Starting phenix.real_space_refine
on Sat Oct 11 11:24:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t7e_41091/10_2025/8t7e_41091_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t7e_41091/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t7e_41091/10_2025/8t7e_41091_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t7e_41091/10_2025/8t7e_41091_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t7e_41091/10_2025/8t7e_41091.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t7e_41091/10_2025/8t7e_41091.map"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3}
          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: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 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: 3.46, per 1000 atoms: 0.24
  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: 1.20
  Conformation dependent library (CDL) restraints added in 593.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.69
  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: 2.48

  Time building geometry restraints manager: 1.58 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:             2.080
  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:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.380
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.290
-------------------------------------------------------------------------------
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 : 6.76
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.94 (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
 ARG   0.009   0.001   ARG A1187 
 TYR   0.033   0.002   TYR A 150 
 PHE   0.025   0.002   PHE A 197 
 TRP   0.026   0.002   TRP C 241 
 HIS   0.011   0.001   HIS C 454 

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

*********************** 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  : 0.583 
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: 0.6992 (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: 0.6770 (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: 0.1365
  time to fit residues: 59.5221
Evaluate side-chains
  199 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.0870
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 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 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: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.191213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.149229 restraints weight = 25491.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 2.97
r_work: 0.3840 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1699

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= 0.141
  Angle     :  0.721  24.056  20090  Z= 0.356
  Chirality :  0.065   2.308   2184
  Planarity :  0.005   0.066   2452
  Dihedral  : 17.320 173.756   2232
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.56 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.16 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.20), residues: 1680
  helix: -0.53 (0.21), residues: 591
  sheet: -0.53 (0.34), residues: 213
  loop : -2.07 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1187 
 TYR   0.016   0.002   TYR A 150 
 PHE   0.018   0.002   PHE A 377 
 TRP   0.027   0.001   TRP A1118 
 HIS   0.010   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (14702)
  covalent geometry    : angle       0.72114 (20090)
  hydrogen bonds       : bond        0.04178 (  507)
  hydrogen bonds       : angle       5.29551 ( 1440)

*********************** 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
  256 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 231
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6486 (pp30) cc_final: 0.6229 (pp30)
REVERT: A  279 ARG cc_start: 0.5666 (tpm170) cc_final: 0.5014 (ttp80)
REVERT: A  544 MET cc_start: 0.7748 (ppp) cc_final: 0.7490 (ppp)
REVERT: A  744 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8256 (mm)
REVERT: A  768 LYS cc_start: 0.7255 (mttp) cc_final: 0.7050 (mmmt)
REVERT: A  907 PHE cc_start: 0.8038 (t80) cc_final: 0.6870 (t80)
REVERT: A  955 TYR cc_start: 0.7444 (m-80) cc_final: 0.7180 (m-80)
REVERT: A 1093 MET cc_start: 0.5567 (tpt) cc_final: 0.4526 (ptp)
REVERT: B   74 GLN cc_start: 0.7443 (mp10) cc_final: 0.7226 (mp10)
REVERT: C  400 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: C  466 MET cc_start: 0.7622 (ttm) cc_final: 0.7207 (ttt)
  outliers start: 25
  outliers final: 12
  residues processed: 247
  average time/residue: 0.1243
  time to fit residues: 45.0454
Evaluate side-chains
  219 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 206
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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  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 146 optimal weight:    0.0570
   chunk 52 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 152 optimal weight:    0.6980
   chunk 132 optimal weight:    2.9990
   chunk 157 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.0900

-------------------------------------------------------------------------------
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 368 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.188187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.145108 restraints weight = 27709.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 3.09
r_work: 0.3781 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2191

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     :  0.708  24.195  20090  Z= 0.347
  Chirality :  0.061   2.044   2184
  Planarity :  0.005   0.053   2452
  Dihedral  : 17.189 173.085   2231
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.56 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.34 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.20), residues: 1680
  helix:  0.15 (0.22), residues: 598
  sheet: -0.78 (0.33), residues: 224
  loop : -1.92 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 386 
 TYR   0.018   0.001   TYR A 434 
 PHE   0.023   0.002   PHE A 961 
 TRP   0.020   0.001   TRP A 312 
 HIS   0.008   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (14702)
  covalent geometry    : angle       0.70824 (20090)
  hydrogen bonds       : bond        0.03909 (  507)
  hydrogen bonds       : angle       4.95013 ( 1440)

