Starting phenix.real_space_refine
on Wed Sep 17 05:26:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nu1_49792/09_2025/9nu1_49792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nu1_49792/09_2025/9nu1_49792.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/9nu1_49792/09_2025/9nu1_49792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nu1_49792/09_2025/9nu1_49792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nu1_49792/09_2025/9nu1_49792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nu1_49792/09_2025/9nu1_49792.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    3178      2.51       5
     N     849      2.21       5
     O    1012      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5092
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1972
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 10, 'TRANS': 241}
    Chain: "C"
      Number of atoms: 909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 909
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "B"
      Number of atoms: 1099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1099
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
    Chain: "S"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 914
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "S"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.61, per 1000 atoms: 0.32
  Number of scatterers: 5092
  At special positions: 0
  Unit cell: (75.18, 97.734, 150.36, 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      53     16.00
     O    1012      8.00
     N     849      7.00
     C    3178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 335 " - pdb=" SG  CYS A 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 389 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 506 " - pdb=" SG  CYS A 566 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 571 " - pdb=" SG  CYS A 578 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 335 " - pdb=" SG  CYS C 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 366 " - pdb=" SG  CYS C 389 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 506 " - pdb=" SG  CYS B 566 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 527 " - pdb=" SG  CYS B 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 571 " - pdb=" SG  CYS B 578 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 174 " - pdb=" SG  CYS S 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 195 " - pdb=" SG  CYS S 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 217 " - pdb=" SG  CYS S 255 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 223 " - pdb=" SG  CYS S 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 248 " - pdb=" SG  CYS S 256 " distance=2.03

  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
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
      " BMA F   3 " - " MAN F   4 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 513 "
      " NAG E   1 " - " ASN A 396 "
      " NAG F   1 " - " ASN C 396 "
      " NAG G   1 " - " ASN B 513 "
      " NAG H   1 " - " ASN S 275 "
      " NAG S 701 " - " ASN S 232 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 192.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1168

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 15 sheets defined
      3.3% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 4.311A  pdb=" N   SER A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 469
      removed outlier: 3.729A  pdb=" N   TYR A 468 " --> pdb=" O   THR A 465 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 469 " --> pdb=" O   PRO A 466 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 465 through 469'
    Processing helix  chain 'C' and resid 346 through 353
    Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 335
      removed outlier: 3.520A  pdb=" N   ARG A 332 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS A 341 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359
      removed outlier: 3.615A  pdb=" N   ALA A 409 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395
      removed outlier: 6.363A  pdb=" N   ASN A 418 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ILE B 448 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LYS A 420 " --> pdb=" O   ILE B 448 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL B 450 " --> pdb=" O   LYS A 420 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASN A 422 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   GLY B 452 " --> pdb=" O   ASN A 422 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ALA A 424 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434
      removed outlier: 3.731A  pdb=" N   ASN B 505 " --> pdb=" O   GLU B 567 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TYR B 569 " --> pdb=" O   MET B 503 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   MET B 503 " --> pdb=" O   TYR B 569 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ALA B 508 " --> pdb=" O   PHE B 521 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   PHE B 521 " --> pdb=" O   ALA B 508 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 453
      removed outlier: 4.268A  pdb=" N   ILE C 419 " --> pdb=" O   LEU C 408 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   CYS C 425 " --> pdb=" O   TYR C 402 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR C 401 " --> pdb=" O   THR C 394 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 458 through 463
      removed outlier: 3.782A  pdb=" N   TYR A 486 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG A 547 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 538 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 478
    Processing sheet with id=AA9, first strand: chain 'A' and resid 527 through 528
      removed outlier: 6.496A  pdb=" N   CYS A 506 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   GLN A 524 " --> pdb=" O   THR A 504 " (cutoff:3.500A)
      removed outlier: 8.755A  pdb=" N   THR A 504 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU A 501 " --> pdb=" O   CYS A 571 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   CYS A 571 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   MET A 503 " --> pdb=" O   TYR A 569 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   TYR A 569 " --> pdb=" O   MET A 503 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASN A 505 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU A 567 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 332 through 335
      removed outlier: 3.515A  pdb=" N   LYS C 341 " --> pdb=" O   GLU C 334 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 414
    Processing sheet with id=AB3, first strand: chain 'B' and resid 458 through 462
      removed outlier: 7.000A  pdb=" N   ARG B 547 " --> pdb=" O   VAL B 538 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 499 through 500
    Processing sheet with id=AB5, first strand: chain 'S' and resid 178 through 181
      removed outlier: 3.510A  pdb=" N   LEU S 180 " --> pdb=" O   ARG S 204 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLY S 201 " --> pdb=" O   LEU S 276 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   PHE S 205 " --> pdb=" O   TYR S 272 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   TYR S 272 " --> pdb=" O   PHE S 205 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 254 through 262
      removed outlier: 4.889A  pdb=" N   CYS S 255 " --> pdb=" O   TRP S 251 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   TRP S 251 " --> pdb=" O   CYS S 255 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ALA S 249 " --> pdb=" O   LEU S 257 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   ASP S 259 " --> pdb=" O   ALA S 247 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ALA S 247 " --> pdb=" O   ASP S 259 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   SER S 261 " --> pdb=" O   ARG S 245 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ARG S 245 " --> pdb=" O   SER S 261 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA S 285 " --> pdb=" O   ALA S 227 " (cutoff:3.500A)

    131 hydrogen bonds defined for protein.
