Starting phenix.real_space_refine
on Fri May 16 12:48:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g5j_29746/05_2025/8g5j_29746_neut.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
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      40      5.49       5
     S      80      5.16       5
     C    9131      2.51       5
     N    2562      2.21       5
     O    2731      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14544
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 941, 7369
          Classifications: {'peptide': 941}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 60, 'TRANS': 880}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 187
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 4, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 94
    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: 3168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3168
          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: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "P"
      Number of atoms: 413
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 19, 393
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 19, 393
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 419
    Chain: "T"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" P  A DA P  28 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C4 B DA P  28 " occ=0.50
    residue:
      pdb=" P    DG T   3 " occ=0.50
      ... (20 atoms not shown)
      pdb=" C4   DG T   3 " occ=0.50
  Time building chain proxies: 8.56, per 1000 atoms: 0.59
  Number of scatterers: 14544
  At special positions: 0
  Unit cell: (102.424, 102.424, 145.376, 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      80     16.00
     P      40     15.00
     O    2731      8.00
     N    2562      7.00
     C    9131      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.41
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3242

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 10 sheets defined
      41.1% alpha, 12.2% beta
      17 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 4.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 109
      removed outlier: 3.509A  pdb=" N   GLU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 159
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 6.890A  pdb=" N   GLU A 280 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR A 282 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 283 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.725A  pdb=" N   GLY A 303 " --> pdb=" O   MET A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 316
    Processing helix  chain 'A' and resid 355 through 364
    Processing helix  chain 'A' and resid 381 through 388
    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: 4.063A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 471
      removed outlier: 3.501A  pdb=" N   ARG A 443 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 475
      removed outlier: 4.007A  pdb=" N   SER A 475 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 472 through 475'
    Processing helix  chain 'A' and resid 537 through 548
    Processing helix  chain 'A' and resid 551 through 556
      removed outlier: 4.041A  pdb=" N   THR A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 577
    Processing helix  chain 'A' and resid 597 through 604
      removed outlier: 4.002A  pdb=" N   LYS A 601 " --> pdb=" O   ARG A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 777
    Processing helix  chain 'A' and resid 786 through 810
      removed outlier: 4.719A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.597A  pdb=" N   ILE A 826 " --> pdb=" O   PRO A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 853
      removed outlier: 4.166A  pdb=" N   ARG A 853 " --> pdb=" O   ILE A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 878
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 903 through 908
    Processing helix  chain 'A' and resid 914 through 922
    Processing helix  chain 'A' and resid 930 through 939
      removed outlier: 3.503A  pdb=" N   THR A 938 " --> pdb=" O   LYS A 934 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A 939 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 954
      removed outlier: 4.629A  pdb=" N   GLY A 952 " --> pdb=" O   ILE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 971
    Processing helix  chain 'A' and resid 973 through 984
      removed outlier: 4.264A  pdb=" N   LYS A 981 " --> pdb=" O   GLU A 977 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ALA A 982 " --> pdb=" O   ALA A 978 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN A 983 " --> pdb=" O   ALA A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 988
    Processing helix  chain 'A' and resid 1057 through 1066
      removed outlier: 4.029A  pdb=" N   LEU A1061 " --> pdb=" O   MET A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1124
      removed outlier: 3.762A  pdb=" N   VAL A1101 " --> pdb=" O   VAL A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1168
    Processing helix  chain 'A' and resid 1216 through 1221
      removed outlier: 3.624A  pdb=" N   ASP A1219 " --> pdb=" O   GLU A1216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 77