*********************** 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
  252 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 215
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TYR cc_start: 0.3050 (m-80) cc_final: 0.2672 (m-80)
REVERT: A  544 MET cc_start: 0.7792 (ppp) cc_final: 0.7424 (ppp)
REVERT: A  550 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7144 (tm-30)
REVERT: A  744 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8312 (mm)
REVERT: A  907 PHE cc_start: 0.8153 (t80) cc_final: 0.7051 (t80)
REVERT: A  964 ARG cc_start: 0.6395 (mpt90) cc_final: 0.6128 (mpt180)
REVERT: A 1108 TYR cc_start: 0.7267 (t80) cc_final: 0.6998 (t80)
REVERT: A 1112 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7272 (mtt)
REVERT: A 1116 MET cc_start: 0.6841 (mtm) cc_final: 0.6638 (mtt)
REVERT: C  219 PHE cc_start: 0.6730 (m-10) cc_final: 0.6520 (m-10)
REVERT: C  281 GLU cc_start: 0.7685 (mp0) cc_final: 0.7370 (pp20)
REVERT: C  325 ARG cc_start: 0.6134 (tpp-160) cc_final: 0.5542 (tpp-160)
REVERT: C  400 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7325 (tm-30)
  outliers start: 37
  outliers final: 22
  residues processed: 240
  average time/residue: 0.1237
  time to fit residues: 43.9428
Evaluate side-chains
  228 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
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  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 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  331 VAL
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 B residue  453 ILE
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  261 GLN
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 100 optimal weight:    8.9990
   chunk 115 optimal weight:    0.0070
   chunk 14 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 116 optimal weight:    0.6980
   chunk 140 optimal weight:    7.9990
   chunk 93 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0970
   chunk 149 optimal weight:    0.5980
   chunk 144 optimal weight:    4.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 950 ASN
A 959 GLN
B 216 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.189862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.146543 restraints weight = 29289.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 3.24
r_work: 0.3799 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3809
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3809 r_free = 0.3809    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3809 r_free = 0.3809    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3809
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2382

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= 0.123
  Angle     :  0.686  24.278  20090  Z= 0.330
  Chirality :  0.060   2.042   2184
  Planarity :  0.004   0.050   2452
  Dihedral  : 17.065 173.820   2231
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.14 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.72 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.21), residues: 1680
  helix:  0.51 (0.22), residues: 592
  sheet: -0.56 (0.34), residues: 209
  loop : -1.88 (0.21), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 275 
 TYR   0.016   0.001   TYR A 434 
 PHE   0.014   0.001   PHE B 403 
 TRP   0.027   0.001   TRP A 312 
 HIS   0.005   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (14702)
  covalent geometry    : angle       0.68600 (20090)
  hydrogen bonds       : bond        0.03502 (  507)
  hydrogen bonds       : angle       4.73121 ( 1440)

*********************** 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
  250 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 214
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  544 MET cc_start: 0.7782 (ppp) cc_final: 0.7416 (ppp)
REVERT: A  744 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  907 PHE cc_start: 0.8128 (t80) cc_final: 0.6936 (t80)
REVERT: A  955 TYR cc_start: 0.7722 (m-80) cc_final: 0.7128 (m-80)
REVERT: A  964 ARG cc_start: 0.6410 (mpt90) cc_final: 0.6118 (mpt180)
REVERT: A 1093 MET cc_start: 0.5231 (tpt) cc_final: 0.4310 (ptt)
REVERT: C  400 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7220 (tm-30)
REVERT: C  479 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6553 (pt)
  outliers start: 36
  outliers final: 22
  residues processed: 237
  average time/residue: 0.1190
  time to fit residues: 42.3684
Evaluate side-chains
  223 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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  189 ILE
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 1074 VAL
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue   75 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  367 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  261 GLN
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 34 optimal weight:    1.9990
   chunk 170 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 564 GLN
A 565 HIS
A 894 GLN
A 911 HIS
B 132 HIS
** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 HIS
B 323 HIS
B 427 GLN
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 427 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.178871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.133880 restraints weight = 29857.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 3.20
r_work: 0.3629 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3635
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086  14702  Z= 0.314
  Angle     :  0.856  24.604  20090  Z= 0.425
  Chirality :  0.065   2.008   2184
  Planarity :  0.006   0.065   2452
  Dihedral  : 17.188 174.440   2231
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.51 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 17.49 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.20), residues: 1680
  helix:  0.02 (0.21), residues: 601
  sheet: -1.09 (0.32), residues: 234
  loop : -2.07 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 617 
 TYR   0.029   0.003   TYR A 434 
 PHE   0.028   0.003   PHE B 266 
 TRP   0.027   0.002   TRP A 312 
 HIS   0.010   0.002   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 (14702)
  covalent geometry    : angle       0.85642 (20090)
  hydrogen bonds       : bond        0.04852 (  507)
  hydrogen bonds       : angle       5.29175 ( 1440)