    342 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: 0.64

  Time building geometry restraints manager: 0.66 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: 1514
        1.33 -     1.46: 1060
        1.46 -     1.58: 2550
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 5199
  Sorted by residual:
  bond pdb=" CA  ALA S 194 "
       pdb=" CB  ALA S 194 "
    ideal  model  delta    sigma   weight residual
    1.529  1.470  0.059 1.69e-02 3.50e+03 1.23e+01
  bond pdb=" N   ILE A 535 "
       pdb=" CA  ILE A 535 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.14e-02 7.69e+03 1.14e+01
  bond pdb=" N   GLU S 191 "
       pdb=" CA  GLU S 191 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.031 1.18e-02 7.18e+03 6.97e+00
  bond pdb=" CA  THR A 382 "
       pdb=" C   THR A 382 "
    ideal  model  delta    sigma   weight residual
    1.522  1.494  0.028 1.08e-02 8.57e+03 6.83e+00
  bond pdb=" N   GLN B 464 "
       pdb=" CA  GLN B 464 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.33e-02 5.65e+03 5.90e+00
  ... (remaining 5194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 6808
        1.93 -     3.87: 190
        3.87 -     5.80: 33
        5.80 -     7.73: 13
        7.73 -     9.67: 6
  Bond angle restraints: 7050
  Sorted by residual:
  angle pdb=" CA  LYS B 577 "
        pdb=" CB  LYS B 577 "
        pdb=" CG  LYS B 577 "
      ideal   model   delta    sigma   weight residual
     114.10  123.38   -9.28 2.00e+00 2.50e-01 2.15e+01
  angle pdb=" C   GLU S 191 "
        pdb=" CA  GLU S 191 "
        pdb=" CB  GLU S 191 "
      ideal   model   delta    sigma   weight residual
     109.86  101.57    8.29 1.80e+00 3.09e-01 2.12e+01
  angle pdb=" N   GLY C 387 "
        pdb=" CA  GLY C 387 "
        pdb=" C   GLY C 387 "
      ideal   model   delta    sigma   weight residual
     112.34  121.03   -8.69 2.04e+00 2.40e-01 1.82e+01
  angle pdb=" C   CYS S 282 "
        pdb=" N   HIS S 283 "
        pdb=" CA  HIS S 283 "
      ideal   model   delta    sigma   weight residual
     122.74  128.68   -5.94 1.44e+00 4.82e-01 1.70e+01
  angle pdb=" N   LEU C 429 "
        pdb=" CA  LEU C 429 "
        pdb=" C   LEU C 429 "
      ideal   model   delta    sigma   weight residual
     113.50  108.87    4.63 1.23e+00 6.61e-01 1.41e+01
  ... (remaining 7045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.47: 3006
       24.47 -    48.95: 258
       48.95 -    73.42: 30
       73.42 -    97.90: 15
       97.90 -   122.37: 25
  Dihedral angle restraints: 3334
    sinusoidal: 1510
      harmonic: 1824
  Sorted by residual:
  dihedral pdb=" CB  CYS S 248 "
           pdb=" SG  CYS S 248 "
           pdb=" SG  CYS S 256 "
           pdb=" CB  CYS S 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.81  -68.19     1      1.00e+01 1.00e-02 6.03e+01
  dihedral pdb=" CB  CYS C 366 "
           pdb=" SG  CYS C 366 "
           pdb=" SG  CYS C 389 "
           pdb=" CB  CYS C 389 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.04  -53.04     1      1.00e+01 1.00e-02 3.83e+01
  dihedral pdb=" C2  MAN E   4 "
           pdb=" C1  MAN E   4 "
           pdb=" O5  MAN E   4 "
           pdb=" C5  MAN E   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   64.75 -122.37     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 3331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 720
       0.069 -    0.138: 101
       0.138 -    0.207: 3
       0.207 -    0.275: 1
       0.275 -    0.344: 1
  Chirality restraints: 826
  Sorted by residual:
  chirality pdb=" CA  ILE A 535 "
            pdb=" N   ILE A 535 "
            pdb=" C   ILE A 535 "
            pdb=" CB  ILE A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" C1  NAG S 701 "
            pdb=" ND2 ASN S 232 "
            pdb=" C2  NAG S 701 "
            pdb=" O5  NAG S 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" C4  NAG H   1 "
            pdb=" C3  NAG H   1 "
            pdb=" C5  NAG H   1 "
            pdb=" O4  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.36   -0.17 2.00e-01 2.50e+01 7.34e-01
  ... (remaining 823 not shown)

  Planarity restraints: 893
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY S 190 "   -0.012 2.00e-02 2.50e+03   2.26e-02 5.10e+00
        pdb=" C   GLY S 190 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLY S 190 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU S 191 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S 200 "   -0.176 9.50e-02 1.11e+02   7.90e-02 4.44e+00
        pdb=" NE  ARG S 200 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG S 200 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG S 200 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG S 200 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP S 198 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   ASP S 198 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ASP S 198 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LEU S 199 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 890 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 2430
        2.96 -     3.45: 4625