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 185 through 192
    Processing helix  chain 'B' and resid 192 through 200
      removed outlier: 3.515A  pdb=" N   VAL B 200 " --> pdb=" O   CYS B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 265
    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 308 through 315
    Processing helix  chain 'B' and resid 319 through 323
    Processing helix  chain 'B' and resid 342 through 354
    Processing helix  chain 'B' and resid 394 through 409
      removed outlier: 4.062A  pdb=" N   VAL B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 435
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.918A  pdb=" N   LEU B 448 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'C' and resid 68 through 76
    Processing helix  chain 'C' and resid 88 through 93
    Processing helix  chain 'C' and resid 100 through 119
    Processing helix  chain 'C' and resid 185 through 192
    Processing helix  chain 'C' and resid 192 through 200
      removed outlier: 3.794A  pdb=" N   ASP C 198 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU C 199 " --> pdb=" O   ASN C 195 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL C 200 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 246
      No H-bonds generated for 'chain 'C' and resid 244 through 246'
    Processing helix  chain 'C' and resid 247 through 266
      removed outlier: 4.158A  pdb=" N   PHE C 266 " --> pdb=" O   TRP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 271
      No H-bonds generated for 'chain 'C' and resid 269 through 271'
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 318 through 323
      removed outlier: 3.982A  pdb=" N   LEU C 322 " --> pdb=" O   ASN C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 354
    Processing helix  chain 'C' and resid 391 through 409
    Processing helix  chain 'C' and resid 424 through 435
    Processing helix  chain 'C' and resid 444 through 451
      removed outlier: 3.584A  pdb=" N   LEU C 448 " --> pdb=" O   THR C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 484
      removed outlier: 4.590A  pdb=" N   ASP C 473 " --> pdb=" O   SER C 469 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.808A  pdb=" N   TRP A 175 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP A 220 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 211 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU A 200 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A 195 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLN A 264 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   LEU A 292 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 6.326A  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 438
      removed outlier: 4.689A  pdb=" N   TYR A 837 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1133
    Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127
      removed outlier: 6.294A  pdb=" N   PHE B 126 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 8.560A  pdb=" N   ILE B 211 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B 300 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   LYS B 297 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE B 293 " --> pdb=" O   LYS B 297 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   LEU B 299 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN B 305 " --> pdb=" O   LYS B 285 " (cutoff:3.500A)
      removed outlier: 5.087A  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 325
    Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415
      removed outlier: 7.157A  pdb=" N   VAL B 383 " --> pdb=" O   TRP B 414 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ALA B 384 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.516A  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: 6.263A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE C 300 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   LEU C 299 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 6.063A  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: 6.865A  pdb=" N   VAL C 383 " --> pdb=" O   TRP C 414 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ALA C 384 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   VAL C 443 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ASP C 386 " --> pdb=" O   VAL C 443 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 4.92

  Time building geometry restraints manager: 4.01 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: 4473
        1.34 -     1.46: 2636
        1.46 -     1.58: 7664
        1.58 -     1.70: 79
        1.70 -     1.82: 126
  Bond restraints: 14978
  Sorted by residual:
  bond pdb=" P    DC T   4 "
       pdb=" OP2  DC T   4 "
    ideal  model  delta    sigma   weight residual
    1.480  1.621 -0.141 2.00e-02 2.50e+03 4.96e+01
  bond pdb=" C2'  DG T   3 "
       pdb=" C1'  DG T   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.438  0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" C1'  DA P  15 "
       pdb=" N9   DA P  15 "
    ideal  model  delta    sigma   weight residual
    1.460  1.381  0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" C1'  DG P  16 "
       pdb=" N9   DG P  16 "
    ideal  model  delta    sigma   weight residual
    1.460  1.382  0.078 2.00e-02 2.50e+03 1.52e+01
