_start: 0.6837 (p) cc_final: 0.6516 (t)
REVERT: A 1214 GLN cc_start: 0.6138 (tm-30) cc_final: 0.5812 (tm-30)
REVERT: B   75 ARG cc_start: 0.7113 (ttp-170) cc_final: 0.6850 (mtp180)
REVERT: C  256 LEU cc_start: 0.7922 (tt) cc_final: 0.7709 (tp)
REVERT: C  400 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: C  479 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6771 (pt)
  outliers start: 36
  outliers final: 29
  residues processed: 229
  average time/residue: 0.2663
  time to fit residues: 90.9179
Evaluate side-chains
  229 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  279 ARG
Chi-restraints excluded: chain A residue  420 HIS
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 155 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 427 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 = 0.4400 r_free = 0.4400 target = 0.181692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.137155 restraints weight = 29087.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 3.16
r_work: 0.3678 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3685 r_free = 0.3685    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3685 r_free = 0.3685    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14702  Z= 0.175
  Angle     :  0.724  11.625  20090  Z= 0.363
  Chirality :  0.044   0.190   2184
  Planarity :  0.005   0.055   2452
  Dihedral  : 17.125 175.231   2230
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.75 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.97 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.21), residues: 1680
  helix:  0.28 (0.22), residues: 603
  sheet: -0.75 (0.34), residues: 216
  loop : -2.05 (0.21), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 312 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.027   0.002   PHE A 961 
 TYR   0.040   0.002   TYR A1108 
 ARG   0.010   0.001   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  507)
  hydrogen bonds       : angle       4.94418 ( 1440)
  covalent geometry    : bond        0.00398 (14702)
  covalent geometry    : angle       0.72390 (20090)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 1.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6907 (pp30) cc_final: 0.6660 (pp30)
REVERT: A  275 ARG cc_start: 0.7691 (tmt170) cc_final: 0.7364 (tpt-90)
REVERT: A  279 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5409 (tpm170)
REVERT: A  345 TRP cc_start: 0.6286 (m-90) cc_final: 0.4552 (t-100)
REVERT: A  454 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7112 (mm-30)
REVERT: A  812 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6980 (ptm)
REVERT: A  907 PHE cc_start: 0.8459 (t80) cc_final: 0.7498 (t80)
REVERT: A  964 ARG cc_start: 0.6497 (mpt90) cc_final: 0.6144 (mpt180)
REVERT: A 1093 MET cc_start: 0.5106 (tpt) cc_final: 0.4366 (ppp)
REVERT: A 1094 THR cc_start: 0.6817 (p) cc_final: 0.5109 (t)
REVERT: A 1214 GLN cc_start: 0.6163 (tm-30) cc_final: 0.5831 (tm-30)
REVERT: B   75 ARG cc_start: 0.7127 (ttp-170) cc_final: 0.6870 (mtp180)
REVERT: C  197 LEU cc_start: 0.8236 (tt) cc_final: 0.7995 (tt)
REVERT: C  256 LEU cc_start: 0.7970 (tt) cc_final: 0.7750 (tp)
REVERT: C  400 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7604 (tm-30)
REVERT: C  479 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6859 (pt)
  outliers start: 40
  outliers final: 32
  residues processed: 230
  average time/residue: 0.2559
  time to fit residues: 87.7463
Evaluate side-chains
  232 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  279 ARG
Chi-restraints excluded: chain A residue  420 HIS
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  812 MET
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1119 LEU
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  427 GLN
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  479 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 132 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0010
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 959 GLN
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 427 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 = 0.4424 r_free = 0.4424 target = 0.183932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.140454 restraints weight = 25527.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.95
r_work: 0.3726 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14702  Z= 0.136
  Angle     :  0.709  11.832  20090  Z= 0.353
  Chirality :  0.044   0.191   2184
  Planarity :  0.004   0.054   2452
  Dihedral  : 17.063 175.326   2230
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.10 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.66 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.21), residues: 1680
  helix:  0.37 (0.22), residues: 599
  sheet: -0.51 (0.34), residues: 204
  loop : -2.03 (0.21), residues: 877

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP A 312 
 HIS   0.004   0.001   HIS C 187 
 PHE   0.026   0.001   PHE A 961 
 TYR   0.018   0.001   TYR A1108 
 ARG   0.009   0.001   ARG A 275 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  507)
  hydrogen bonds       : angle       4.85035 ( 1440)
  covalent geometry    : bond        0.00302 (14702)
  covalent geometry    : angle       0.70866 (20090)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9236.08 seconds
wall clock time: 162 minutes 59.52 seconds (9779.52 seconds total)