        3.45 -     3.93: 7753
        3.93 -     4.42: 8362
        4.42 -     4.90: 14387
  Nonbonded interactions: 37557
  Sorted by model distance:
  nonbonded pdb=" O   THR A 382 "
            pdb=" CG2 THR A 382 "
     model   vdw
     2.475 3.460
  nonbonded pdb=" N   ASP S 198 "
            pdb=" OD1 ASP S 198 "
     model   vdw
     2.520 3.120
  nonbonded pdb=" N   GLU B 576 "
            pdb=" OE1 GLU B 576 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" N   GLU A 576 "
            pdb=" OE1 GLU A 576 "
     model   vdw
     2.552 3.120
  nonbonded pdb=" O5  BMA F   3 "
            pdb=" O6  BMA F   3 "
     model   vdw
     2.568 2.432
  ... (remaining 37552 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 'D'
  selection = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             3.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
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      :  0.004   0.059   5228  Z= 0.199
  Angle     :  0.871   9.666   7123  Z= 0.436
  Chirality :  0.048   0.344    826
  Planarity :  0.005   0.079    887
  Dihedral  : 20.811 122.370   2124
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 33.21 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.34), residues: 620
  helix: -1.99 (0.98), residues: 15
  sheet: -0.92 (0.33), residues: 225
  loop : -1.23 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG S 200 
 TYR   0.022   0.001   TYR B 468 
 PHE   0.013   0.001   PHE C 423 
 TRP   0.013   0.001   TRP S 258 
 HIS   0.005   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5199)
  covalent geometry    : angle       0.83204 ( 7050)
  SS BOND              : bond        0.00334 (   14)
  SS BOND              : angle       1.22920 (   28)
  hydrogen bonds       : bond        0.28560 (  131)
  hydrogen bonds       : angle      11.26851 (  342)
  link_ALPHA1-3        : bond        0.00492 (    2)
  link_ALPHA1-3        : angle       1.61666 (    6)
  link_BETA1-4         : bond        0.00801 (    7)
  link_BETA1-4         : angle       3.35925 (   21)
  link_NAG-ASN         : bond        0.00500 (    6)
  link_NAG-ASN         : angle       3.60134 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ASP cc_start: 0.8271 (p0) cc_final: 0.8022 (p0)
REVERT: A  356 LYS cc_start: 0.7389 (ptpp) cc_final: 0.7163 (pttp)
REVERT: A  558 ASN cc_start: 0.7983 (p0) cc_final: 0.7607 (p0)
REVERT: C  442 MET cc_start: 0.7218 (pmm) cc_final: 0.6053 (pmm)
REVERT: S  283 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7345 (m90)
  outliers start: 10
  outliers final: 5
  residues processed: 137
  average time/residue: 0.0863
  time to fit residues: 14.8439
Evaluate side-chains
  130 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  578 CYS
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain S residue  229 MET
Chi-restraints excluded: chain S residue  283 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
C 418 ASN
B 464 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.134364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.104666 restraints weight = 9023.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.108254 restraints weight = 5022.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.110520 restraints weight = 3489.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.111630 restraints weight = 2781.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.112600 restraints weight = 2448.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5228  Z= 0.198
  Angle     :  0.843   9.465   7123  Z= 0.387
  Chirality :  0.048   0.196    826
  Planarity :  0.004   0.034    887
  Dihedral  : 15.322 114.096   1008
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 29.17 %
    Favored  : 64.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.34), residues: 620
  helix: -2.01 (0.88), residues: 18
  sheet: -0.72 (0.33), residues: 235
  loop : -1.22 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 200 
 TYR   0.015   0.001   TYR S 274 
 PHE   0.014   0.001   PHE B 548 
 TRP   0.008   0.001   TRP S 258 
 HIS   0.005   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 5199)
  covalent geometry    : angle       0.79484 ( 7050)
  SS BOND              : bond        0.00415 (   14)
  SS BOND              : angle       1.16361 (   28)
  hydrogen bonds       : bond        0.04463 (  131)
  hydrogen bonds       : angle       7.84807 (  342)
  link_ALPHA1-3        : bond        0.00382 (    2)
  link_ALPHA1-3        : angle       3.24273 (    6)
  link_BETA1-4         : bond        0.00708 (    7)
  link_BETA1-4         : angle       3.32822 (   21)
  link_NAG-ASN         : bond        0.00580 (    6)
  link_NAG-ASN         : angle       3.90028 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  459 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7761 (ttp-110)
REVERT: A  507 TYR cc_start: 0.8681 (p90) cc_final: 0.8472 (p90)
REVERT: A  558 ASN cc_start: 0.8072 (p0) cc_final: 0.7717 (p0)
REVERT: C  341 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7978 (ptpp)
REVERT: C  414 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8038 (tp)