  bond pdb=" C1'  DG T  13 "
       pdb=" N9   DG T  13 "
    ideal  model  delta    sigma   weight residual
    1.460  1.387  0.073 2.00e-02 2.50e+03 1.33e+01
  ... (remaining 14973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.44: 20371
        5.44 -    10.87: 90
       10.87 -    16.31: 8
       16.31 -    21.74: 0
       21.74 -    27.18: 1
  Bond angle restraints: 20470
  Sorted by residual:
  angle pdb=" C3'  DG T   3 "
        pdb=" O3'  DG T   3 "
        pdb=" P    DC T   4 "
      ideal   model   delta    sigma   weight residual
     120.20   93.02   27.18 1.50e+00 4.44e-01 3.28e+02
  angle pdb=" C4'  DG T   3 "
        pdb=" C3'  DG T   3 "
        pdb=" O3'  DG T   3 "
      ideal   model   delta    sigma   weight residual
     110.00  125.79  -15.79 1.50e+00 4.44e-01 1.11e+02
  angle pdb=" O3'  DG T   3 "
        pdb=" C3'  DG T   3 "
        pdb=" C2'  DG T   3 "
      ideal   model   delta    sigma   weight residual
     111.50   96.44   15.06 1.50e+00 4.44e-01 1.01e+02
  angle pdb=" N   PRO C 137 "
        pdb=" CA  PRO C 137 "
        pdb=" C   PRO C 137 "
      ideal   model   delta    sigma   weight residual
     113.65  100.84   12.81 1.35e+00 5.49e-01 9.00e+01
  angle pdb=" C3'  DC T   2 "
        pdb=" O3'  DC T   2 "
        pdb=" P    DG T   3 "
      ideal   model   delta    sigma   weight residual
     120.20  107.81   12.39 1.50e+00 4.44e-01 6.83e+01
  ... (remaining 20465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.66: 8082
       28.66 -    57.32: 668
       57.32 -    85.97: 81
       85.97 -   114.63: 0
      114.63 -   143.29: 3
  Dihedral angle restraints: 8834
    sinusoidal: 3819
      harmonic: 5015
  Sorted by residual:
  dihedral pdb=" CD  ARG A 102 "
           pdb=" NE  ARG A 102 "
           pdb=" CZ  ARG A 102 "
           pdb=" NH1 ARG A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -69.84   69.84     1      1.00e+01 1.00e-02 6.29e+01
  dihedral pdb=" CD  ARG B 257 "
           pdb=" NE  ARG B 257 "
           pdb=" CZ  ARG B 257 "
           pdb=" NH1 ARG B 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -57.20   57.20     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CD  ARG B 154 "
           pdb=" NE  ARG B 154 "
           pdb=" CZ  ARG B 154 "
           pdb=" NH1 ARG B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   55.71  -55.71     1      1.00e+01 1.00e-02 4.19e+01
  ... (remaining 8831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.236: 2195
       0.236 -    0.472: 24
       0.472 -    0.708: 8
       0.708 -    0.944: 0
       0.944 -    1.179: 1
  Chirality restraints: 2228
  Sorted by residual:
  chirality pdb=" P    DC T   4 "
            pdb=" OP1  DC T   4 "
            pdb=" OP2  DC T   4 "
            pdb=" O5'  DC T   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.53   -1.18 2.00e-01 2.50e+01 3.48e+01
  chirality pdb=" P    DC T   2 "
            pdb=" OP1  DC T   2 "
            pdb=" OP2  DC T   2 "
            pdb=" O5'  DC T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" P    DA P  10 "
            pdb=" OP1  DA P  10 "
            pdb=" OP2  DA P  10 "
            pdb=" O5'  DA P  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.60 2.00e-01 2.50e+01 9.15e+00
  ... (remaining 2225 not shown)

  Planarity restraints: 2497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 102 "   -1.036 9.50e-02 1.11e+02   4.64e-01 1.30e+02
        pdb=" NE  ARG A 102 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 102 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 102 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 102 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 257 "   -0.923 9.50e-02 1.11e+02   4.14e-01 1.04e+02
        pdb=" NE  ARG B 257 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 257 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 257 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 257 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 154 "   -0.904 9.50e-02 1.11e+02   4.05e-01 9.96e+01
        pdb=" NE  ARG B 154 "    0.054 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 154 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 154 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 154 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 2494 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 283
        2.67 -     3.22: 13525
        3.22 -     3.78: 23408
        3.78 -     4.34: 31799
        4.34 -     4.90: 51352
  Nonbonded interactions: 120367
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 892 "
            pdb=" OG  SER A1181 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" NH2 ARG B  75 "
            pdb=" O   GLY B  81 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG1 THR A 885 "
            pdb=" O   ASP A1186 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   ASP A 491 "
            pdb=" NH2 ARG A 574 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" C2'  DG T   3 "
            pdb=" P    DC T   4 "
     model   vdw
     2.229 3.040
  ... (remaining 120362 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 through 285 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 286 through 355 or resid 368 through 485))
