Starting phenix.real_space_refine
on Wed Mar  4 02:08:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sz5_25561/03_2026/7sz5_25561.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 847 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     114      5.16       5
     C    5793      2.51       5
     N    1668      2.21       5
     O    1792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9367
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4723
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 30, 'TRANS': 583}
    Chain: "C"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 386
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "B"
      Number of atoms: 3872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3872
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 21, 'TRANS': 478}
    Chain: "D"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 386
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
  Time building chain proxies: 2.30, per 1000 atoms: 0.25
  Number of scatterers: 9367
  At special positions: 0
  Unit cell: (64.764, 145.719, 130.607, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     114     16.00
     O    1792      8.00
     N    1668      7.00
     C    5793      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=48, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  34 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 163 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 170 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 207 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 224 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 227 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 267 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 271 " - pdb=" SG  CYS A 283 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 302 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 305 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 482 " - pdb=" SG  CYS A 491 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 486 " - pdb=" SG  CYS A 499 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 502 " - pdb=" SG  CYS A 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 555 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 558 " - pdb=" SG  CYS A 567 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 571 " - pdb=" SG  CYS A 593 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 604 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 600 " - pdb=" SG  CYS A 612 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   8 " - pdb=" SG  CYS C  21 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  16 " - pdb=" SG  CYS C  32 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  34 " - pdb=" SG  CYS C  43 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  34 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 163 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 166 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 191 " - pdb=" SG  CYS B 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 195 " - pdb=" SG  CYS B 207 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B 208 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 224 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 227 " - pdb=" SG  CYS B 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 267 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 283 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 287 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 305 " - pdb=" SG  CYS B 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 338 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 446 " - pdb=" SG  CYS B 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 482 " - pdb=" SG  CYS B 491 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 499 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D   8 " - pdb=" SG  CYS D  21 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  16 " - pdb=" SG  CYS D  32 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  34 " - pdb=" SG  CYS D  43 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 394.4 milliseconds
  

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 23 sheets defined
      11.0% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 32
      removed outlier: 3.654A  pdb=" N   PHE A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   MET A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 139 through 144
      removed outlier: 4.083A  pdb=" N   ILE A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 170 through 174
    Processing helix  chain 'A' and resid 366 through 374
      removed outlier: 3.636A  pdb=" N   LYS A 372 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   THR A 373 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 410
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 452 through 457
      removed outlier: 3.567A  pdb=" N   LEU A 456 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 476
    Processing helix  chain 'A' and resid 551 through 555
      removed outlier: 3.843A  pdb=" N   ASN A 554 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 611
      removed outlier: 3.650A  pdb=" N   GLU A 610 " --> pdb=" O   PRO A 607 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY A 611 " --> pdb=" O   GLY A 608 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 607 through 611'
    Processing helix  chain 'B' and resid 19 through 31
      removed outlier: 3.704A  pdb=" N   PHE B  24 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG B  29 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   PHE B  31 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 57
    Processing helix  chain 'B' and resid 146 through 151
    Processing helix  chain 'B' and resid 170 through 174
    Processing helix  chain 'B' and resid 331 through 335
    Processing helix  chain 'B' and resid 364 through 368
      removed outlier: 3.641A  pdb=" N   GLU B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 411
    Processing helix  chain 'B' and resid 452 through 456
    Processing helix  chain 'B' and resid 475 through 479
      removed outlier: 4.180A  pdb=" N   GLY B 479 " --> pdb=" O   LYS B 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17
    Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68
      removed outlier: 7.334A  pdb=" N   ARG A 125 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA A  96 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262
    Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 277
    Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.229A  pdb=" N   CYS A 313 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347
      removed outlier: 6.502A  pdb=" N   LEU A 345 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ILE A 438 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ALA A 415 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   SER A 440 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL A 417 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 505 through 507
      removed outlier: 4.162A  pdb=" N   GLU A 510 " --> pdb=" O   ARG A 507 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 527
    Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576
      removed outlier: 4.067A  pdb=" N   VAL A 575 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 586 through 587
      removed outlier: 3.792A  pdb=" N   TYR A 586 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 6
    Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 39
    Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7
    Processing sheet with id=AB6, first strand: chain 'B' and resid 16 through 17
    Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44
      removed outlier: 6.559A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   ALA B  68 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE B  43 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B  65 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   LEU B  98 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B  67 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   TYR B  93 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ARG B 125 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU B  95 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 244 through 246
    Processing sheet with id=AB9, first strand: chain 'B' and resid 261 through 262
    Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 277
    Processing sheet with id=AC2, first strand: chain 'B' and resid 291 through 295
    Processing sheet with id=AC3, first strand: chain 'B' and resid 340 through 341
    Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 347
      removed outlier: 6.244A  pdb=" N   LEU B 381 " --> pdb=" O   ALA B 415 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   LEU B 414 " --> pdb=" O   ILE B 438 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 5 through 7

    103 hydrogen bonds defined for protein.