*********************** 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
  270 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 210
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6934 (pp30) cc_final: 0.6702 (pp30)
REVERT: A  211 LEU cc_start: 0.6475 (mm) cc_final: 0.6218 (mm)
REVERT: A  279 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5723 (tpm170)
REVERT: A  454 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7243 (mm-30)
REVERT: A  544 MET cc_start: 0.8143 (ppp) cc_final: 0.7849 (ppp)
REVERT: A  744 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (mm)
REVERT: A  755 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5113 (ptpt)
REVERT: A  907 PHE cc_start: 0.8419 (t80) cc_final: 0.7108 (t80)
REVERT: A  955 TYR cc_start: 0.7754 (m-80) cc_final: 0.7413 (m-80)
REVERT: A  964 ARG cc_start: 0.6574 (mpt90) cc_final: 0.6275 (mpt180)
REVERT: A 1093 MET cc_start: 0.5187 (tpt) cc_final: 0.4197 (ptt)
REVERT: A 1116 MET cc_start: 0.7151 (mtm) cc_final: 0.6442 (mtt)
REVERT: A 1128 ARG cc_start: 0.7306 (mmt-90) cc_final: 0.6832 (mmm160)
REVERT: A 1214 GLN cc_start: 0.5998 (tm-30) cc_final: 0.5624 (tm-30)
REVERT: B  261 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7040 (tp40)
REVERT: C  256 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7839 (tp)
REVERT: C  325 ARG cc_start: 0.6148 (tpp-160) cc_final: 0.4723 (tpt170)
REVERT: C  385 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.5083 (mt)
REVERT: C  400 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: C  466 MET cc_start: 0.7704 (ttm) cc_final: 0.7347 (ttm)
REVERT: C  479 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7003 (pt)
  outliers start: 60
  outliers final: 37
  residues processed: 251
  average time/residue: 0.1223
  time to fit residues: 45.1350
Evaluate side-chains
  231 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 187
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
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  279 ARG
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  445 LEU
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  610 PHE
Chi-restraints excluded: chain A residue  613 HIS
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  755 LYS
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  920 THR
Chi-restraints excluded: chain A residue  927 ARG
Chi-restraints excluded: chain A residue 1074 VAL
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  197 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  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  147 LEU
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  444 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 131 optimal weight:    0.3980
   chunk 114 optimal weight:    0.8980
   chunk 138 optimal weight:    2.9990
   chunk 142 optimal weight:    0.0980
   chunk 95 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 94 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS
A 565 HIS
A 959 GLN
B 124 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 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 = 0.4423 r_free = 0.4423 target = 0.183755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.139133 restraints weight = 31471.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 3.31
r_work: 0.3694 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
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 = 0.10   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 = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.3235

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= 0.142
  Angle     :  0.724  24.355  20090  Z= 0.354
  Chirality :  0.061   2.015   2184
  Planarity :  0.004   0.052   2452
  Dihedral  : 17.098 175.379   2231
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.62 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.88 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.21), residues: 1680
  helix:  0.38 (0.22), residues: 601
  sheet: -0.93 (0.33), residues: 221
  loop : -1.93 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 597 
 TYR   0.019   0.001   TYR A 434 
 PHE   0.014   0.001   PHE B 403 
 TRP   0.031   0.001   TRP A 312 
 HIS   0.005   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14702)
  covalent geometry    : angle       0.72412 (20090)
  hydrogen bonds       : bond        0.03767 (  507)
  hydrogen bonds       : angle       4.92912 ( 1440)

