Starting phenix.real_space_refine
on Sat Jul 26 08:38:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2025/9mdi_48171.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.085
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      11      5.16       5
     C    5077      2.51       5
     N    1323      2.21       5
     O    1722      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8139
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4076
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 20, 'TRANS': 502}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4057
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 20, 'TRANS': 499}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.27, per 1000 atoms: 0.77
  Number of scatterers: 8139
  At special positions: 0
  Unit cell: (92.88, 89.44, 101.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      11     16.00
     O    1722      8.00
     N    1323      7.00
     C    5077      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 972.7 milliseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 18 sheets defined
      12.2% alpha, 32.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 272 through 277
    Processing helix  chain 'A' and resid 286 through 291
      removed outlier: 4.100A  pdb=" N   ASP A 291 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 473
      removed outlier: 3.992A  pdb=" N   GLY A 473 " --> pdb=" O   LYS A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 512
      removed outlier: 4.015A  pdb=" N   GLN A 509 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 556
    Processing helix  chain 'A' and resid 581 through 592
    Processing helix  chain 'A' and resid 659 through 663
    Processing helix  chain 'B' and resid 227 through 233
      removed outlier: 3.784A  pdb=" N   ASN B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 278
    Processing helix  chain 'B' and resid 286 through 290
    Processing helix  chain 'B' and resid 425 through 429
      removed outlier: 3.918A  pdb=" N   GLN B 428 " --> pdb=" O   GLN B 425 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE B 429 " --> pdb=" O   GLU B 426 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 425 through 429'
    Processing helix  chain 'B' and resid 463 through 472
    Processing helix  chain 'B' and resid 506 through 512
      removed outlier: 3.845A  pdb=" N   SER B 512 " --> pdb=" O   SER B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 555
    Processing helix  chain 'B' and resid 581 through 595
      removed outlier: 4.286A  pdb=" N   ASN B 586 " --> pdb=" O   ASP B 582 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LYS B 587 " --> pdb=" O   ASN B 583 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS B 593 " --> pdb=" O   LYS B 589 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   THR B 594 " --> pdb=" O   ASP B 590 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 595 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 663
    Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 423
      removed outlier: 6.968A  pdb=" N   LEU A 412 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR A 421 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   THR A 410 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LYS A 423 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR A 407 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL A 483 " --> pdb=" O   THR A 407 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR A 409 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   GLU A 305 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASN A 329 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   GLY A 303 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   VAL A 302 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR A 396 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   MET A 304 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG A 394 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS A 306 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 423
      removed outlier: 6.968A  pdb=" N   LEU A 412 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR A 421 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   THR A 410 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LYS A 423 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR A 407 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL A 483 " --> pdb=" O   THR A 407 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR A 409 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 4.964A  pdb=" N   GLU A 305 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASN A 329 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   GLY A 303 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   VAL A 302 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR A 396 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   MET A 304 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG A 394 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LYS A 306 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 460 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 353