  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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     35.740
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
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      :  0.006   0.141  14978  Z= 0.318
  Angle     :  1.039  27.179  20470  Z= 0.600
  Chirality :  0.076   1.179   2228
  Planarity :  0.021   0.464   2497
  Dihedral  : 19.274 143.288   5592
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.84 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 25.14 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.20), residues: 1713
  helix:  1.05 (0.21), residues: 658
  sheet:  0.29 (0.33), residues: 228
  loop : -1.78 (0.20), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 607 
 HIS   0.016   0.001   HIS C 309 
 PHE   0.039   0.001   PHE A 961 
 TYR   0.018   0.001   TYR C 291 
 ARG   0.024   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14209 (  614)
  hydrogen bonds       : angle       6.84950 ( 1723)
  covalent geometry    : bond        0.00586 (14978)
  covalent geometry    : angle       1.03933 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.664 
Fit side-chains
REVERT: A   87 ILE cc_start: 0.2050 (OUTLIER) cc_final: 0.1459 (pp)
REVERT: A  215 ILE cc_start: 0.7484 (pt) cc_final: 0.7283 (pt)
REVERT: B  329 LYS cc_start: 0.7431 (ptmm) cc_final: 0.7196 (ptmt)
REVERT: B  460 THR cc_start: 0.7615 (p) cc_final: 0.7225 (p)
REVERT: C  397 GLN cc_start: 0.7095 (mp10) cc_final: 0.6506 (mp10)
  outliers start: 32
  outliers final: 12
  residues processed: 207
  average time/residue: 1.1112
  time to fit residues: 256.7938
Evaluate side-chains
  172 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue  353 SER
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 148 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 102 optimal weight:    0.3980
   chunk 159 optimal weight:    2.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 144 GLN
A 550 GLN
A 761 ASN
A 811 GLN
A 843 GLN
A 894 GLN
A 922 GLN
A1059 ASN
A1089 GLN
A1110 HIS
A1222 GLN
B 133 HIS
B 187 HIS
B 272 ASN
C 250 GLN
C 279 GLN
C 309 HIS
C 330 ASN
C 404 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.183398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.129222 restraints weight = 41337.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 4.70
r_work: 0.3433 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14978  Z= 0.210
  Angle     :  0.701  11.870  20470  Z= 0.362
  Chirality :  0.047   0.264   2228
  Planarity :  0.006   0.067   2497
  Dihedral  : 16.462 145.517   2313
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.95 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.11 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.20), residues: 1713
  helix:  1.16 (0.21), residues: 656
  sheet:  0.45 (0.32), residues: 238
  loop : -1.77 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 748 
 HIS   0.008   0.001   HIS A  84 
 PHE   0.019   0.002   PHE A 610 
 TYR   0.015   0.002   TYR C 291 
 ARG   0.013   0.001   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04816 (  614)
  hydrogen bonds       : angle       5.04666 ( 1723)
  covalent geometry    : bond        0.00490 (14978)
  covalent geometry    : angle       0.70088 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 167
  time to evaluate  : 1.584 
Fit side-chains
REVERT: A   87 ILE cc_start: 0.2603 (OUTLIER) cc_final: 0.1783 (pp)
REVERT: A  183 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5951 (pm20)
REVERT: A  372 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6625 (mt-10)
REVERT: A  484 TRP cc_start: 0.7952 (m-90) cc_final: 0.6917 (m-10)
REVERT: A  774 MET cc_start: 0.7229 (mmt) cc_final: 0.7001 (mmt)
REVERT: B  325 ARG cc_start: 0.7360 (mtm110) cc_final: 0.7105 (mtm180)
REVERT: B  421 MET cc_start: 0.6734 (pp-130) cc_final: 0.6432 (pp-130)
REVERT: C  355 GLN cc_start: 0.5058 (OUTLIER) cc_final: 0.3994 (pm20)
  outliers start: 57
  outliers final: 23
  residues processed: 204
  average time/residue: 1.1337
  time to fit residues: 258.0483
Evaluate side-chains
  176 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 1.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  235 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 156 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0050
   chunk 154 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 95 optimal weight:    4.9990
   chunk 151 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 168 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
A 394 GLN
A 550 GLN
A 803 ASN
A1102 GLN
B 124 GLN
C 309 HIS
C 404 ASN
C 409 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.183618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130927 restraints weight = 45075.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 4.99
r_work: 0.3443 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14978  Z= 0.164
  Angle     :  0.636   9.697  20470  Z= 0.330
  Chirality :  0.044   0.161   2228
  Planarity :  0.005   0.070   2497
  Dihedral  : 16.426 146.844   2307
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.42 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 24.45 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.20), residues: 1713
  helix:  1.17 (0.20), residues: 663
  sheet:  0.48 (0.33), residues: 238