REVERT: B  503 MET cc_start: 0.8029 (mtt) cc_final: 0.7757 (mtt)
REVERT: B  552 MET cc_start: 0.8093 (tpp) cc_final: 0.7444 (tpp)
REVERT: S  184 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.7317 (p-90)
REVERT: S  256 CYS cc_start: 0.4861 (t) cc_final: 0.4625 (t)
  outliers start: 36
  outliers final: 22
  residues processed: 149
  average time/residue: 0.0811
  time to fit residues: 15.4365
Evaluate side-chains
  150 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  578 CYS
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  216 THR
Chi-restraints excluded: chain S residue  221 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0870
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.133849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.104050 restraints weight = 9000.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107745 restraints weight = 5054.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.110059 restraints weight = 3492.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.111523 restraints weight = 2771.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.112343 restraints weight = 2395.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5228  Z= 0.190
  Angle     :  0.790  10.174   7123  Z= 0.367
  Chirality :  0.046   0.189    826
  Planarity :  0.004   0.046    887
  Dihedral  : 11.451 111.487   1003
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 28.99 %
    Favored  : 64.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.34), residues: 620
  helix: -1.67 (0.96), residues: 18
  sheet: -0.63 (0.33), residues: 232
  loop : -1.26 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 200 
 TYR   0.011   0.001   TYR S 274 
 PHE   0.012   0.001   PHE C 423 
 TRP   0.010   0.001   TRP C 377 
 HIS   0.005   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 5199)
  covalent geometry    : angle       0.74187 ( 7050)
  SS BOND              : bond        0.00469 (   14)
  SS BOND              : angle       1.03177 (   28)
  hydrogen bonds       : bond        0.04402 (  131)
  hydrogen bonds       : angle       7.15670 (  342)
  link_ALPHA1-3        : bond        0.00965 (    2)
  link_ALPHA1-3        : angle       2.86056 (    6)
  link_BETA1-4         : bond        0.00777 (    7)
  link_BETA1-4         : angle       3.34137 (   21)
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       3.73522 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (p0)
REVERT: A  459 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7589 (ttp-110)
REVERT: A  460 MET cc_start: 0.7880 (ttm) cc_final: 0.7401 (ttm)
REVERT: A  558 ASN cc_start: 0.8069 (p0) cc_final: 0.7799 (p0)
REVERT: C  341 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7923 (ptpp)
REVERT: C  442 MET cc_start: 0.7273 (pmm) cc_final: 0.6026 (pmm)
REVERT: B  552 MET cc_start: 0.8123 (tpp) cc_final: 0.7446 (tpp)
REVERT: S  184 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.7314 (p-90)
  outliers start: 37
  outliers final: 23
  residues processed: 148
  average time/residue: 0.0838
  time to fit residues: 15.7304
Evaluate side-chains
  147 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  578 CYS
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  379 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 30 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.133889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.103636 restraints weight = 9023.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.107398 restraints weight = 4978.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.109774 restraints weight = 3423.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.111256 restraints weight = 2712.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.112224 restraints weight = 2346.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5228  Z= 0.187
  Angle     :  0.784   8.566   7123  Z= 0.363
  Chirality :  0.046   0.185    826
  Planarity :  0.004   0.049    887
  Dihedral  : 11.002 106.960   1002
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 28.81 %
    Favored  : 63.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.34), residues: 620
  helix: -1.40 (0.97), residues: 18
  sheet: -0.74 (0.32), residues: 238
  loop : -1.18 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG S 200 
 TYR   0.012   0.001   TYR S 274 
 PHE   0.014   0.001   PHE B 548 
 TRP   0.010   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5199)
  covalent geometry    : angle       0.73295 ( 7050)
  SS BOND              : bond        0.00436 (   14)
  SS BOND              : angle       1.13421 (   28)
  hydrogen bonds       : bond        0.04049 (  131)
  hydrogen bonds       : angle       6.98744 (  342)
  link_ALPHA1-3        : bond        0.00903 (    2)
  link_ALPHA1-3        : angle       3.31702 (    6)
  link_BETA1-4         : bond        0.00733 (    7)
  link_BETA1-4         : angle       3.34359 (   21)
  link_NAG-ASN         : bond        0.00545 (    6)
  link_NAG-ASN         : angle       3.74198 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6584 (mp0)
