Starting phenix.real_space_refine
on Mon Jul 28 05:49:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_25561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_25561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_25561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_25561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sz5_25561/07_2025/7sz5_25561.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.76, per 1000 atoms: 0.72
  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: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.21
  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: 2.40

  Time building geometry restraints manager: 2.95 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:             4.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.800
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.350
-------------------------------------------------------------------------------
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 : 18.21
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.002   TRP B 176 
 HIS   0.006   0.001   HIS B 409 
 PHE   0.020   0.002   PHE B 156 
 TYR   0.017   0.002   TYR A 447 
 ARG   0.004   0.001   ARG B  48 

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

*********************** 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  : 1.173 
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: 0.2018
  time to fit residues: 25.9766
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  : 1.131 
-------------------------------------------------------------------------------
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 102 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0470
   chunk 50 optimal weight:    0.0010
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.2090

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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 252 GLN
** 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 = 0.3336 r_free = 0.3336 target = 0.047584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.033099 restraints weight = 64747.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.033776 restraints weight = 40888.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.034328 restraints weight = 30063.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9600  Z= 0.163
  Angle     :  0.665  12.094  13013  Z= 0.344
  Chirality :  0.046   0.201   1418
  Planarity :  0.004   0.041   1709
  Dihedral  :  6.352  53.331   1306
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.86 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.01 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.21), residues: 1206
  helix: -4.41 (0.30), residues: 74
  sheet: -3.28 (0.40), residues: 130
  loop : -3.02 (0.17), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 386 
 HIS   0.005   0.001   HIS D  18 
 PHE   0.010   0.001   PHE B 396 
 TYR   0.008   0.001   TYR A 447 
 ARG   0.006   0.001   ARG B 405 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  103)
  hydrogen bonds       : angle       7.01928 (  183)
  SS BOND              : bond        0.00330 (   48)
  SS BOND              : angle       0.92718 (   96)
  covalent geometry    : bond        0.00360 ( 9552)
  covalent geometry    : angle       0.66316 (12917)

*********************** 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
  68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 42
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8705 (pp)
REVERT: A  253 MET cc_start: 0.9299 (mmt) cc_final: 0.8882 (mmm)
REVERT: A  521 GLU cc_start: 0.9657 (mp0) cc_final: 0.9262 (tm-30)
REVERT: B  229 LYS cc_start: 0.9271 (ttmm) cc_final: 0.8878 (ttpt)
REVERT: B  498 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7395 (p0)
  outliers start: 26
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1615
  time to fit residues: 17.2536
Evaluate side-chains
  48 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  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  294 MET
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 46 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0040
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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
A 528 ASN
B 252 GLN
B 334 HIS
** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.047943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.033380 restraints weight = 64767.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.034114 restraints weight = 40560.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.034494 restraints weight = 29550.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9600  Z= 0.114
  Angle     :  0.599  12.713  13013  Z= 0.308
  Chirality :  0.045   0.171   1418
  Planarity :  0.004   0.042   1709
  Dihedral  :  5.589  46.813   1298
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.36 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.65 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.22), residues: 1206
  helix: -3.70 (0.40), residues: 66
  sheet: -2.67 (0.44), residues: 123
  loop : -2.60 (0.18), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 386 
 HIS   0.012   0.001   HIS A 597 
 PHE   0.011   0.001   PHE B  31 
 TYR   0.010   0.001   TYR A 292 
 ARG   0.004   0.000   ARG B 405 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  103)
  hydrogen bonds       : angle       6.19816 (  183)
  SS BOND              : bond        0.00243 (   48)
  SS BOND              : angle       0.89855 (   96)
  covalent geometry    : bond        0.00248 ( 9552)
  covalent geometry    : angle       0.59606 (12917)