    183 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2984
        1.33 -     1.46: 1962
        1.46 -     1.58: 4474
        1.58 -     1.71: 0
        1.71 -     1.83: 132
  Bond restraints: 9552
  Sorted by residual:
  bond pdb=" CA  SER A 196 "
       pdb=" CB  SER A 196 "
    ideal  model  delta    sigma   weight residual
    1.534  1.468  0.066 1.45e-02 4.76e+03 2.05e+01
  bond pdb=" CA  SER B 196 "
       pdb=" CB  SER B 196 "
    ideal  model  delta    sigma   weight residual
    1.533  1.471  0.062 1.60e-02 3.91e+03 1.49e+01
  bond pdb=" CA  SER C   3 "
       pdb=" CB  SER C   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.055 1.52e-02 4.33e+03 1.29e+01
  bond pdb=" N   CYS A 538 "
       pdb=" CA  CYS A 538 "
    ideal  model  delta    sigma   weight residual
    1.453  1.494 -0.042 1.31e-02 5.83e+03 1.01e+01
  bond pdb=" N   ASN A 134 "
       pdb=" CA  ASN A 134 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.66e+00
  ... (remaining 9547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 12079
        1.73 -     3.47: 735
        3.47 -     5.20: 88
        5.20 -     6.94: 13
        6.94 -     8.67: 2
  Bond angle restraints: 12917
  Sorted by residual:
  angle pdb=" CA  PHE B 156 "
        pdb=" CB  PHE B 156 "
        pdb=" CG  PHE B 156 "
      ideal   model   delta    sigma   weight residual
     113.80  119.25   -5.45 1.00e+00 1.00e+00 2.97e+01
  angle pdb=" C   LYS B 430 "
        pdb=" N   GLU B 431 "
        pdb=" CA  GLU B 431 "
      ideal   model   delta    sigma   weight residual
     122.87  116.59    6.28 1.44e+00 4.82e-01 1.90e+01
  angle pdb=" N   VAL A 500 "
        pdb=" CA  VAL A 500 "
        pdb=" C   VAL A 500 "
      ideal   model   delta    sigma   weight residual
     113.53  109.28    4.25 9.80e-01 1.04e+00 1.88e+01
  angle pdb=" N   PRO B 171 "
        pdb=" CA  PRO B 171 "
        pdb=" C   PRO B 171 "
      ideal   model   delta    sigma   weight residual
     112.47  121.14   -8.67 2.06e+00 2.36e-01 1.77e+01
  angle pdb=" N   ILE B 432 "
        pdb=" CA  ILE B 432 "
        pdb=" C   ILE B 432 "
      ideal   model   delta    sigma   weight residual
     109.58  104.48    5.10 1.29e+00 6.01e-01 1.57e+01
  ... (remaining 12912 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5228
       17.97 -    35.95: 562
       35.95 -    53.92: 107
       53.92 -    71.90: 26
       71.90 -    89.87: 11
  Dihedral angle restraints: 5934
    sinusoidal: 2453
      harmonic: 3481
  Sorted by residual:
  dihedral pdb=" CB  CYS A 596 "
           pdb=" SG  CYS A 596 "
           pdb=" SG  CYS A 604 "
           pdb=" CB  CYS A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    7.81   85.19     1      1.00e+01 1.00e-02 8.80e+01
  dihedral pdb=" CB  CYS A 195 "
           pdb=" SG  CYS A 195 "
           pdb=" SG  CYS A 207 "
           pdb=" CB  CYS A 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.50  -82.50     1      1.00e+01 1.00e-02 8.35e+01
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 555 "
           pdb=" CB  CYS A 555 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -16.01  -69.99     1      1.00e+01 1.00e-02 6.31e+01
  ... (remaining 5931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1023
       0.057 -    0.114: 327
       0.114 -    0.170: 53
       0.170 -    0.227: 12
       0.227 -    0.284: 3
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  ILE A  67 "
            pdb=" N   ILE A  67 "
            pdb=" C   ILE A  67 "
            pdb=" CB  ILE A  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  ILE A  43 "
            pdb=" N   ILE A  43 "
            pdb=" C   ILE A  43 "
            pdb=" CB  ILE A  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  ILE B 432 "
            pdb=" N   ILE B 432 "
            pdb=" C   ILE B 432 "
            pdb=" CB  ILE B 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1709
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 158 "    0.014 2.00e-02 2.50e+03   2.79e-02 7.80e+00
        pdb=" C   ASN B 158 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ASN B 158 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 159 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 192 "    0.011 2.00e-02 2.50e+03   2.38e-02 5.68e+00
        pdb=" C   ALA B 192 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ALA B 192 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN B 193 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 168 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   PRO B 168 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PRO B 168 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER B 169 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1706 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 140
        2.54 -     3.13: 7929
        3.13 -     3.72: 13565
        3.72 -     4.31: 19045
        4.31 -     4.90: 31401
  Nonbonded interactions: 72080
  Sorted by model distance:
  nonbonded pdb=" CB  MET B 154 "
            pdb=" CE1 PHE B 156 "
     model   vdw
     1.947 3.740
  nonbonded pdb=" O   ARG A 403 "
            pdb=" OG  SER A 433 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" OH  TYR B 101 "
            pdb=" OE1 GLN D  26 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG1 THR A 391 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   VAL B 437 "
            pdb=" OG1 THR B 464 "
     model   vdw
     2.163 3.040
  ... (remaining 72075 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 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.630
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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      :  0.007   0.066   9600  Z= 0.397
  Angle     :  0.911   8.671  13013  Z= 0.561
  Chirality :  0.057   0.284   1418
  Planarity :  0.005   0.043   1709
  Dihedral  : 14.971  89.870   3550
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 16.83 %
    Favored  : 83.00 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 10.84 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.33 (0.18), residues: 1206
  helix: -5.02 (0.18), residues: 91
  sheet: -3.65 (0.39), residues: 127
  loop : -3.75 (0.16), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  48 
 TYR   0.017   0.002   TYR A 447 
 PHE   0.020   0.002   PHE B 156 
 TRP   0.018   0.002   TRP B 176 
 HIS   0.006   0.001   HIS B 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 ( 9552)
  covalent geometry    : angle       0.90164 (12917)
  SS BOND              : bond        0.00881 (   48)
  SS BOND              : angle       1.79600 (   96)
  hydrogen bonds       : bond        0.29035 (  103)
  hydrogen bonds       : angle      10.28248 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4767 (mm-30)
  outliers start: 30
  outliers final: 5
  residues processed: 87
  average time/residue: 0.0801
  time to fit residues: 10.5300
Evaluate side-chains
  41 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  537 GLU
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  419 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A  40 ASN
** A  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 GLN
** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 GLN
A 462 GLN
A 528 ASN
A 557 GLN
A 597 HIS
B  23 HIS
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
B 134 ASN
** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 442 ASN
D   4 HIS
D  14 GLN
D  18 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.047332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.032842 restraints weight = 66097.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.033596 restraints weight = 41535.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.033964 restraints weight = 30266.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.034469 restraints weight = 25037.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.034638 restraints weight = 21534.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9600  Z= 0.179
  Angle     :  0.675  12.579  13013  Z= 0.348
  Chirality :  0.047   0.206   1418
  Planarity :  0.005   0.041   1709
  Dihedral  :  6.401  52.791   1306
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 13.29 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.35 (0.21), residues: 1206
  helix: -4.40 (0.30), residues: 74
  sheet: -3.29 (0.40), residues: 130
  loop : -3.01 (0.17), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 405 
 TYR   0.008   0.001   TYR A 586 
 PHE   0.009   0.001   PHE B 396 
 TRP   0.012   0.001   TRP B 386 
 HIS   0.005   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9552)
  covalent geometry    : angle       0.67278 (12917)
  SS BOND              : bond        0.00357 (   48)
  SS BOND              : angle       0.96008 (   96)
  hydrogen bonds       : bond        0.03731 (  103)
  hydrogen bonds       : angle       6.99841 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 42
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8709 (pp)
REVERT: A  253 MET cc_start: 0.9298 (mmt) cc_final: 0.8880 (mmm)
REVERT: A  521 GLU cc_start: 0.9654 (mp0) cc_final: 0.9256 (tm-30)
REVERT: B  229 LYS cc_start: 0.9262 (ttmm) cc_final: 0.8853 (ttmt)
REVERT: B  437 VAL cc_start: 0.9476 (OUTLIER) cc_final: 0.9269 (p)
REVERT: B  498 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7261 (p0)
  outliers start: 28
  outliers final: 12
  residues processed: 68
  average time/residue: 0.0697
  time to fit residues: 7.7552
Evaluate side-chains
  53 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  498 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 116 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0670
   chunk 85 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0980
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 100 ASN
B 334 HIS
** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.047676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.033244 restraints weight = 65115.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.033979 restraints weight = 40746.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.034560 restraints weight = 29604.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.034809 restraints weight = 23546.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.035005 restraints weight = 20720.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9600  Z= 0.118
  Angle     :  0.604  12.981  13013  Z= 0.310
  Chirality :  0.046   0.175   1418
  Planarity :  0.004   0.042   1709
  Dihedral  :  5.641  47.310   1298
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.83 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.71 (0.22), residues: 1206
  helix: -3.69 (0.40), residues: 66
  sheet: -2.73 (0.44), residues: 123
  loop : -2.60 (0.18), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 405 
 TYR   0.011   0.001   TYR A 292 
 PHE   0.011   0.001   PHE B  31 
 TRP   0.011   0.001   TRP B 386 
 HIS   0.012   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9552)
  covalent geometry    : angle       0.60095 (12917)
  SS BOND              : bond        0.00386 (   48)
  SS BOND              : angle       0.88515 (   96)
  hydrogen bonds       : bond        0.03307 (  103)
  hydrogen bonds       : angle       6.21260 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 42
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8654 (pp)
REVERT: A  184 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7652 (tm-30)
REVERT: A  253 MET cc_start: 0.9284 (mmt) cc_final: 0.8890 (mmm)
REVERT: B  229 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8820 (ttmt)
REVERT: D   29 LYS cc_start: 0.9281 (mmmm) cc_final: 0.9019 (mmmt)
  outliers start: 26
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0583
  time to fit residues: 6.2304
Evaluate side-chains
  52 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  184 GLN
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 111 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0870
   chunk 38 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    1.1560

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

Flipped N/Q/H residues before XYZ refinement:
A 483 HIS
A 597 HIS
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 GLN
** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.046940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.032689 restraints weight = 66033.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.033323 restraints weight = 41014.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.033757 restraints weight = 29603.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.034065 restraints weight = 24481.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.034345 restraints weight = 21563.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9600  Z= 0.145
  Angle     :  0.598  13.534  13013  Z= 0.307
  Chirality :  0.045   0.154   1418
  Planarity :  0.004   0.040   1709
  Dihedral  :  5.584  50.651   1298
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.97 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.22), residues: 1206
  helix: -3.07 (0.49), residues: 66
  sheet: -2.58 (0.44), residues: 130
  loop : -2.33 (0.19), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 427 
 TYR   0.006   0.001   TYR A 586 
 PHE   0.008   0.001   PHE B  31 
 TRP   0.010   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9552)
  covalent geometry    : angle       0.59468 (12917)
  SS BOND              : bond        0.00292 (   48)
  SS BOND              : angle       0.98203 (   96)
  hydrogen bonds       : bond        0.03040 (  103)
  hydrogen bonds       : angle       5.87321 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 39
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9106 (p)
REVERT: A   98 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8686 (pp)
REVERT: A  253 MET cc_start: 0.9300 (mmt) cc_final: 0.8964 (mmm)
REVERT: B  229 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8793 (ttmt)
REVERT: B  498 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7435 (p0)
  outliers start: 29
  outliers final: 19
  residues processed: 63
  average time/residue: 0.0676
  time to fit residues: 6.9067
Evaluate side-chains
  57 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 35
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    0.0370
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0570
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
A 597 HIS
** C  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 442 ASN
** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.047720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.033326 restraints weight = 65291.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034007 restraints weight = 40346.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.034535 restraints weight = 29423.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.034798 restraints weight = 23635.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.035012 restraints weight = 20745.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9600  Z= 0.094
  Angle     :  0.571  13.135  13013  Z= 0.290
