Starting phenix.real_space_refine
on Thu Jun  5 04:04:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nu1_49792/06_2025/9nu1_49792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nu1_49792/06_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_49792/06_2025/9nu1_49792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nu1_49792/06_2025/9nu1_49792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nu1_49792/06_2025/9nu1_49792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nu1_49792/06_2025/9nu1_49792.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.46, per 1000 atoms: 0.88
  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: 1.56
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.58
  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: 1.45

  Time building geometry restraints manager: 1.74 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:             15.070
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.060
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.001   TRP S 258 
 HIS   0.005   0.001   HIS A 331 
 PHE   0.013   0.001   PHE C 423 
 TYR   0.022   0.001   TYR B 468 
 ARG   0.014   0.001   ARG S 200 

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

*********************** 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  : 0.713 
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: 0.2118
  time to fit residues: 36.1706
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  : 0.675 
-------------------------------------------------------------------------------
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 51 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0020
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5388

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.135422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105902 restraints weight = 8996.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.109474 restraints weight = 5004.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.111733 restraints weight = 3478.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5228  Z= 0.176
  Angle     :  0.831   9.642   7123  Z= 0.380
  Chirality :  0.047   0.193    826
  Planarity :  0.004   0.037    887
  Dihedral  : 14.877 113.597   1008
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 29.36 %
    Favored  : 64.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.34), residues: 620
  helix: -2.01 (0.86), residues: 18
  sheet: -0.74 (0.33), residues: 235
  loop : -1.19 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S 258 
 HIS   0.005   0.001   HIS A 331 
 PHE   0.016   0.001   PHE B 548 
 TYR   0.015   0.001   TYR S 274 
 ARG   0.005   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00586 (    6)
  link_NAG-ASN         : angle       3.88384 (   18)
  link_BETA1-4         : bond        0.00720 (    7)
  link_BETA1-4         : angle       3.32182 (   21)
  link_ALPHA1-3        : bond        0.00563 (    2)
  link_ALPHA1-3        : angle       3.25961 (    6)
  hydrogen bonds       : bond        0.04331 (  131)
  hydrogen bonds       : angle       7.78641 (  342)
  SS BOND              : bond        0.00406 (   14)
  SS BOND              : angle       1.15779 (   28)
  covalent geometry    : bond        0.00407 ( 5199)
  covalent geometry    : angle       0.78229 ( 7050)

*********************** 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
  160 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  459 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7801 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8053 (p0) cc_final: 0.7697 (p0)
REVERT: C  341 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8004 (ptpp)
REVERT: B  503 MET cc_start: 0.7985 (mtt) cc_final: 0.7709 (mtt)
REVERT: B  552 MET cc_start: 0.8037 (tpp) cc_final: 0.7441 (tpp)
REVERT: S  256 CYS cc_start: 0.4829 (t) cc_final: 0.4568 (t)
  outliers start: 34
  outliers final: 24
  residues processed: 146
  average time/residue: 0.2016
  time to fit residues: 37.3084
Evaluate side-chains
  149 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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  431 MET
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  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  403 SER
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  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 48 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.134098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104394 restraints weight = 9069.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.107969 restraints weight = 5045.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.110257 restraints weight = 3517.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5228  Z= 0.181
  Angle     :  0.776   9.781   7123  Z= 0.360
  Chirality :  0.046   0.188    826
  Planarity :  0.004   0.043    887
  Dihedral  : 11.307 110.254   1003
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 29.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.34), residues: 620
  helix: -1.44 (0.95), residues: 18
  sheet: -0.69 (0.33), residues: 237
  loop : -1.23 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 377 
 HIS   0.005   0.001   HIS S 235 
 PHE   0.013   0.001   PHE B 548 
 TYR   0.010   0.001   TYR S 274 
 ARG   0.006   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00527 (    6)
  link_NAG-ASN         : angle       3.68435 (   18)
  link_BETA1-4         : bond        0.00729 (    7)
  link_BETA1-4         : angle       3.32167 (   21)
  link_ALPHA1-3        : bond        0.00927 (    2)
  link_ALPHA1-3        : angle       2.83877 (    6)
  hydrogen bonds       : bond        0.04313 (  131)
  hydrogen bonds       : angle       7.17049 (  342)
  SS BOND              : bond        0.00422 (   14)
  SS BOND              : angle       0.99758 (   28)
  covalent geometry    : bond        0.00425 ( 5199)
  covalent geometry    : angle       0.72828 ( 7050)