  loop : -1.76 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 748 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.015   0.001   PHE A 749 
 TYR   0.013   0.002   TYR C 291 
 ARG   0.015   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  614)
  hydrogen bonds       : angle       4.88582 ( 1723)
  covalent geometry    : bond        0.00376 (14978)
  covalent geometry    : angle       0.63646 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 162
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ILE cc_start: 0.2389 (OUTLIER) cc_final: 0.1578 (pp)
REVERT: A  108 GLN cc_start: 0.6765 (tt0) cc_final: 0.6401 (mt0)
REVERT: A  183 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5864 (pm20)
REVERT: A  372 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6626 (mt-10)
REVERT: A  484 TRP cc_start: 0.7936 (m-90) cc_final: 0.6934 (m-10)
REVERT: A  910 MET cc_start: 0.7844 (mpp) cc_final: 0.7565 (mpt)
REVERT: A 1131 ILE cc_start: 0.5034 (OUTLIER) cc_final: 0.4228 (mt)
REVERT: B  314 MET cc_start: 0.8372 (ttm) cc_final: 0.8105 (mtp)
REVERT: B  325 ARG cc_start: 0.7421 (mtm110) cc_final: 0.7196 (mtm180)
REVERT: B  421 MET cc_start: 0.6793 (pp-130) cc_final: 0.6413 (pp-130)
REVERT: C  355 GLN cc_start: 0.5014 (OUTLIER) cc_final: 0.3964 (pm20)
REVERT: C  400 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6877 (tm-30)
  outliers start: 55
  outliers final: 26
  residues processed: 198
  average time/residue: 1.0722
  time to fit residues: 236.9071
Evaluate side-chains
  186 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 136 optimal weight:    0.7980
   chunk 143 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0170
   chunk 124 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 151 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0270
   chunk 113 optimal weight:    4.9990
   chunk 148 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 564 GLN
A 803 ASN
A 828 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.188262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135344 restraints weight = 36478.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.98
r_work: 0.3509 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14978  Z= 0.117
  Angle     :  0.588  13.240  20470  Z= 0.302
  Chirality :  0.042   0.339   2228
  Planarity :  0.005   0.061   2497
  Dihedral  : 16.254 147.014   2306
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.45 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.20), residues: 1713
  helix:  1.39 (0.21), residues: 663
  sheet:  0.64 (0.33), residues: 232
  loop : -1.70 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 607 
 HIS   0.006   0.001   HIS C  77 
 PHE   0.014   0.001   PHE A 766 
 TYR   0.009   0.001   TYR C 193 
 ARG   0.009   0.000   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  614)
  hydrogen bonds       : angle       4.66427 ( 1723)
  covalent geometry    : bond        0.00252 (14978)
  covalent geometry    : angle       0.58805 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 169
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ILE cc_start: 0.2365 (OUTLIER) cc_final: 0.1619 (pp)
REVERT: A  108 GLN cc_start: 0.6850 (tt0) cc_final: 0.6237 (mt0)
REVERT: A  183 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5802 (pm20)
REVERT: A  372 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6479 (mt-10)
REVERT: A  780 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6653 (mt0)
REVERT: A  890 ASP cc_start: 0.7886 (p0) cc_final: 0.7556 (p0)
REVERT: A  910 MET cc_start: 0.7759 (mpp) cc_final: 0.7498 (mpt)
REVERT: A 1131 ILE cc_start: 0.4811 (OUTLIER) cc_final: 0.4063 (mt)
REVERT: B  314 MET cc_start: 0.8361 (ttm) cc_final: 0.8103 (mtp)
REVERT: B  325 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7158 (mtm180)
REVERT: B  394 GLU cc_start: 0.7934 (tp30) cc_final: 0.7424 (tp30)
REVERT: B  421 MET cc_start: 0.6700 (pp-130) cc_final: 0.6164 (pp-130)
REVERT: B  460 THR cc_start: 0.7978 (p) cc_final: 0.7692 (p)
REVERT: C  400 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6756 (tm-30)
  outliers start: 59
  outliers final: 19
  residues processed: 206
  average time/residue: 1.1340
  time to fit residues: 262.5986
Evaluate side-chains
  183 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 158
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  279 GLN
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 104 optimal weight:    8.9990
   chunk 145 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0570
   chunk 155 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 138 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    0.9904

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 803 ASN
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 GLN
C 409 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.184720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.131371 restraints weight = 37997.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 4.04
r_work: 0.3461 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14978  Z= 0.149
  Angle     :  0.614  11.773  20470  Z= 0.315
  Chirality :  0.043   0.195   2228
  Planarity :  0.005   0.061   2497
  Dihedral  : 16.279 146.674   2305