*********************** 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
  259 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 213
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6903 (pp30) cc_final: 0.6550 (pp30)
REVERT: A  279 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.5484 (tpm170)
REVERT: A  304 LEU cc_start: 0.6758 (mm) cc_final: 0.6442 (mm)
REVERT: A  345 TRP cc_start: 0.6146 (m-90) cc_final: 0.4223 (t-100)
REVERT: A  420 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7366 (m-70)
REVERT: A  544 MET cc_start: 0.7965 (ppp) cc_final: 0.7647 (ppp)
REVERT: A  559 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5408 (mt)
REVERT: A  812 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7003 (ptm)
REVERT: A  907 PHE cc_start: 0.8335 (t80) cc_final: 0.7023 (t80)
REVERT: A  955 TYR cc_start: 0.7765 (m-80) cc_final: 0.7494 (m-80)
REVERT: A  964 ARG cc_start: 0.6522 (mpt90) cc_final: 0.6221 (mpt180)
REVERT: A 1175 GLN cc_start: 0.8109 (tp40) cc_final: 0.7640 (tp40)
REVERT: A 1214 GLN cc_start: 0.6071 (tm-30) cc_final: 0.5732 (tm-30)
REVERT: B  256 LEU cc_start: 0.8562 (tt) cc_final: 0.8312 (tt)
REVERT: C  400 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: C  479 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6726 (pt)
  outliers start: 46
  outliers final: 26
  residues processed: 245
  average time/residue: 0.1213
  time to fit residues: 43.8836
Evaluate side-chains
  238 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 207
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  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  559 LEU
Chi-restraints excluded: chain A residue  610 PHE
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  920 THR
Chi-restraints excluded: chain A residue 1074 VAL
Chi-restraints excluded: chain A residue 1112 MET
Chi-restraints excluded: chain A residue 1170 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  387 VAL
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  405 GLU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 90 optimal weight:    0.6980
   chunk 162 optimal weight:    3.9990
   chunk 150 optimal weight:    5.9990
   chunk 153 optimal weight:    3.9990
   chunk 158 optimal weight:    0.0170
   chunk 12 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    2.3424

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

Flipped N/Q/H residues before XYZ refinement:
A 906 HIS
A 959 GLN
B 368 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.179855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.135675 restraints weight = 26798.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 3.01
r_work: 0.3660 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  14702  Z= 0.236
  Angle     :  0.783  24.816  20090  Z= 0.387
  Chirality :  0.063   1.993   2184
  Planarity :  0.005   0.051   2452
  Dihedral  : 17.074 174.877   2231
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.51 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.47 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.20), residues: 1680
  helix:  0.18 (0.22), residues: 601
  sheet: -0.84 (0.34), residues: 216
  loop : -2.05 (0.21), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 597 
 TYR   0.020   0.002   TYR A 434 
 PHE   0.026   0.002   PHE A 961 
 TRP   0.034   0.002   TRP A 312 
 HIS   0.007   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (14702)
  covalent geometry    : angle       0.78335 (20090)
  hydrogen bonds       : bond        0.04218 (  507)
  hydrogen bonds       : angle       5.09282 ( 1440)

*********************** 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
  239 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 197
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.7002 (pp30) cc_final: 0.6682 (pp30)
REVERT: A  304 LEU cc_start: 0.6993 (mm) cc_final: 0.6638 (mm)
REVERT: A  420 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (m-70)
REVERT: A  544 MET cc_start: 0.8039 (ppp) cc_final: 0.7758 (ppp)
REVERT: A  907 PHE cc_start: 0.8465 (t80) cc_final: 0.7285 (t80)
REVERT: A  955 TYR cc_start: 0.7818 (m-80) cc_final: 0.7590 (m-80)
REVERT: A  964 ARG cc_start: 0.6609 (mpt90) cc_final: 0.6288 (mpt180)
REVERT: A 1093 MET cc_start: 0.5711 (tpt) cc_final: 0.5122 (ptp)
REVERT: A 1214 GLN cc_start: 0.6033 (tm-30) cc_final: 0.5683 (tm-30)
REVERT: C  325 ARG cc_start: 0.6166 (tpp-160) cc_final: 0.4810 (tpt170)
REVERT: C  400 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: C  479 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6893 (pt)
  outliers start: 42
  outliers final: 29
  residues processed: 228
  average time/residue: 0.1234
  time to fit residues: 41.6501
Evaluate side-chains
  226 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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  610 PHE
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  920 THR
Chi-restraints excluded: chain A residue  927 ARG
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  152 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  258 HIS
Chi-restraints excluded: chain C residue  440 THR
Chi-restraints excluded: chain C residue  444 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 100 optimal weight:    7.9990
   chunk 166 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0030
   chunk 164 optimal weight:    1.9990
   chunk 143 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0980
   chunk 115 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
A 906 HIS
A 959 GLN
B 368 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 427 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.183336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.139722 restraints weight = 27301.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 3.04
r_work: 0.3713 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3719 r_free = 0.3719    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14702  Z= 0.141
  Angle     :  0.726  24.979  20090  Z= 0.355
  Chirality :  0.061   1.995   2184
  Planarity :  0.004   0.050   2452
  Dihedral  : 16.967 175.028   2231
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.98 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.61 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.21), residues: 1680
  helix:  0.40 (0.22), residues: 601
  sheet: -0.84 (0.34), residues: 221
  loop : -1.91 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 597 
 TYR   0.024   0.001   TYR B 432 
 PHE   0.028   0.001   PHE A 961 
 TRP   0.038   0.001   TRP A 312 
 HIS   0.014   0.001   HIS C 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (14702)
  covalent geometry    : angle       0.72582 (20090)
  hydrogen bonds       : bond        0.03726 (  507)
  hydrogen bonds       : angle       4.87544 ( 1440)