*********************** 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  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8406 (p0)
REVERT: A  459 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7607 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8173 (p0) cc_final: 0.7917 (p0)
REVERT: C  341 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7926 (ptpp)
REVERT: B  503 MET cc_start: 0.7958 (mtt) cc_final: 0.7668 (mtt)
REVERT: B  552 MET cc_start: 0.8120 (tpp) cc_final: 0.7462 (tpp)
REVERT: S  184 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7313 (p-90)
  outliers start: 37
  outliers final: 22
  residues processed: 147
  average time/residue: 0.2151
  time to fit residues: 40.2466
Evaluate side-chains
  141 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
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  447 ASN
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  523 ILE
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
Chi-restraints excluded: chain S residue  216 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3952 r_free = 0.3952 target = 0.133305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.103409 restraints weight = 9264.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.107034 restraints weight = 5134.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.109356 restraints weight = 3569.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5228  Z= 0.207
  Angle     :  0.805  10.879   7123  Z= 0.371
  Chirality :  0.046   0.184    826
  Planarity :  0.004   0.047    887
  Dihedral  : 10.971 106.192   1002
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 28.99 %
    Favored  : 63.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.34), residues: 620
  helix: -1.22 (1.00), residues: 18
  sheet: -0.76 (0.32), residues: 238
  loop : -1.22 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 377 
 HIS   0.005   0.001   HIS S 235 
 PHE   0.014   0.001   PHE B 548 
 TYR   0.013   0.001   TYR S 274 
 ARG   0.008   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00551 (    6)
  link_NAG-ASN         : angle       3.76980 (   18)
  link_BETA1-4         : bond        0.00687 (    7)
  link_BETA1-4         : angle       3.34112 (   21)
  link_ALPHA1-3        : bond        0.00872 (    2)
  link_ALPHA1-3        : angle       3.39391 (    6)
  hydrogen bonds       : bond        0.04005 (  131)
  hydrogen bonds       : angle       6.96308 (  342)
  SS BOND              : bond        0.00571 (   14)
  SS BOND              : angle       1.18041 (   28)
  covalent geometry    : bond        0.00491 ( 5199)
  covalent geometry    : angle       0.75437 ( 7050)

*********************** 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
  163 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6731 (mp0)
REVERT: A  447 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8447 (p0)
REVERT: A  459 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7516 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8135 (p0) cc_final: 0.7857 (p0)
REVERT: C  341 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8098 (ptpp)
REVERT: C  414 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.7980 (tp)
REVERT: B  503 MET cc_start: 0.8039 (mtt) cc_final: 0.7780 (mtt)
REVERT: B  552 MET cc_start: 0.8155 (tpp) cc_final: 0.7452 (tpp)
REVERT: S  184 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.7280 (p-90)
  outliers start: 43
  outliers final: 29
  residues processed: 151
  average time/residue: 0.2202
  time to fit residues: 41.7601
Evaluate side-chains
  152 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  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  535 ILE
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  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  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 34 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.134261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104316 restraints weight = 9044.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.107938 restraints weight = 5053.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.110278 restraints weight = 3523.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5228  Z= 0.182
  Angle     :  0.793   9.588   7123  Z= 0.364
  Chirality :  0.046   0.181    826
  Planarity :  0.004   0.056    887
  Dihedral  : 10.715 104.720   1002
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 29.72 %
    Favored  : 63.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.34), residues: 620
  helix: -0.94 (0.99), residues: 18
  sheet: -0.72 (0.32), residues: 237
  loop : -1.22 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 
 PHE   0.013   0.001   PHE B 548 
 TYR   0.012   0.001   TYR S 274 
 ARG   0.009   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00556 (    6)
  link_NAG-ASN         : angle       3.72130 (   18)
  link_BETA1-4         : bond        0.00711 (    7)
  link_BETA1-4         : angle       3.33872 (   21)
  link_ALPHA1-3        : bond        0.00959 (    2)
  link_ALPHA1-3        : angle       3.38558 (    6)
  hydrogen bonds       : bond        0.03767 (  131)
  hydrogen bonds       : angle       6.77843 (  342)
  SS BOND              : bond        0.00427 (   14)
  SS BOND              : angle       1.04751 (   28)
  covalent geometry    : bond        0.00430 ( 5199)
  covalent geometry    : angle       0.74294 ( 7050)