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.30 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.86 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.20), residues: 1713
  helix:  1.26 (0.21), residues: 669
  sheet:  0.64 (0.34), residues: 232
  loop : -1.72 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 748 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.015   0.001   PHE C 403 
 TYR   0.011   0.001   TYR A 434 
 ARG   0.009   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  614)
  hydrogen bonds       : angle       4.72321 ( 1723)
  covalent geometry    : bond        0.00342 (14978)
  covalent geometry    : angle       0.61358 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 165
  time to evaluate  : 1.620 
Fit side-chains
REVERT: A  108 GLN cc_start: 0.6927 (tt0) cc_final: 0.6207 (mt0)
REVERT: A  183 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5841 (pm20)
REVERT: A  372 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6539 (mt-10)
REVERT: A  484 TRP cc_start: 0.7911 (m-90) cc_final: 0.6934 (m-10)
REVERT: A  780 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6748 (mt0)
REVERT: A  947 LYS cc_start: 0.5913 (tptt) cc_final: 0.5078 (ttmt)
REVERT: A 1131 ILE cc_start: 0.4986 (OUTLIER) cc_final: 0.4167 (mt)
REVERT: B  325 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7235 (mtm180)
REVERT: B  394 GLU cc_start: 0.7989 (tp30) cc_final: 0.7492 (tp30)
REVERT: B  421 MET cc_start: 0.6682 (pp-130) cc_final: 0.6171 (pp-130)
REVERT: B  460 THR cc_start: 0.7999 (p) cc_final: 0.7738 (p)
REVERT: C  400 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6813 (tm-30)
  outliers start: 57
  outliers final: 25
  residues processed: 205
  average time/residue: 1.0532
  time to fit residues: 242.1930
Evaluate side-chains
  185 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 150 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 167 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 169 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 803 ASN
A 911 HIS
A1214 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.181709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.128063 restraints weight = 38930.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 4.07
r_work: 0.3421 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14978  Z= 0.187
  Angle     :  0.659  13.912  20470  Z= 0.337
  Chirality :  0.044   0.168   2228
  Planarity :  0.005   0.068   2497
  Dihedral  : 16.343 147.023   2303
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.01 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.48 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.20), residues: 1713
  helix:  1.15 (0.20), residues: 666
  sheet:  0.60 (0.34), residues: 232
  loop : -1.79 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 748 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.026   0.002   PHE A 961 
 TYR   0.014   0.002   TYR C 291 
 ARG   0.011   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  614)
  hydrogen bonds       : angle       4.86794 ( 1723)
  covalent geometry    : bond        0.00438 (14978)
  covalent geometry    : angle       0.65864 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 164
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6923 (tt0) cc_final: 0.6195 (mt0)
REVERT: A  372 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6564 (mt-10)
REVERT: A  442 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8254 (mm-30)
REVERT: A  484 TRP cc_start: 0.7916 (m-90) cc_final: 0.6946 (m-10)
REVERT: A  780 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7140 (pt0)
REVERT: A  947 LYS cc_start: 0.5697 (tptt) cc_final: 0.5000 (ttmt)
REVERT: B  256 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8019 (tp)
REVERT: B  394 GLU cc_start: 0.8048 (tp30) cc_final: 0.7748 (tp30)
REVERT: B  421 MET cc_start: 0.6720 (pp-130) cc_final: 0.6275 (pp-130)
REVERT: B  453 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7322 (pp)
REVERT: C  400 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6883 (tm-30)
REVERT: C  409 ASN cc_start: 0.7736 (m-40) cc_final: 0.7475 (m-40)
  outliers start: 59
  outliers final: 27
  residues processed: 207
  average time/residue: 1.0807
  time to fit residues: 249.4640
Evaluate side-chains
  185 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 137 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.183784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.130365 restraints weight = 42440.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 4.81
r_work: 0.3437 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14978  Z= 0.142
  Angle     :  0.626  14.210  20470  Z= 0.319
  Chirality :  0.043   0.175   2228
  Planarity :  0.005   0.063   2497
  Dihedral  : 16.297 147.230   2303
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.60 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 26.17 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.20), residues: 1713
  helix:  1.28 (0.21), residues: 656
  sheet:  0.62 (0.34), residues: 232
  loop : -1.71 (0.21), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 918 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.019   0.001   PHE A 961 
 TYR   0.012   0.001   TYR A 233 
 ARG   0.009   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  614)
  hydrogen bonds       : angle       4.78593 ( 1723)