  Chirality :  0.044   0.152   1418
  Planarity :  0.004   0.041   1709
  Dihedral  :  5.380  53.863   1298
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.53 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.23), residues: 1206
  helix: -2.84 (0.52), residues: 72
  sheet: -2.54 (0.41), residues: 150
  loop : -2.11 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 427 
 TYR   0.006   0.001   TYR B 292 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.010   0.001   TRP B 386 
 HIS   0.015   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 9552)
  covalent geometry    : angle       0.56908 (12917)
  SS BOND              : bond        0.00175 (   48)
  SS BOND              : angle       0.82122 (   96)
  hydrogen bonds       : bond        0.02707 (  103)
  hydrogen bonds       : angle       5.51617 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 38
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8580 (pp)
REVERT: A  253 MET cc_start: 0.9285 (mmt) cc_final: 0.8951 (mmm)
REVERT: B  229 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8866 (ttmt)
REVERT: B  244 MET cc_start: 0.9196 (mmm) cc_final: 0.8961 (mmm)
REVERT: B  498 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7651 (p0)
  outliers start: 29
  outliers final: 16
  residues processed: 64
  average time/residue: 0.0726
  time to fit residues: 7.3619
Evaluate side-chains
  53 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 35
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0040
   chunk 56 optimal weight:   20.0000
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 597 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.047426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033037 restraints weight = 65974.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.033752 restraints weight = 41029.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.034253 restraints weight = 29786.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034542 restraints weight = 23906.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.034868 restraints weight = 20480.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9600  Z= 0.105
  Angle     :  0.574  13.950  13013  Z= 0.286
  Chirality :  0.044   0.154   1418
  Planarity :  0.004   0.039   1709
  Dihedral  :  5.294  55.651   1298
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.04 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.23), residues: 1206
  helix: -2.59 (0.55), residues: 72
  sheet: -2.52 (0.40), residues: 150
  loop : -1.99 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 427 
 TYR   0.005   0.001   TYR A 586 
 PHE   0.008   0.001   PHE B 156 
 TRP   0.010   0.001   TRP B 386 
 HIS   0.012   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9552)
  covalent geometry    : angle       0.57229 (12917)
  SS BOND              : bond        0.00213 (   48)
  SS BOND              : angle       0.78128 (   96)
  hydrogen bonds       : bond        0.02621 (  103)
  hydrogen bonds       : angle       5.35691 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 39
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9289 (mmt) cc_final: 0.8958 (mmm)
REVERT: A  382 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9302 (pt)
REVERT: B  229 LYS cc_start: 0.9306 (ttmm) cc_final: 0.8857 (ttmt)
REVERT: B  498 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7634 (p0)
  outliers start: 27
  outliers final: 19
  residues processed: 61
  average time/residue: 0.0807
  time to fit residues: 7.6536
Evaluate side-chains
  58 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0370
   chunk 86 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 88 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.3258

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 597 HIS
** C  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.047803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.033450 restraints weight = 65852.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.034176 restraints weight = 40981.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.034742 restraints weight = 29628.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.035036 restraints weight = 23489.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.035360 restraints weight = 20613.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9600  Z= 0.088
  Angle     :  0.567  13.678  13013  Z= 0.282
  Chirality :  0.044   0.165   1418
  Planarity :  0.004   0.040   1709
  Dihedral  :  4.969  59.819   1297
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.94 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.23), residues: 1206
  helix: -2.61 (0.53), residues: 78