*********************** 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
  158 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6640 (mp0)
REVERT: A  447 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (p0)
REVERT: A  459 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7539 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8162 (p0) cc_final: 0.7912 (p0)
REVERT: C  341 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8078 (ptpp)
REVERT: B  503 MET cc_start: 0.8029 (mtt) cc_final: 0.7750 (mtt)
REVERT: B  524 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7897 (tp40)
REVERT: B  552 MET cc_start: 0.8164 (tpp) cc_final: 0.7489 (tpp)
REVERT: S  184 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.7285 (p-90)
  outliers start: 39
  outliers final: 30
  residues processed: 146
  average time/residue: 0.1861
  time to fit residues: 34.2610
Evaluate side-chains
  150 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 115
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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  442 MET
Chi-restraints excluded: chain A residue  446 LEU
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  535 ILE
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  379 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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0570
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5298

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.134558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.104727 restraints weight = 9036.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.108415 restraints weight = 4989.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.110739 restraints weight = 3450.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2026

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     :  0.795  13.118   7123  Z= 0.360
  Chirality :  0.045   0.180    826
  Planarity :  0.004   0.049    887
  Dihedral  : 10.352 103.733   1001
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  8.44 %
    Allowed  : 28.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.33), residues: 620
  helix: -0.68 (1.03), residues: 18
  sheet: -0.69 (0.32), residues: 237
  loop : -1.24 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 
 PHE   0.012   0.001   PHE B 548 
 TYR   0.011   0.001   TYR S 274 
 ARG   0.008   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00573 (    6)
  link_NAG-ASN         : angle       3.72527 (   18)
  link_BETA1-4         : bond        0.00717 (    7)
  link_BETA1-4         : angle       3.34834 (   21)
  link_ALPHA1-3        : bond        0.01103 (    2)
  link_ALPHA1-3        : angle       3.46999 (    6)
  hydrogen bonds       : bond        0.03632 (  131)
  hydrogen bonds       : angle       6.56452 (  342)
  SS BOND              : bond        0.00436 (   14)
  SS BOND              : angle       0.92603 (   28)
  covalent geometry    : bond        0.00396 ( 5199)
  covalent geometry    : angle       0.74583 ( 7050)

*********************** 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
  163 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 117
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6645 (mp0)
REVERT: A  459 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7569 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8282 (p0) cc_final: 0.7994 (p0)
REVERT: C  341 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8045 (ptpp)
REVERT: B  503 MET cc_start: 0.8046 (mtt) cc_final: 0.7813 (mtt)
REVERT: B  524 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7920 (tp40)
REVERT: B  552 MET cc_start: 0.8156 (tpp) cc_final: 0.7477 (tpp)
REVERT: S  184 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7286 (p-90)
  outliers start: 46
  outliers final: 35
  residues processed: 150
  average time/residue: 0.2365
  time to fit residues: 44.9010
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  : 0.655 
-------------------------------------------------------------------------------
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  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  446 LEU
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  535 ILE
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  379 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.134807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.105218 restraints weight = 8891.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.108832 restraints weight = 4923.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.111159 restraints weight = 3415.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5228  Z= 0.157
  Angle     :  0.792  12.045   7123  Z= 0.359
  Chirality :  0.045   0.177    826
  Planarity :  0.003   0.037    887
  Dihedral  :  9.746 103.608   1001
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 29.72 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.33), residues: 620
  helix: -0.52 (1.05), residues: 18
  sheet: -0.65 (0.33), residues: 231
  loop : -1.22 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 377 
 HIS   0.003   0.001   HIS A 529 
 PHE   0.012   0.001   PHE B 548 
 TYR   0.010   0.001   TYR S 274 
 ARG   0.011   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00565 (    6)
  link_NAG-ASN         : angle       3.73898 (   18)
  link_BETA1-4         : bond        0.00735 (    7)
  link_BETA1-4         : angle       3.33094 (   21)
  link_ALPHA1-3        : bond        0.01326 (    2)
  link_ALPHA1-3        : angle       3.21889 (    6)
  hydrogen bonds       : bond        0.03475 (  131)
  hydrogen bonds       : angle       6.38308 (  342)
  SS BOND              : bond        0.00412 (   14)
  SS BOND              : angle       0.91340 (   28)
  covalent geometry    : bond        0.00366 ( 5199)
  covalent geometry    : angle       0.74395 ( 7050)