*********************** 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
  70 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 44
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8644 (pp)
REVERT: A  152 MET cc_start: 0.9204 (ptm) cc_final: 0.8908 (ptp)
REVERT: A  184 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7662 (tm-30)
REVERT: A  253 MET cc_start: 0.9275 (mmt) cc_final: 0.8891 (mmm)
REVERT: A  521 GLU cc_start: 0.9682 (mp0) cc_final: 0.9223 (tm-30)
REVERT: B  152 MET cc_start: 0.8573 (tmm) cc_final: 0.8360 (tmm)
REVERT: B  229 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8840 (ttmt)
REVERT: D   29 LYS cc_start: 0.9281 (mmmm) cc_final: 0.9026 (mmmt)
  outliers start: 26
  outliers final: 14
  residues processed: 68
  average time/residue: 0.1566
  time to fit residues: 17.2247
Evaluate side-chains
  54 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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  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 B residue   43 ILE
Chi-restraints excluded: chain B residue  207 CYS
Chi-restraints excluded: chain B residue  294 MET
Chi-restraints excluded: chain B residue  347 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 110 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 HIS
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  45 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.045957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.031787 restraints weight = 67089.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.032460 restraints weight = 41958.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.032938 restraints weight = 30635.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9600  Z= 0.252
  Angle     :  0.688  13.909  13013  Z= 0.350
  Chirality :  0.046   0.161   1418
  Planarity :  0.004   0.039   1709
  Dihedral  :  5.890  50.556   1298
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.35 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.34 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.22), residues: 1206
  helix: -3.40 (0.43), residues: 78
  sheet: -2.64 (0.43), residues: 130
  loop : -2.43 (0.19), residues: 998

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 386 
 HIS   0.005   0.001   HIS A 121 
 PHE   0.011   0.001   PHE B  31 
 TYR   0.009   0.001   TYR A 586 
 ARG   0.004   0.000   ARG A 497 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03480 (  103)
  hydrogen bonds       : angle       6.12722 (  183)
  SS BOND              : bond        0.00478 (   48)
  SS BOND              : angle       1.31167 (   96)
  covalent geometry    : bond        0.00547 ( 9552)
  covalent geometry    : angle       0.68132 (12917)

*********************** 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
  66 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 36
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9138 (p)
REVERT: A   98 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8834 (pp)
REVERT: A  184 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7914 (tm-30)
REVERT: A  253 MET cc_start: 0.9318 (mmt) cc_final: 0.8985 (mmm)
REVERT: B  152 MET cc_start: 0.8797 (tmm) cc_final: 0.8572 (tmm)
REVERT: B  229 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8787 (ttmt)
REVERT: B  498 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7460 (p0)
  outliers start: 30
  outliers final: 21
  residues processed: 63
  average time/residue: 0.1652
  time to fit residues: 16.9269
Evaluate side-chains
  58 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 33
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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  184 GLN
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  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 C residue   33 VAL
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  426 LEU
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 60 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 117 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 54 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.3586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.046373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.032017 restraints weight = 66619.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.032750 restraints weight = 41006.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.033271 restraints weight = 29532.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9600  Z= 0.162
  Angle     :  0.615  13.479  13013  Z= 0.312
  Chirality :  0.045   0.152   1418
  Planarity :  0.004   0.040   1709
  Dihedral  :  5.725  53.681   1298
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.10 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.23), residues: 1206
  helix: -2.84 (0.50), residues: 72
  sheet: -2.72 (0.41), residues: 140
  loop : -2.22 (0.19), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 386 
 HIS   0.010   0.001   HIS A 597 
 PHE   0.009   0.001   PHE A 380 
 TYR   0.006   0.001   TYR A 586 
 ARG   0.003   0.000   ARG B 405 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03037 (  103)
  hydrogen bonds       : angle       5.78888 (  183)
  SS BOND              : bond        0.00309 (   48)
  SS BOND              : angle       1.03076 (   96)
  covalent geometry    : bond        0.00357 ( 9552)
  covalent geometry    : angle       0.61119 (12917)