REVERT: A  447 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8471 (p0)
REVERT: A  459 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7509 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8153 (p0) cc_final: 0.7882 (p0)
REVERT: C  341 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8042 (ptpp)
REVERT: C  442 MET cc_start: 0.7275 (pmm) cc_final: 0.5990 (pmm)
REVERT: B  552 MET cc_start: 0.8171 (tpp) cc_final: 0.7461 (tpp)
REVERT: S  184 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.7337 (p-90)
  outliers start: 42
  outliers final: 30
  residues processed: 153
  average time/residue: 0.0851
  time to fit residues: 16.5068
Evaluate side-chains
  153 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain A residue  578 CYS
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  379 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0980
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 14 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.135205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.105473 restraints weight = 9017.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.109127 restraints weight = 4977.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.111475 restraints weight = 3459.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.112835 restraints weight = 2742.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.113807 restraints weight = 2394.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5228  Z= 0.151
  Angle     :  0.789  12.058   7123  Z= 0.359
  Chirality :  0.045   0.182    826
  Planarity :  0.004   0.056    887
  Dihedral  : 10.689 105.418   1002
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 30.46 %
    Favored  : 62.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.34), residues: 620
  helix: -0.96 (0.96), residues: 18
  sheet: -0.71 (0.32), residues: 237
  loop : -1.14 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG S 200 
 TYR   0.009   0.001   TYR S 274 
 PHE   0.014   0.001   PHE B 548 
 TRP   0.011   0.001   TRP C 377 
 HIS   0.003   0.001   HIS A 529 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5199)
  covalent geometry    : angle       0.74041 ( 7050)
  SS BOND              : bond        0.00398 (   14)
  SS BOND              : angle       0.97121 (   28)
  hydrogen bonds       : bond        0.03744 (  131)
  hydrogen bonds       : angle       6.76599 (  342)
  link_ALPHA1-3        : bond        0.01032 (    2)
  link_ALPHA1-3        : angle       3.27504 (    6)
  link_BETA1-4         : bond        0.00754 (    7)
  link_BETA1-4         : angle       3.34851 (   21)
  link_NAG-ASN         : bond        0.00540 (    6)
  link_NAG-ASN         : angle       3.63937 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6514 (mp0)
REVERT: A  447 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8449 (p0)
REVERT: A  459 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7524 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8110 (p0) cc_final: 0.7856 (p0)
REVERT: C  341 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8014 (ptpp)
REVERT: C  414 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.7878 (tp)
REVERT: C  442 MET cc_start: 0.7272 (pmm) cc_final: 0.5989 (pmm)
REVERT: B  552 MET cc_start: 0.8129 (tpp) cc_final: 0.7466 (tpp)
  outliers start: 39
  outliers final: 28
  residues processed: 146
  average time/residue: 0.0877
  time to fit residues: 16.1693
Evaluate side-chains
  146 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain A residue  578 CYS
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  215 GLU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 56 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.134261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104421 restraints weight = 9154.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.108207 restraints weight = 4914.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.110586 restraints weight = 3351.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.112075 restraints weight = 2646.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.112768 restraints weight = 2282.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5228  Z= 0.169
  Angle     :  0.791  11.027   7123  Z= 0.360
  Chirality :  0.045   0.179    826
  Planarity :  0.004   0.060    887
  Dihedral  : 10.411 104.198   1002
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 28.44 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.34), residues: 620
  helix: -0.67 (1.02), residues: 18
  sheet: -0.69 (0.32), residues: 237
  loop : -1.12 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG S 200 
 TYR   0.011   0.001   TYR S 274 
 PHE   0.014   0.001   PHE B 548 
 TRP   0.010   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5199)
  covalent geometry    : angle       0.74239 ( 7050)
  SS BOND              : bond        0.00362 (   14)
  SS BOND              : angle       0.96569 (   28)
  hydrogen bonds       : bond        0.03716 (  131)
  hydrogen bonds       : angle       6.59950 (  342)
  link_ALPHA1-3        : bond        0.01031 (    2)