      removed outlier: 6.372A  pdb=" N   SER A 516 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ILE A 613 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE A 518 " --> pdb=" O   ILE A 613 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490
    Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 560
    Processing sheet with id=AA7, first strand: chain 'A' and resid 618 through 620
      removed outlier: 3.590A  pdb=" N   LEU A 733 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620
      removed outlier: 5.244A  pdb=" N   LEU A 733 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LYS A 676 " --> pdb=" O   LEU A 733 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   ASN A 735 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   TYR A 674 " --> pdb=" O   ASN A 735 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ARG A 668 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 658
    Processing sheet with id=AB1, first strand: chain 'B' and resid 235 through 238
    Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 448
      removed outlier: 3.828A  pdb=" N   ILE B 460 " --> pdb=" O   ILE B 389 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 448
      removed outlier: 3.944A  pdb=" N   LYS B 306 " --> pdb=" O   ASN B 392 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ARG B 394 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   MET B 304 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   TYR B 396 " --> pdb=" O   VAL B 302 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   VAL B 302 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 8.356A  pdb=" N   GLY B 303 " --> pdb=" O   ASN B 329 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ASN B 329 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   GLU B 305 " --> pdb=" O   THR B 327 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 353
      removed outlier: 6.557A  pdb=" N   ASN B 352 " --> pdb=" O   PHE B 580 " (cutoff:3.500A)
      removed outlier: 9.460A  pdb=" N   ILE B 611 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   SER B 516 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ILE B 613 " --> pdb=" O   SER B 516 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ILE B 518 " --> pdb=" O   ILE B 613 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 413 through 414
    Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 560
      removed outlier: 3.910A  pdb=" N   LEU B 564 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 618 through 620
      removed outlier: 3.607A  pdb=" N   TYR B 618 " --> pdb=" O   ILE B 738 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 618 through 620
      removed outlier: 3.607A  pdb=" N   TYR B 618 " --> pdb=" O   ILE B 738 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   LEU B 733 " --> pdb=" O   LYS B 676 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS B 676 " --> pdb=" O   LEU B 733 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   ASN B 735 " --> pdb=" O   TYR B 674 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   TYR B 674 " --> pdb=" O   ASN B 735 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ARG B 668 " --> pdb=" O   LEU B 741 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 675 " --> pdb=" O   THR B 705 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   THR B 705 " --> pdb=" O   SER B 675 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 653 through 658
      removed outlier: 3.648A  pdb=" N   GLU B 722 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    618 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2642
        1.34 -     1.46: 1367
        1.46 -     1.57: 4240
        1.57 -     1.69: 2
        1.69 -     1.81: 20
  Bond restraints: 8271
  Sorted by residual:
  bond pdb=" CB  PRO B 435 "
       pdb=" CG  PRO B 435 "
    ideal  model  delta    sigma   weight residual
    1.492  1.607 -0.115 5.00e-02 4.00e+02 5.32e+00
  bond pdb=" CB  PRO A 570 "
       pdb=" CG  PRO A 570 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.88e+00
  bond pdb=" CB  ASP B 218 "
       pdb=" CG  ASP B 218 "
    ideal  model  delta    sigma   weight residual
    1.516  1.563 -0.047 2.50e-02 1.60e+03 3.55e+00
  bond pdb=" CA  ASP B 218 "
       pdb=" CB  ASP B 218 "
    ideal  model  delta    sigma   weight residual
    1.530  1.564 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" CB  LYS B 490 "
       pdb=" CG  LYS B 490 "
    ideal  model  delta    sigma   weight residual
    1.520  1.571 -0.051 3.00e-02 1.11e+03 2.94e+00
  ... (remaining 8266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 10959
        2.41 -     4.81: 223
        4.81 -     7.22: 35
        7.22 -     9.62: 5
        9.62 -    12.03: 2
  Bond angle restraints: 11224
  Sorted by residual:
  angle pdb=" CA  PRO B 435 "
        pdb=" N   PRO B 435 "
        pdb=" CD  PRO B 435 "
      ideal   model   delta    sigma   weight residual
     112.00  101.59   10.41 1.40e+00 5.10e-01 5.52e+01
  angle pdb=" CB  LYS B 490 "
        pdb=" CG  LYS B 490 "
        pdb=" CD  LYS B 490 "
      ideal   model   delta    sigma   weight residual
     111.30  123.33  -12.03 2.30e+00 1.89e-01 2.73e+01
  angle pdb=" C   ARG A 232 "
        pdb=" N   ASN A 233 "
        pdb=" CA  ASN A 233 "
      ideal   model   delta    sigma   weight residual