*********************** 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
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 34
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9182 (p)
REVERT: A   98 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8722 (pp)
REVERT: A  253 MET cc_start: 0.9299 (mmt) cc_final: 0.8934 (mmm)
REVERT: A  331 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7525 (p0)
REVERT: B   87 MET cc_start: 0.8800 (mtm) cc_final: 0.8573 (ptp)
REVERT: B  229 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8775 (ttmt)
REVERT: B  244 MET cc_start: 0.9307 (mmm) cc_final: 0.9084 (mmm)
REVERT: B  498 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7493 (p0)
  outliers start: 38
  outliers final: 22
  residues processed: 68
  average time/residue: 0.1643
  time to fit residues: 17.8247
Evaluate side-chains
  60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 34
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  500 VAL
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  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 100 optimal weight:    6.9990
   chunk 81 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 ASN
** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 HIS
B 134 ASN
B 366 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.045119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.030943 restraints weight = 68852.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.031610 restraints weight = 43023.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.032099 restraints weight = 31606.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   9600  Z= 0.315
  Angle     :  0.770  15.070  13013  Z= 0.383
  Chirality :  0.046   0.159   1418
  Planarity :  0.005   0.041   1709
  Dihedral  :  6.194  55.592   1298
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.13 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.22), residues: 1206
  helix: -2.53 (0.54), residues: 72
  sheet: -2.82 (0.40), residues: 140
  loop : -2.25 (0.19), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 140 
 HIS   0.014   0.001   HIS A 597 
 PHE   0.010   0.002   PHE C  17 
 TYR   0.011   0.001   TYR A 586 
 ARG   0.006   0.001   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  103)
  hydrogen bonds       : angle       5.97933 (  183)
  SS BOND              : bond        0.00617 (   48)
  SS BOND              : angle       1.50425 (   96)
  covalent geometry    : bond        0.00676 ( 9552)
  covalent geometry    : angle       0.76195 (12917)

*********************** 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
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 32
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9182 (p)
REVERT: A   98 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8851 (pp)
REVERT: A  195 CYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6910 (m)
REVERT: A  253 MET cc_start: 0.9298 (mmt) cc_final: 0.8969 (mmm)
REVERT: A  331 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7928 (p0)
REVERT: B  229 LYS cc_start: 0.9300 (ttmm) cc_final: 0.8792 (ttmt)
REVERT: B  498 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7335 (p0)
  outliers start: 40
  outliers final: 29
  residues processed: 68
  average time/residue: 0.1496
  time to fit residues: 17.0494
Evaluate side-chains
  65 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 31
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
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  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  500 VAL
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 C residue   32 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue   43 ILE
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  369 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 111 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3300 r_free = 0.3300 target = 0.045554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.031283 restraints weight = 68784.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.031931 restraints weight = 42632.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.032419 restraints weight = 31024.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9600  Z= 0.206
  Angle     :  0.670  14.848  13013  Z= 0.335
  Chirality :  0.046   0.168   1418
  Planarity :  0.004   0.043   1709
  Dihedral  :  6.028  58.980   1298
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.02 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.23 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.23), residues: 1206
  helix: -1.95 (0.60), residues: 66
  sheet: -2.79 (0.40), residues: 140
  loop : -2.10 (0.19), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 176 
 HIS   0.004   0.001   HIS A 597 
 PHE   0.011   0.001   PHE B 412 
 TYR   0.007   0.001   TYR A 586 
 ARG   0.006   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03139 (  103)
  hydrogen bonds       : angle       5.77510 (  183)
  SS BOND              : bond        0.00404 (   48)
  SS BOND              : angle       1.20736 (   96)
  covalent geometry    : bond        0.00449 ( 9552)
  covalent geometry    : angle       0.66395 (12917)