  sheet: -2.43 (0.41), residues: 150
  loop : -1.89 (0.19), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 427 
 TYR   0.006   0.001   TYR B 292 
 PHE   0.007   0.001   PHE B 156 
 TRP   0.013   0.001   TRP B 386 
 HIS   0.012   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 9552)
  covalent geometry    : angle       0.56551 (12917)
  SS BOND              : bond        0.00160 (   48)
  SS BOND              : angle       0.72338 (   96)
  hydrogen bonds       : bond        0.02503 (  103)
  hydrogen bonds       : angle       5.18039 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 41
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.9140 (ptm) cc_final: 0.8889 (ptp)
REVERT: A  253 MET cc_start: 0.9299 (mmt) cc_final: 0.8942 (mmm)
REVERT: A  382 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9312 (pt)
REVERT: B  229 LYS cc_start: 0.9295 (ttmm) cc_final: 0.8845 (ttmt)
REVERT: B  442 ASN cc_start: 0.8739 (m110) cc_final: 0.7935 (t0)
REVERT: B  498 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7620 (p0)
  outliers start: 31
  outliers final: 19
  residues processed: 69
  average time/residue: 0.0699
  time to fit residues: 7.6302
Evaluate side-chains
  58 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  113 MET
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  538 CYS
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 108 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 33 optimal weight:    0.5980
   chunk 115 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 597 HIS
B 252 GLN
D  45 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.046517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.032209 restraints weight = 66901.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.032908 restraints weight = 41602.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.033391 restraints weight = 30311.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.033644 restraints weight = 24584.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.033914 restraints weight = 21737.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9600  Z= 0.169
  Angle     :  0.627  13.724  13013  Z= 0.310
  Chirality :  0.044   0.177   1418
  Planarity :  0.004   0.036   1709
  Dihedral  :  5.179  58.298   1297
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.32 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.23), residues: 1206
  helix: -2.41 (0.52), residues: 78
  sheet: -2.36 (0.43), residues: 140
  loop : -1.86 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 427 
 TYR   0.007   0.001   TYR A 586 
 PHE   0.013   0.001   PHE B 156 
 TRP   0.009   0.001   TRP B 386 
 HIS   0.008   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9552)
  covalent geometry    : angle       0.62312 (12917)
  SS BOND              : bond        0.00314 (   48)
  SS BOND              : angle       0.98419 (   96)
  hydrogen bonds       : bond        0.02770 (  103)
  hydrogen bonds       : angle       5.22044 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 35
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9298 (mmt) cc_final: 0.8978 (mmm)
REVERT: A  331 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7414 (p0)
REVERT: A  382 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9345 (pt)
REVERT: B  229 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8863 (ttmt)
REVERT: B  442 ASN cc_start: 0.8949 (m110) cc_final: 0.8046 (t0)
REVERT: B  498 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7592 (p0)
  outliers start: 31
  outliers final: 18
  residues processed: 64
  average time/residue: 0.0719
  time to fit residues: 7.2820
Evaluate side-chains
  55 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 117 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.047077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.033012 restraints weight = 67230.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.033703 restraints weight = 41286.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.034254 restraints weight = 29681.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034604 restraints weight = 23660.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.034771 restraints weight = 20493.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9600  Z= 0.117
  Angle     :  0.604  11.660  13013  Z= 0.300
  Chirality :  0.044   0.194   1418
  Planarity :  0.004   0.038   1709
  Dihedral  :  4.861  19.648   1296
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.98 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.23), residues: 1206
  helix: -2.13 (0.55), residues: 78
  sheet: -2.31 (0.43), residues: 140
  loop : -1.78 (0.20), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.006   0.001   TYR A 586 
 PHE   0.008   0.001   PHE B 412 
 TRP   0.009   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9552)
  covalent geometry    : angle       0.60126 (12917)
  SS BOND              : bond        0.00224 (   48)