*********************** 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
  251 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 208
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6927 (pp30) cc_final: 0.6588 (pp30)
REVERT: A  279 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5553 (tpm170)
REVERT: A  304 LEU cc_start: 0.6904 (mm) cc_final: 0.6537 (mm)
REVERT: A  345 TRP cc_start: 0.6149 (m-90) cc_final: 0.4238 (t-100)
REVERT: A  812 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7083 (ptm)
REVERT: A  907 PHE cc_start: 0.8447 (t80) cc_final: 0.7276 (t80)
REVERT: A  964 ARG cc_start: 0.6564 (mpt90) cc_final: 0.6257 (mpt180)
REVERT: A 1093 MET cc_start: 0.5588 (tpt) cc_final: 0.5025 (ptp)
REVERT: A 1214 GLN cc_start: 0.6129 (tm-30) cc_final: 0.5806 (tm-30)
REVERT: C  325 ARG cc_start: 0.6108 (tpp-160) cc_final: 0.4538 (tpt170)
REVERT: C  400 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: C  479 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6715 (pt)
  outliers start: 43
  outliers final: 24
  residues processed: 239
  average time/residue: 0.1185
  time to fit residues: 41.8552
Evaluate side-chains
  225 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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  279 ARG
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  552 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  813 VAL
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 140 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 135 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0010
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 959 GLN
B 368 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 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 = 0.4435 r_free = 0.4435 target = 0.184746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.141464 restraints weight = 25653.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 2.94
r_work: 0.3737 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3744 r_free = 0.3744    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3744 r_free = 0.3744    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14702  Z= 0.137
  Angle     :  0.729  25.362  20090  Z= 0.354
  Chirality :  0.060   1.972   2184
  Planarity :  0.004   0.050   2452
  Dihedral  : 16.826 174.623   2231
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.04 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.65 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.21), residues: 1680
  helix:  0.51 (0.22), residues: 604
  sheet: -0.52 (0.34), residues: 206
  loop : -1.94 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 597 
 TYR   0.021   0.001   TYR A1108 
 PHE   0.028   0.001   PHE A 961 
 TRP   0.045   0.001   TRP A 312 
 HIS   0.006   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (14702)
  covalent geometry    : angle       0.72922 (20090)
  hydrogen bonds       : bond        0.03574 (  507)
  hydrogen bonds       : angle       4.78163 ( 1440)