*********************** 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: 38
    poor density    : 34
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9200 (p)
REVERT: A   98 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (pp)
REVERT: A  253 MET cc_start: 0.9297 (mmt) cc_final: 0.8944 (mmm)
REVERT: A  331 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7683 (p0)
REVERT: A  431 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7480 (tp30)
REVERT: B   87 MET cc_start: 0.8654 (ptp) cc_final: 0.8334 (ptp)
REVERT: B  498 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7431 (p0)
  outliers start: 38
  outliers final: 27
  residues processed: 69
  average time/residue: 0.1527
  time to fit residues: 17.4641
Evaluate side-chains
  64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 32
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
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  331 ASN
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  500 VAL
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 C residue   32 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   43 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 43 optimal weight:    0.4980
   chunk 117 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 597 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.045690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.031384 restraints weight = 70375.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.032116 restraints weight = 42235.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.032613 restraints weight = 30267.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9600  Z= 0.213
  Angle     :  0.678  14.447  13013  Z= 0.337
  Chirality :  0.045   0.183   1418
  Planarity :  0.004   0.044   1709
  Dihedral  :  5.904  56.978   1298
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.02 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.76 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.23), residues: 1206
  helix: -1.55 (0.62), residues: 66
  sheet: -2.49 (0.43), residues: 130
  loop : -2.04 (0.19), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 176 
 HIS   0.005   0.001   HIS A 121 
 PHE   0.008   0.001   PHE A 412 
 TYR   0.009   0.001   TYR A 586 
 ARG   0.006   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  103)
  hydrogen bonds       : angle       5.58209 (  183)
  SS BOND              : bond        0.00414 (   48)
  SS BOND              : angle       1.16767 (   96)
  covalent geometry    : bond        0.00463 ( 9552)
  covalent geometry    : angle       0.67325 (12917)

*********************** 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
  77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 33
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9184 (p)
REVERT: A   98 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8724 (pp)
REVERT: A  253 MET cc_start: 0.9313 (mmt) cc_final: 0.8980 (mmm)
REVERT: A  293 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8273 (mp0)
REVERT: A  331 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7755 (p0)
REVERT: A  431 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7615 (tp30)
REVERT: B   87 MET cc_start: 0.8739 (ptp) cc_final: 0.8369 (ptp)
REVERT: B  229 LYS cc_start: 0.9324 (ttmm) cc_final: 0.8760 (ttmt)
REVERT: B  498 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7238 (p0)
  outliers start: 44
  outliers final: 30
  residues processed: 74
  average time/residue: 0.1501
  time to fit residues: 18.2607
Evaluate side-chains
  71 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 35
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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  175 CYS
Chi-restraints excluded: chain A residue  293 GLU
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  406 THR
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  434 ASP
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  500 VAL
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   32 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain B residue    6 VAL
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   43 ILE
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  424 LEU
Chi-restraints excluded: chain B residue  426 LEU
Chi-restraints excluded: chain B residue  473 ASN
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Chi-restraints excluded: chain D residue   20 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 56 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
A 384 GLN
A 483 HIS
A 597 HIS
B 134 ASN
B 442 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.046564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.032306 restraints weight = 66556.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.032907 restraints weight = 41401.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.033300 restraints weight = 30072.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9600  Z= 0.102
  Angle     :  0.616  12.449  13013  Z= 0.307
  Chirality :  0.046   0.162   1418
  Planarity :  0.004   0.048   1709
  Dihedral  :  5.173  20.387   1296
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.74 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.23), residues: 1206
  helix: -1.73 (0.60), residues: 72
  sheet: -2.26 (0.44), residues: 133
  loop : -1.87 (0.20), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 492 
 HIS   0.008   0.001   HIS A 597 
 PHE   0.009   0.001   PHE A 380 
 TYR   0.008   0.001   TYR A 101 
 ARG   0.006   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02639 (  103)
  hydrogen bonds       : angle       5.36801 (  183)
  SS BOND              : bond        0.00221 (   48)
  SS BOND              : angle       0.87975 (   96)
  covalent geometry    : bond        0.00229 ( 9552)
  covalent geometry    : angle       0.61361 (12917)