*********************** 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
  157 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 115
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6628 (mp0)
REVERT: A  447 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8466 (p0)
REVERT: A  459 ARG cc_start: 0.8110 (ttp-170) cc_final: 0.7595 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8289 (p0) cc_final: 0.8019 (p0)
REVERT: C  341 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8028 (ptpp)
REVERT: C  372 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6674 (mtp-110)
REVERT: B  503 MET cc_start: 0.8048 (mtt) cc_final: 0.7788 (mtt)
REVERT: B  524 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7921 (tp40)
REVERT: B  552 MET cc_start: 0.8126 (tpp) cc_final: 0.7476 (tpp)
REVERT: S  184 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.7416 (p-90)
  outliers start: 42
  outliers final: 32
  residues processed: 145
  average time/residue: 0.1800
  time to fit residues: 32.7657
Evaluate side-chains
  150 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 112
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
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  446 LEU
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  535 ILE
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  372 ARG
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 43 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0040
   chunk 57 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.134707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.105014 restraints weight = 9036.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.108675 restraints weight = 4961.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.111026 restraints weight = 3431.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5228  Z= 0.179
  Angle     :  0.802  11.467   7123  Z= 0.366
  Chirality :  0.045   0.176    826
  Planarity :  0.003   0.033    887
  Dihedral  :  9.514 104.189   1001
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 29.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.33), residues: 620
  helix: -0.45 (1.06), residues: 18
  sheet: -0.62 (0.33), residues: 231
  loop : -1.29 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 377 
 HIS   0.004   0.001   HIS S 235 
 PHE   0.012   0.001   PHE B 548 
 TYR   0.012   0.001   TYR S 274 
 ARG   0.009   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00562 (    6)
  link_NAG-ASN         : angle       3.74429 (   18)
  link_BETA1-4         : bond        0.00707 (    7)
  link_BETA1-4         : angle       3.26310 (   21)
  link_ALPHA1-3        : bond        0.01250 (    2)
  link_ALPHA1-3        : angle       3.06797 (    6)
  hydrogen bonds       : bond        0.03616 (  131)
  hydrogen bonds       : angle       6.40556 (  342)
  SS BOND              : bond        0.00435 (   14)
  SS BOND              : angle       1.37013 (   28)
  covalent geometry    : bond        0.00421 ( 5199)
  covalent geometry    : angle       0.75327 ( 7050)

*********************** 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
  160 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6659 (mp0)
REVERT: A  459 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7593 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8334 (p0) cc_final: 0.8050 (p0)
REVERT: C  341 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8034 (ptpp)
REVERT: B  524 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7957 (tp40)
REVERT: B  552 MET cc_start: 0.8157 (tpp) cc_final: 0.7493 (tpp)
REVERT: S  184 TRP cc_start: 0.8691 (OUTLIER) cc_final: 0.7307 (p-90)
  outliers start: 43
  outliers final: 34
  residues processed: 148
  average time/residue: 0.1790
  time to fit residues: 33.3599
Evaluate side-chains
  153 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
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  446 LEU
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  535 ILE
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  465 THR
Chi-restraints excluded: chain B residue  480 SER
Chi-restraints excluded: chain B residue  490 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.132305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.102298 restraints weight = 9008.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.105980 restraints weight = 4960.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.108311 restraints weight = 3420.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   5228  Z= 0.255
  Angle     :  0.856  11.659   7123  Z= 0.399
  Chirality :  0.047   0.170    826
  Planarity :  0.004   0.034    887
  Dihedral  :  9.591 104.699   1001
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 30.28 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.33), residues: 620
  helix: -0.68 (1.07), residues: 18
  sheet: -0.69 (0.32), residues: 241
  loop : -1.50 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 377 
 HIS   0.005   0.001   HIS S 235 
 PHE   0.014   0.001   PHE C 423 
 TYR   0.017   0.002   TYR S 274 
 ARG   0.009   0.001   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00638 (    6)
  link_NAG-ASN         : angle       3.98205 (   18)
  link_BETA1-4         : bond        0.00662 (    7)
  link_BETA1-4         : angle       3.30629 (   21)
  link_ALPHA1-3        : bond        0.01066 (    2)
  link_ALPHA1-3        : angle       3.19071 (    6)
  hydrogen bonds       : bond        0.03971 (  131)
  hydrogen bonds       : angle       6.46411 (  342)
  SS BOND              : bond        0.00592 (   14)
  SS BOND              : angle       1.37222 (   28)
  covalent geometry    : bond        0.00601 ( 5199)
  covalent geometry    : angle       0.80719 ( 7050)