  link_ALPHA1-3        : angle       3.42284 (    6)
  link_BETA1-4         : bond        0.00717 (    7)
  link_BETA1-4         : angle       3.33528 (   21)
  link_NAG-ASN         : bond        0.00536 (    6)
  link_NAG-ASN         : angle       3.67408 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 116
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6521 (mp0)
REVERT: A  447 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (p0)
REVERT: A  459 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7558 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8294 (p0) cc_final: 0.8003 (p0)
REVERT: C  341 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8013 (ptpp)
REVERT: B  524 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7787 (tp40)
REVERT: B  552 MET cc_start: 0.8177 (tpp) cc_final: 0.7491 (tpp)
REVERT: S  184 TRP cc_start: 0.8686 (OUTLIER) cc_final: 0.7342 (p-90)
  outliers start: 43
  outliers final: 31
  residues processed: 147
  average time/residue: 0.0768
  time to fit residues: 14.5361
Evaluate side-chains
  151 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  484 PHE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  524 GLN
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 3 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0970
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.135194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.105423 restraints weight = 9097.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.109171 restraints weight = 4981.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.111526 restraints weight = 3425.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.112983 restraints weight = 2717.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.113903 restraints weight = 2357.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5228  Z= 0.146
  Angle     :  0.784  10.107   7123  Z= 0.356
  Chirality :  0.045   0.179    826
  Planarity :  0.004   0.054    887
  Dihedral  :  9.947 104.370   1001
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 28.62 %
    Favored  : 64.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.34), residues: 620
  helix: -0.51 (1.04), residues: 18
  sheet: -0.64 (0.33), residues: 231
  loop : -1.10 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG S 200 
 TYR   0.009   0.001   TYR S 274 
 PHE   0.013   0.001   PHE B 548 
 TRP   0.010   0.001   TRP C 377 
 HIS   0.003   0.001   HIS A 529 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5199)
  covalent geometry    : angle       0.73602 ( 7050)
  SS BOND              : bond        0.00343 (   14)
  SS BOND              : angle       0.86770 (   28)
  hydrogen bonds       : bond        0.03565 (  131)
  hydrogen bonds       : angle       6.44549 (  342)
  link_ALPHA1-3        : bond        0.01242 (    2)
  link_ALPHA1-3        : angle       3.36212 (    6)
  link_BETA1-4         : bond        0.00748 (    7)
  link_BETA1-4         : angle       3.32462 (   21)
  link_NAG-ASN         : bond        0.00553 (    6)
  link_NAG-ASN         : angle       3.65464 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6529 (mp0)
REVERT: A  447 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (p0)
REVERT: A  459 ARG cc_start: 0.8092 (ttp-170) cc_final: 0.7583 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8251 (p0) cc_final: 0.7956 (p0)
REVERT: C  341 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.7992 (ptpp)
REVERT: B  524 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7807 (tp40)
REVERT: B  552 MET cc_start: 0.8091 (tpp) cc_final: 0.7445 (tpp)
REVERT: S  184 TRP cc_start: 0.8691 (OUTLIER) cc_final: 0.7387 (p-90)
  outliers start: 39
  outliers final: 29
  residues processed: 145
  average time/residue: 0.0755
  time to fit residues: 14.0991
Evaluate side-chains
  147 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  524 GLN
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  215 GLU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 18 optimal weight:    0.4980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN
** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.134842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.104968 restraints weight = 9150.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.108679 restraints weight = 5011.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.111016 restraints weight = 3455.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.112482 restraints weight = 2757.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.113359 restraints weight = 2391.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5228  Z= 0.172
  Angle     :  0.812  14.019   7123  Z= 0.368
  Chirality :  0.046   0.178    826
  Planarity :  0.004   0.066    887
  Dihedral  :  9.614 104.821   1001
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 28.81 %
    Favored  : 63.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.34), residues: 620
  helix: -0.47 (1.04), residues: 18
  sheet: -0.60 (0.33), residues: 237
  loop : -1.22 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG S 200 
 TYR   0.011   0.001   TYR S 274 