  covalent geometry    : bond        0.00322 (14978)
  covalent geometry    : angle       0.62581 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 161
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6899 (tt0) cc_final: 0.6244 (mt0)
REVERT: A  372 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6574 (mt-10)
REVERT: A  484 TRP cc_start: 0.7876 (m-90) cc_final: 0.6925 (m-10)
REVERT: A  780 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7061 (pt0)
REVERT: A  890 ASP cc_start: 0.7967 (p0) cc_final: 0.7650 (p0)
REVERT: A  947 LYS cc_start: 0.5628 (tptt) cc_final: 0.4966 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7449 (tm-30)
REVERT: A 1131 ILE cc_start: 0.4992 (OUTLIER) cc_final: 0.4195 (mt)
REVERT: B  256 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8065 (tp)
REVERT: B  394 GLU cc_start: 0.8028 (tp30) cc_final: 0.7479 (tp30)
REVERT: B  421 MET cc_start: 0.6761 (pp-130) cc_final: 0.6322 (pp-130)
REVERT: C  400 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6848 (tm-30)
REVERT: C  409 ASN cc_start: 0.7693 (m-40) cc_final: 0.7428 (m-40)
  outliers start: 53
  outliers final: 24
  residues processed: 199
  average time/residue: 1.0445
  time to fit residues: 232.2295
Evaluate side-chains
  189 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0170
   chunk 72 optimal weight:   10.0000
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0570
   chunk 57 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0980
   chunk 160 optimal weight:    0.6980
   overall best weight:    0.2936

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.188051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.135423 restraints weight = 37260.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 4.38
r_work: 0.3512 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14978  Z= 0.115
  Angle     :  0.604  16.216  20470  Z= 0.306
  Chirality :  0.041   0.177   2228
  Planarity :  0.005   0.065   2497
  Dihedral  : 16.209 147.019   2301
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.84 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 26.99 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.21), residues: 1713
  helix:  1.36 (0.21), residues: 669
  sheet:  0.68 (0.34), residues: 232
  loop : -1.68 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 918 
 HIS   0.005   0.001   HIS C  77 
 PHE   0.026   0.001   PHE A 961 
 TYR   0.010   0.001   TYR C 193 
 ARG   0.008   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03277 (  614)
  hydrogen bonds       : angle       4.66027 ( 1723)
  covalent geometry    : bond        0.00251 (14978)
  covalent geometry    : angle       0.60363 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 1.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6950 (tt0) cc_final: 0.6174 (mt0)
REVERT: A  372 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6512 (mt-10)
REVERT: A  484 TRP cc_start: 0.7812 (m-90) cc_final: 0.6935 (m-10)
REVERT: A  890 ASP cc_start: 0.7964 (p0) cc_final: 0.7613 (p0)
REVERT: A  947 LYS cc_start: 0.5634 (tptt) cc_final: 0.4951 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7423 (tm-30)
REVERT: A 1131 ILE cc_start: 0.4843 (OUTLIER) cc_final: 0.4077 (mt)
REVERT: B  124 GLN cc_start: 0.5805 (mm-40) cc_final: 0.5465 (mm-40)
REVERT: B  394 GLU cc_start: 0.8036 (tp30) cc_final: 0.7668 (tp30)
REVERT: B  421 MET cc_start: 0.6638 (pp-130) cc_final: 0.6207 (pp-130)
REVERT: B  460 THR cc_start: 0.7999 (p) cc_final: 0.7711 (p)
REVERT: C  397 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6500 (mp10)
REVERT: C  400 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6854 (tm-30)
  outliers start: 45
  outliers final: 19
  residues processed: 195
  average time/residue: 1.1160
  time to fit residues: 243.6190
Evaluate side-chains
  184 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  397 GLN
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 45 optimal weight:    0.0670
   chunk 165 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 174 optimal weight:   10.0000
   overall best weight:    0.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
B 287 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.185883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.132679 restraints weight = 38710.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 4.49
r_work: 0.3465 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3487
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3487 r_free = 0.3487    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3487
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14978  Z= 0.135
  Angle     :  0.618  14.935  20470  Z= 0.312
  Chirality :  0.042   0.203   2228
  Planarity :  0.005   0.064   2497
  Dihedral  : 16.251 146.829   2301
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.42 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 27.54 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.21), residues: 1713
  helix:  1.34 (0.21), residues: 669
  sheet:  0.74 (0.34), residues: 232
  loop : -1.70 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 918 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.030   0.001   PHE A 961 
 TYR   0.012   0.001   TYR A 233 
 ARG   0.008   0.000   ARG A 546 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  614)