*********************** 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
  151 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6802 (mp0)
REVERT: A  460 MET cc_start: 0.7741 (ttm) cc_final: 0.7506 (ttm)
REVERT: A  558 ASN cc_start: 0.8460 (p0) cc_final: 0.8165 (p0)
REVERT: C  341 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8015 (ptpp)
REVERT: C  372 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.6782 (mtp-110)
REVERT: B  524 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7984 (tp40)
REVERT: B  542 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: B  552 MET cc_start: 0.8296 (tpp) cc_final: 0.7552 (tpp)
REVERT: S  184 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.7045 (p-90)
  outliers start: 39
  outliers final: 29
  residues processed: 143
  average time/residue: 0.1767
  time to fit residues: 31.9907
Evaluate side-chains
  145 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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  382 THR
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  446 LEU
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  535 ILE
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  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  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 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   chunk 50 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5178

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.134285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.104452 restraints weight = 8945.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.108202 restraints weight = 4839.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.110618 restraints weight = 3312.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2327

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= 0.167
  Angle     :  0.803  11.242   7123  Z= 0.367
  Chirality :  0.045   0.181    826
  Planarity :  0.004   0.037    887
  Dihedral  :  9.257 103.830   1001
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 30.64 %
    Favored  : 62.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.33), residues: 620
  helix: -0.54 (1.06), residues: 18
  sheet: -0.61 (0.33), residues: 236
  loop : -1.45 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 377 
 HIS   0.003   0.001   HIS A 529 
 PHE   0.011   0.001   PHE C 423 
 TYR   0.011   0.001   TYR S 274 
 ARG   0.007   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00600 (    6)
  link_NAG-ASN         : angle       3.77501 (   18)
  link_BETA1-4         : bond        0.00742 (    7)
  link_BETA1-4         : angle       3.41081 (   21)
  link_ALPHA1-3        : bond        0.01095 (    2)
  link_ALPHA1-3        : angle       2.71309 (    6)
  hydrogen bonds       : bond        0.03580 (  131)
  hydrogen bonds       : angle       6.38376 (  342)
  SS BOND              : bond        0.00421 (   14)
  SS BOND              : angle       1.18093 (   28)
  covalent geometry    : bond        0.00393 ( 5199)
  covalent geometry    : angle       0.75394 ( 7050)

********************** 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
  153 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6607 (mp0)
REVERT: A  459 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7640 (ttp-110)
REVERT: A  558 ASN cc_start: 0.8390 (p0) cc_final: 0.8109 (p0)
REVERT: C  341 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7926 (ptpp)
REVERT: C  372 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6712 (mtp-110)
REVERT: B  524 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8008 (tp40)
REVERT: B  542 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7971 (mm-30)
REVERT: B  552 MET cc_start: 0.8233 (tpp) cc_final: 0.7661 (tpp)
REVERT: S  184 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.7124 (p-90)
  outliers start: 36
  outliers final: 29
  residues processed: 144
  average time/residue: 0.1891
  time to fit residues: 34.0311
Evaluate side-chains
  146 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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  442 MET
Chi-restraints excluded: chain A residue  446 LEU
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  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  490 MET
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  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 42 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0770
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
A 540 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.134684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.105144 restraints weight = 9087.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.108826 restraints weight = 4986.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.111183 restraints weight = 3438.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5228  Z= 0.169
  Angle     :  0.810  11.067   7123  Z= 0.372
  Chirality :  0.045   0.177    826
  Planarity :  0.004   0.040    887
  Dihedral  :  9.120 102.472   1001
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 31.19 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.34), residues: 620
  helix: -0.61 (1.03), residues: 18
  sheet: -0.55 (0.33), residues: 236
  loop : -1.39 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 377 
 HIS   0.007   0.001   HIS A 565 
 PHE   0.011   0.001   PHE C 423 
 TYR   0.011   0.001   TYR S 274 
 ARG   0.007   0.000   ARG S 200 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00573 (    6)
  link_NAG-ASN         : angle       3.77161 (   18)
  link_BETA1-4         : bond        0.00736 (    7)
  link_BETA1-4         : angle       3.41518 (   21)
  link_ALPHA1-3        : bond        0.01024 (    2)
  link_ALPHA1-3        : angle       2.66407 (    6)
  hydrogen bonds       : bond        0.03589 (  131)
  hydrogen bonds       : angle       6.33935 (  342)
  SS BOND              : bond        0.00397 (   14)
  SS BOND              : angle       1.10103 (   28)
  covalent geometry    : bond        0.00398 ( 5199)
  covalent geometry    : angle       0.76225 ( 7050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2597.08 seconds
wall clock time: 47 minutes 35.14 seconds (2855.14 seconds total)