 PHE   0.013   0.001   PHE B 548 
 TRP   0.011   0.001   TRP C 377 
 HIS   0.003   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5199)
  covalent geometry    : angle       0.76540 ( 7050)
  SS BOND              : bond        0.00407 (   14)
  SS BOND              : angle       1.30793 (   28)
  hydrogen bonds       : bond        0.03682 (  131)
  hydrogen bonds       : angle       6.39689 (  342)
  link_ALPHA1-3        : bond        0.01308 (    2)
  link_ALPHA1-3        : angle       3.16345 (    6)
  link_BETA1-4         : bond        0.00715 (    7)
  link_BETA1-4         : angle       3.25145 (   21)
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       3.66115 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 116
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6562 (mp0)
REVERT: A  447 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8505 (p0)
REVERT: A  459 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7577 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8301 (p0) cc_final: 0.8013 (p0)
REVERT: C  341 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7981 (ptpp)
REVERT: B  524 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7751 (tp40)
REVERT: B  552 MET cc_start: 0.8164 (tpp) cc_final: 0.7476 (tpp)
REVERT: S  184 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7312 (p-90)
  outliers start: 42
  outliers final: 32
  residues processed: 146
  average time/residue: 0.0807
  time to fit residues: 15.0100
Evaluate side-chains
  150 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  524 GLN
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  215 GLU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0770
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN
** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.134696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.104645 restraints weight = 9105.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.108453 restraints weight = 4947.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.110877 restraints weight = 3388.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.112222 restraints weight = 2683.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.113266 restraints weight = 2339.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5228  Z= 0.168
  Angle     :  0.805  13.629   7123  Z= 0.367
  Chirality :  0.046   0.179    826
  Planarity :  0.004   0.055    887
  Dihedral  :  9.400 105.334   1001
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  7.52 %
    Allowed  : 28.99 %
    Favored  : 63.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.34), residues: 620
  helix: -0.46 (1.05), residues: 18
  sheet: -0.57 (0.33), residues: 237
  loop : -1.25 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 200 
 TYR   0.011   0.001   TYR S 274 
 PHE   0.013   0.001   PHE B 548 
 TRP   0.011   0.001   TRP C 377 
 HIS   0.003   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 5199)
  covalent geometry    : angle       0.75875 ( 7050)
  SS BOND              : bond        0.00408 (   14)
  SS BOND              : angle       1.14424 (   28)
  hydrogen bonds       : bond        0.03694 (  131)
  hydrogen bonds       : angle       6.34158 (  342)
  link_ALPHA1-3        : bond        0.01245 (    2)
  link_ALPHA1-3        : angle       2.96108 (    6)
  link_BETA1-4         : bond        0.00720 (    7)
  link_BETA1-4         : angle       3.27571 (   21)
  link_NAG-ASN         : bond        0.00561 (    6)
  link_NAG-ASN         : angle       3.69034 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 117
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6551 (mp0)
REVERT: A  447 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8548 (p0)
REVERT: A  459 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7569 (ttp-110)
REVERT: A  520 TYR cc_start: 0.8458 (t80) cc_final: 0.7984 (t80)
REVERT: A  558 ASN cc_start: 0.8343 (p0) cc_final: 0.8049 (p0)
REVERT: C  341 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7949 (ptpp)
REVERT: B  524 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7745 (tp40)
REVERT: B  552 MET cc_start: 0.8184 (tpp) cc_final: 0.7487 (tpp)
REVERT: S  184 TRP cc_start: 0.8680 (OUTLIER) cc_final: 0.7274 (p-90)
  outliers start: 41
  outliers final: 33
  residues processed: 146
  average time/residue: 0.0805
  time to fit residues: 14.9815
Evaluate side-chains
  152 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 114
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  524 GLN
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  215 GLU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.134134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.104320 restraints weight = 9186.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.108066 restraints weight = 4961.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.110479 restraints weight = 3406.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.111931 restraints weight = 2686.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.112548 restraints weight = 2330.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   5228  Z= 0.198