*********************** 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
  65 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9356 (mmt) cc_final: 0.9010 (mmm)
REVERT: A  431 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7519 (tp30)
REVERT: B   82 ILE cc_start: 0.9384 (mm) cc_final: 0.9119 (mm)
REVERT: B  442 ASN cc_start: 0.9050 (m110) cc_final: 0.7931 (t0)
REVERT: B  498 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7597 (p0)
  outliers start: 26
  outliers final: 17
  residues processed: 62
  average time/residue: 0.1717
  time to fit residues: 17.2136
Evaluate side-chains
  53 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 34
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  113 MET
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  594 HIS
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  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Chi-restraints excluded: chain D residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 57 optimal weight:   30.0000
   chunk 33 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 115 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
B 442 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.046345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.032099 restraints weight = 68198.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.032769 restraints weight = 42216.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.033231 restraints weight = 30718.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9600  Z= 0.118
  Angle     :  0.624  13.767  13013  Z= 0.308
  Chirality :  0.045   0.157   1418
  Planarity :  0.004   0.044   1709
  Dihedral  :  5.052  20.728   1296
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.74 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.23), residues: 1206
  helix: -1.79 (0.58), residues: 78
  sheet: -2.32 (0.43), residues: 140
  loop : -1.81 (0.20), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 386 
 HIS   0.002   0.001   HIS A 535 
 PHE   0.006   0.001   PHE B 412 
 TYR   0.006   0.001   TYR A 586 
 ARG   0.006   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02571 (  103)
  hydrogen bonds       : angle       5.21974 (  183)
  SS BOND              : bond        0.00230 (   48)
  SS BOND              : angle       0.89821 (   96)
  covalent geometry    : bond        0.00269 ( 9552)
  covalent geometry    : angle       0.62123 (12917)

********************** 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: 27
    poor density    : 34
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 MET cc_start: 0.9337 (mmt) cc_final: 0.8991 (mmm)
REVERT: A  431 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7450 (tp30)
REVERT: B   82 ILE cc_start: 0.9377 (mm) cc_final: 0.9126 (mm)
REVERT: B  229 LYS cc_start: 0.9328 (ttmm) cc_final: 0.8894 (ttmt)
REVERT: B  498 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7533 (p0)
  outliers start: 27
  outliers final: 22
  residues processed: 58
  average time/residue: 0.1567
  time to fit residues: 15.2018
Evaluate side-chains
  57 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 33
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
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  113 MET
Chi-restraints excluded: chain A residue  195 CYS
Chi-restraints excluded: chain A residue  309 CYS
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain C residue   32 CYS
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  426 LEU
Chi-restraints excluded: chain B residue  498 ASP
Chi-restraints excluded: chain D residue   12 HIS
Chi-restraints excluded: chain D residue   13 THR
Chi-restraints excluded: chain D residue   20 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 111 optimal weight:    0.4980
   chunk 87 optimal weight:    0.0170
   chunk 91 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 119 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    1.2222

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.046083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.031853 restraints weight = 68129.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.032614 restraints weight = 42447.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.033084 restraints weight = 30922.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.3666

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= 0.151
  Angle     :  0.643  16.152  13013  Z= 0.317
  Chirality :  0.045   0.169   1418
  Planarity :  0.004   0.045   1709
  Dihedral  :  5.090  19.952   1296
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.11 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.23), residues: 1206
  helix: -1.69 (0.59), residues: 78
  sheet: -2.35 (0.43), residues: 140
  loop : -1.80 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 176 
 HIS   0.003   0.001   HIS A 121 
 PHE   0.007   0.001   PHE C  17 
 TYR   0.007   0.001   TYR A 586 
 ARG   0.006   0.000   ARG A 507 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02630 (  103)
  hydrogen bonds       : angle       5.22872 (  183)
  SS BOND              : bond        0.00300 (   48)
  SS BOND              : angle       0.97813 (   96)
  covalent geometry    : bond        0.00338 ( 9552)
  covalent geometry    : angle       0.63948 (12917)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3142.65 seconds
wall clock time: 55 minutes 28.73 seconds (3328.73 seconds total)