  SS BOND              : angle       0.91222 (   96)
  hydrogen bonds       : bond        0.02682 (  103)
  hydrogen bonds       : angle       5.18348 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7439 (p0)
REVERT: A  382 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9317 (pt)
REVERT: B  229 LYS cc_start: 0.9307 (ttmm) cc_final: 0.8861 (ttmt)
REVERT: B  442 ASN cc_start: 0.8863 (m110) cc_final: 0.8060 (t0)
REVERT: B  498 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7632 (p0)
  outliers start: 25
  outliers final: 20
  residues processed: 60
  average time/residue: 0.0693
  time to fit residues: 6.9260
Evaluate side-chains
  59 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 36
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 THR
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  431 GLU
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 91 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 597 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.046703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.032507 restraints weight = 66667.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.033146 restraints weight = 41649.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.033627 restraints weight = 30360.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.033870 restraints weight = 24432.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.034276 restraints weight = 21951.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9600  Z= 0.136
  Angle     :  0.622  10.796  13013  Z= 0.307
  Chirality :  0.044   0.214   1418
  Planarity :  0.004   0.037   1709
  Dihedral  :  4.885  19.810   1296
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.17 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.24), residues: 1206
  helix: -1.87 (0.57), residues: 78
  sheet: -2.30 (0.42), residues: 145
  loop : -1.74 (0.20), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.007   0.001   TYR A 586 
 PHE   0.008   0.001   PHE B 412 
 TRP   0.009   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9552)
  covalent geometry    : angle       0.61940 (12917)
  SS BOND              : bond        0.00263 (   48)
  SS BOND              : angle       0.92560 (   96)
  hydrogen bonds       : bond        0.02674 (  103)
  hydrogen bonds       : angle       5.14763 (  183)

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

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

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2412 Ramachandran restraints generated.
    1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 36
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9304 (mmt) cc_final: 0.8928 (mmm)
REVERT: A  331 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7528 (p0)
REVERT: A  382 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9332 (pt)
REVERT: B  154 MET cc_start: 0.8767 (tpp) cc_final: 0.8258 (tpp)
REVERT: B  229 LYS cc_start: 0.9321 (ttmm) cc_final: 0.8867 (ttmt)
REVERT: B  442 ASN cc_start: 0.8952 (m110) cc_final: 0.8111 (t0)
REVERT: B  498 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7578 (p0)
  outliers start: 25
  outliers final: 21
  residues processed: 59
  average time/residue: 0.0651
  time to fit residues: 6.1632
Evaluate side-chains
  59 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  431 GLU
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0980
   chunk 97 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.046569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.032389 restraints weight = 66506.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.033068 restraints weight = 41621.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.033592 restraints weight = 30394.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.033827 restraints weight = 24412.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.034143 restraints weight = 21635.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9600  Z= 0.149
  Angle     :  0.630  11.020  13013  Z= 0.311
  Chirality :  0.044   0.198   1418
  Planarity :  0.004   0.037   1709
  Dihedral  :  4.903  19.899   1296
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.26 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.24), residues: 1206
  helix: -1.60 (0.59), residues: 78
  sheet: -2.30 (0.42), residues: 145
  loop : -1.73 (0.20), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.007   0.001   TYR A 586 
 PHE   0.008   0.001   PHE B 412 
 TRP   0.009   0.001   TRP B 386 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9552)
  covalent geometry    : angle       0.62698 (12917)
  SS BOND              : bond        0.00279 (   48)
  SS BOND              : angle       0.95488 (   96)
  hydrogen bonds       : bond        0.02688 (  103)
  hydrogen bonds       : angle       5.14575 (  183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.45 seconds
wall clock time: 30 minutes 5.92 seconds (1805.92 seconds total)