*********************** 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
  246 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 209
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6897 (pp30) cc_final: 0.6597 (pp30)
REVERT: A  304 LEU cc_start: 0.6963 (mm) cc_final: 0.6532 (mm)
REVERT: A  812 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7061 (ptm)
REVERT: A  907 PHE cc_start: 0.8448 (t80) cc_final: 0.7302 (t80)
REVERT: A  964 ARG cc_start: 0.6561 (mpt90) cc_final: 0.6262 (mpt180)
REVERT: A 1093 MET cc_start: 0.5395 (tpt) cc_final: 0.5011 (ptt)
REVERT: A 1108 TYR cc_start: 0.7770 (t80) cc_final: 0.7530 (t80)
REVERT: A 1214 GLN cc_start: 0.6138 (tm-30) cc_final: 0.5827 (tm-30)
REVERT: C  325 ARG cc_start: 0.6091 (tpp-160) cc_final: 0.4747 (tpt170)
REVERT: C  400 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: C  479 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6773 (pt)
  outliers start: 37
  outliers final: 27
  residues processed: 236
  average time/residue: 0.1207
  time to fit residues: 42.3492
Evaluate side-chains
  228 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 199
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
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  559 LEU
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  920 THR
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  219 PHE
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  448 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 ILE
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 28 optimal weight:    4.9990
   chunk 145 optimal weight:    2.9990
   chunk 88 optimal weight:    0.1980
   chunk 53 optimal weight:    0.2980
   chunk 1 optimal weight:    8.9990
   chunk 164 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 121 optimal weight:    0.9980
   chunk 15 optimal weight:   20.0000
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 HIS
B 368 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 187 HIS
** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.185053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.141272 restraints weight = 28353.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 3.15
r_work: 0.3733 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14702  Z= 0.134
  Angle     :  0.732  25.766  20090  Z= 0.354
  Chirality :  0.060   1.944   2184
  Planarity :  0.004   0.050   2452
  Dihedral  : 16.730 174.766   2231
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.21 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.37 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.21), residues: 1680
  helix:  0.52 (0.22), residues: 601
  sheet: -0.48 (0.34), residues: 206
  loop : -1.92 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 275 
 TYR   0.015   0.001   TYR A 434 
 PHE   0.028   0.001   PHE A 961 
 TRP   0.049   0.001   TRP A 312 
 HIS   0.008   0.001   HIS A 906 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (14702)
  covalent geometry    : angle       0.73186 (20090)
  hydrogen bonds       : bond        0.03618 (  507)
  hydrogen bonds       : angle       4.74673 ( 1440)

********************** 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
  238 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 202
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLN cc_start: 0.6871 (pp30) cc_final: 0.6579 (pp30)
REVERT: A  304 LEU cc_start: 0.6932 (mm) cc_final: 0.6430 (mm)
REVERT: A  615 SER cc_start: 0.4990 (OUTLIER) cc_final: 0.3232 (m)
REVERT: A  812 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7019 (ptm)
REVERT: A  907 PHE cc_start: 0.8391 (t80) cc_final: 0.7333 (t80)
REVERT: A  964 ARG cc_start: 0.6567 (mpt90) cc_final: 0.6264 (mpt180)
REVERT: A 1093 MET cc_start: 0.5500 (tpt) cc_final: 0.5124 (ptt)
REVERT: A 1214 GLN cc_start: 0.6093 (tm-30) cc_final: 0.5789 (tm-30)
REVERT: C  197 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7621 (tt)
REVERT: C  325 ARG cc_start: 0.6096 (tpp-160) cc_final: 0.4811 (tpt170)
REVERT: C  400 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7439 (tm-30)
REVERT: C  479 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6707 (pt)
  outliers start: 36
  outliers final: 31
  residues processed: 228
  average time/residue: 0.1136
  time to fit residues: 39.2505
Evaluate side-chains
  230 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 195
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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  559 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  615 SER
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  906 HIS
Chi-restraints excluded: chain A residue  920 THR
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  219 PHE
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  405 GLU
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  268 MET
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 150 optimal weight:    7.9990
   chunk 134 optimal weight:    4.9990
   chunk 121 optimal weight:    0.0370
   chunk 10 optimal weight:    0.2980
   chunk 74 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 133 optimal weight:    1.9990
   chunk 132 optimal weight:    0.5980
   chunk 157 optimal weight:    0.6980
   chunk 151 optimal weight:    0.6980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 HIS
B 368 HIS
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 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 = 0.4447 r_free = 0.4447 target = 0.185884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.141946 restraints weight = 36776.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 4.06
r_work: 0.3688 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14702  Z= 0.128
  Angle     :  0.723  26.168  20090  Z= 0.349
  Chirality :  0.059   1.913   2184
  Planarity :  0.004   0.051   2452
  Dihedral  : 16.648 174.792   2231
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.10 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.79 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.21), residues: 1680
  helix:  0.59 (0.22), residues: 601
  sheet: -0.46 (0.35), residues: 206
  loop : -1.86 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 325 
 TYR   0.026   0.001   TYR A1108 
 PHE   0.028   0.001   PHE A 961 
 TRP   0.052   0.001   TRP A 312 
 HIS   0.005   0.001   HIS C 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14702)
  covalent geometry    : angle       0.72340 (20090)
  hydrogen bonds       : bond        0.03465 (  507)
  hydrogen bonds       : angle       4.65241 ( 1440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4423.10 seconds
wall clock time: 76 minutes 26.55 seconds (4586.55 seconds total)