  hydrogen bonds       : angle       4.69225 ( 1723)
  covalent geometry    : bond        0.00306 (14978)
  covalent geometry    : angle       0.61752 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6931 (tt0) cc_final: 0.6294 (mt0)
REVERT: A  372 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6523 (mt-10)
REVERT: A  890 ASP cc_start: 0.7966 (p0) cc_final: 0.7603 (p0)
REVERT: A  947 LYS cc_start: 0.5589 (tptt) cc_final: 0.4916 (ttmt)
REVERT: A 1131 ILE cc_start: 0.4965 (OUTLIER) cc_final: 0.4158 (mt)
REVERT: B  124 GLN cc_start: 0.5806 (mm-40) cc_final: 0.5450 (mm-40)
REVERT: B  394 GLU cc_start: 0.8055 (tp30) cc_final: 0.7696 (tp30)
REVERT: B  421 MET cc_start: 0.6639 (pp-130) cc_final: 0.6209 (pp-130)
REVERT: B  460 THR cc_start: 0.7991 (p) cc_final: 0.7721 (p)
REVERT: C  355 GLN cc_start: 0.4899 (OUTLIER) cc_final: 0.3779 (pm20)
REVERT: C  409 ASN cc_start: 0.7635 (m-40) cc_final: 0.7356 (m-40)
  outliers start: 39
  outliers final: 23
  residues processed: 189
  average time/residue: 1.1956
  time to fit residues: 250.5810
Evaluate side-chains
  184 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  314 MET
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 173 optimal weight:   10.0000
   chunk 112 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0060
   chunk 169 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.186879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.133831 restraints weight = 36863.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 4.59
r_work: 0.3472 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14978  Z= 0.130
  Angle     :  0.620  14.924  20470  Z= 0.312
  Chirality :  0.042   0.195   2228
  Planarity :  0.005   0.070   2497
  Dihedral  : 16.254 146.895   2301
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.48 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 27.75 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.21), residues: 1713
  helix:  1.38 (0.21), residues: 663
  sheet:  0.74 (0.34), residues: 232
  loop : -1.60 (0.22), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 918 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.030   0.001   PHE A 961 
 TYR   0.012   0.001   TYR A 233 
 ARG   0.024   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  614)
  hydrogen bonds       : angle       4.68165 ( 1723)
  covalent geometry    : bond        0.00294 (14978)
  covalent geometry    : angle       0.62020 (20470)

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

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

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6915 (tt0) cc_final: 0.6134 (mt0)
REVERT: A  372 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6520 (mt-10)
REVERT: A  890 ASP cc_start: 0.7974 (p0) cc_final: 0.7612 (p0)
REVERT: A  910 MET cc_start: 0.7858 (mpp) cc_final: 0.7593 (mpt)
REVERT: A  947 LYS cc_start: 0.5693 (tptt) cc_final: 0.5028 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7498 (tm-30)
REVERT: A 1131 ILE cc_start: 0.4963 (OUTLIER) cc_final: 0.4157 (mt)
REVERT: B   75 ARG cc_start: 0.6673 (mmm160) cc_final: 0.6172 (mpp-170)
REVERT: B  124 GLN cc_start: 0.5796 (mm-40) cc_final: 0.5448 (mm-40)
REVERT: B  394 GLU cc_start: 0.8065 (tp30) cc_final: 0.7709 (tp30)
REVERT: B  421 MET cc_start: 0.6556 (pp-130) cc_final: 0.6240 (pp-130)
REVERT: B  460 THR cc_start: 0.7979 (p) cc_final: 0.7709 (p)
REVERT: C  355 GLN cc_start: 0.4906 (OUTLIER) cc_final: 0.3792 (pm20)
  outliers start: 35
  outliers final: 24
  residues processed: 184
  average time/residue: 1.1404
  time to fit residues: 233.2047
Evaluate side-chains
  183 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 1.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 157 optimal weight:    0.4980
   chunk 141 optimal weight:    0.9990
   chunk 69 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 144 optimal weight:    1.9990
   chunk 174 optimal weight:   10.0000
   chunk 172 optimal weight:    0.7980
   chunk 134 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.186012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.133628 restraints weight = 30885.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.68
r_work: 0.3498 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14978  Z= 0.134
  Angle     :  0.615  14.641  20470  Z= 0.311
  Chirality :  0.042   0.190   2228
  Planarity :  0.005   0.087   2497
  Dihedral  : 16.289 146.953   2301
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.71 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 28.09 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.21), residues: 1713
  helix:  1.37 (0.21), residues: 663
  sheet:  0.74 (0.35), residues: 232
  loop : -1.60 (0.22), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 918 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.030   0.001   PHE A 961 
 TYR   0.012   0.001   TYR A 233 
 ARG   0.020   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03466 (  614)
  hydrogen bonds       : angle       4.67820 ( 1723)
  covalent geometry    : bond        0.00305 (14978)
  covalent geometry    : angle       0.61494 (20470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11658.08 seconds
wall clock time: 200 minutes 59.41 seconds (12059.41 seconds total)