  Angle     :  0.822  13.192   7123  Z= 0.379
  Chirality :  0.047   0.190    826
  Planarity :  0.004   0.074    887
  Dihedral  :  9.338 104.984   1001
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 29.91 %
    Favored  : 62.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.34), residues: 620
  helix: -0.44 (1.04), residues: 18
  sheet: -0.41 (0.33), residues: 231
  loop : -1.37 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG S 200 
 TYR   0.013   0.001   TYR S 274 
 PHE   0.011   0.001   PHE C 423 
 TRP   0.011   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 5199)
  covalent geometry    : angle       0.77664 ( 7050)
  SS BOND              : bond        0.00449 (   14)
  SS BOND              : angle       1.14945 (   28)
  hydrogen bonds       : bond        0.03755 (  131)
  hydrogen bonds       : angle       6.41475 (  342)
  link_ALPHA1-3        : bond        0.01116 (    2)
  link_ALPHA1-3        : angle       2.95922 (    6)
  link_BETA1-4         : bond        0.00713 (    7)
  link_BETA1-4         : angle       3.28981 (   21)
  link_NAG-ASN         : bond        0.00554 (    6)
  link_NAG-ASN         : angle       3.71053 (   18)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6606 (mp0)
REVERT: A  359 MET cc_start: 0.8408 (mmt) cc_final: 0.8099 (mmt)
REVERT: A  447 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8523 (p0)
REVERT: A  459 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7588 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8379 (p0) cc_final: 0.8089 (p0)
REVERT: C  341 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7995 (ptpp)
REVERT: C  372 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.6682 (mtp-110)
REVERT: B  522 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.8004 (mt)
REVERT: B  524 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7806 (tp40)
REVERT: B  552 MET cc_start: 0.8230 (tpp) cc_final: 0.7498 (tpp)
REVERT: S  184 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7290 (p-90)
  outliers start: 39
  outliers final: 32
  residues processed: 143
  average time/residue: 0.0825
  time to fit residues: 14.9134
Evaluate side-chains
  151 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  347 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  366 CYS
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ASN
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  527 CYS
Chi-restraints excluded: chain A residue  563 TYR
Chi-restraints excluded: chain C residue  341 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  351 SER
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  412 ILE
Chi-restraints excluded: chain C residue  414 ILE
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  465 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  522 ILE
Chi-restraints excluded: chain B residue  524 GLN
Chi-restraints excluded: chain B residue  529 HIS
Chi-restraints excluded: chain B residue  553 PHE
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  582 CYS
Chi-restraints excluded: chain S residue  184 TRP
Chi-restraints excluded: chain S residue  199 LEU
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 473 GLN
** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.134089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103997 restraints weight = 9254.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.107796 restraints weight = 4974.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.110218 restraints weight = 3402.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.111690 restraints weight = 2690.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.112368 restraints weight = 2329.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   5228  Z= 0.190
  Angle     :  0.816  13.035   7123  Z= 0.376
  Chirality :  0.046   0.199    826
  Planarity :  0.004   0.052    887
  Dihedral  :  9.169 103.395   1001
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 29.17 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.34), residues: 620
  helix: -0.17 (1.14), residues: 18
  sheet: -0.44 (0.33), residues: 231
  loop : -1.43 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 200 
 TYR   0.013   0.001   TYR S 274 
 PHE   0.011   0.001   PHE C 423 
 TRP   0.013   0.001   TRP C 377 
 HIS   0.006   0.001   HIS A 529 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5199)
  covalent geometry    : angle       0.76892 ( 7050)
  SS BOND              : bond        0.00435 (   14)
  SS BOND              : angle       1.10164 (   28)
  hydrogen bonds       : bond        0.03718 (  131)
  hydrogen bonds       : angle       6.34708 (  342)
  link_ALPHA1-3        : bond        0.01055 (    2)
  link_ALPHA1-3        : angle       2.78133 (    6)
  link_BETA1-4         : bond        0.00719 (    7)
  link_BETA1-4         : angle       3.39975 (   21)
  link_NAG-ASN         : bond        0.00588 (    6)
  link_NAG-ASN         : angle       3.77750 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1230.19 seconds
wall clock time: 21 minutes 56.34 seconds (1316.34 seconds total)