     122.61  129.77   -7.16 1.56e+00 4.11e-01 2.11e+01
  angle pdb=" C   LEU A 414 "
        pdb=" N   ASP A 415 "
        pdb=" CA  ASP A 415 "
      ideal   model   delta    sigma   weight residual
     121.54  130.26   -8.72 1.91e+00 2.74e-01 2.09e+01
  angle pdb=" CA  PRO A 570 "
        pdb=" N   PRO A 570 "
        pdb=" CD  PRO A 570 "
      ideal   model   delta    sigma   weight residual
     112.00  105.69    6.31 1.40e+00 5.10e-01 2.03e+01
  ... (remaining 11219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.02: 4211
       18.02 -    36.04: 597
       36.04 -    54.07: 166
       54.07 -    72.09: 33
       72.09 -    90.11: 10
  Dihedral angle restraints: 5017
    sinusoidal: 1970
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CA  GLU A 710 "
           pdb=" C   GLU A 710 "
           pdb=" N   PHE A 711 "
           pdb=" CA  PHE A 711 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.19   22.81     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  SER B 434 "
           pdb=" C   SER B 434 "
           pdb=" N   PRO B 435 "
           pdb=" CA  PRO B 435 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.61  -21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  TYR A 464 "
           pdb=" C   TYR A 464 "
           pdb=" N   ASP A 465 "
           pdb=" CA  ASP A 465 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.40   20.60     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 5014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1112
       0.076 -    0.152: 154
       0.152 -    0.229: 10
       0.229 -    0.305: 2
       0.305 -    0.381: 1
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" CB  VAL A 302 "
            pdb=" CA  VAL A 302 "
            pdb=" CG1 VAL A 302 "
            pdb=" CG2 VAL A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CB  ILE B 658 "
            pdb=" CA  ILE B 658 "
            pdb=" CG1 ILE B 658 "
            pdb=" CG2 ILE B 658 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  ASP A 415 "
            pdb=" N   ASP A 415 "
            pdb=" C   ASP A 415 "
            pdb=" CB  ASP A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1276 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 434 "   -0.076 5.00e-02 4.00e+02   1.09e-01 1.92e+01
        pdb=" N   PRO B 435 "    0.189 5.00e-02 4.00e+02
        pdb=" CA  PRO B 435 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 435 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 537 "   -0.055 5.00e-02 4.00e+02   8.44e-02 1.14e+01
        pdb=" N   PRO B 538 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 628 "    0.054 5.00e-02 4.00e+02   8.20e-02 1.08e+01
        pdb=" N   PRO A 629 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 629 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 629 "    0.045 5.00e-02 4.00e+02
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1676
        2.78 -     3.31: 6629
        3.31 -     3.84: 12729
        3.84 -     4.37: 13641
        4.37 -     4.90: 25523
  Nonbonded interactions: 60198
  Sorted by model distance:
  nonbonded pdb="CA    CA B 901 "
            pdb="CA    CA B 902 "
     model   vdw
     2.248 1.980
  nonbonded pdb=" O   SER A 280 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR B 409 "
            pdb=" O   GLN B 482 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG  SER B 434 "
            pdb=" OD2 ASP B 437 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   VAL A 302 "
            pdb=" ND2 ASN A 363 "
     model   vdw
     2.332 3.120
  ... (remaining 60193 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 'A' and (resid 218 through 313 or resid 320 through 678 or resid 682 thro \ 
ugh 746 or resid 901 through 903))
  selection = (chain 'B' and (resid 218 through 451 or resid 457 through 746 or resid 901 thro \ 
ugh 903))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.200
  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:          0.400
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     24.610
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
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   0.115   8271  Z= 0.182
  Angle     :  0.813  12.027  11224  Z= 0.447
  Chirality :  0.053   0.381   1279
  Planarity :  0.006   0.109   1460
  Dihedral  : 18.387  90.109   3067
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 33.62 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.24), residues: 1031
  helix: -2.92 (0.34), residues: 112
  sheet:  0.07 (0.32), residues: 275
  loop : -2.46 (0.22), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 503 
 HIS   0.000   0.000   HIS B 359 
 PHE   0.018   0.002   PHE A 281 
 TYR   0.041   0.001   TYR B 261 
 ARG   0.002   0.000   ARG B 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16973 (  214)
  hydrogen bonds       : angle       7.04091 (  618)
  covalent geometry    : bond        0.00427 ( 8271)
  covalent geometry    : angle       0.81342 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLU cc_start: 0.7321 (pm20) cc_final: 0.6883 (pm20)
REVERT: B  654 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (p)
  outliers start: 7
  outliers final: 2
  residues processed: 106
  average time/residue: 0.1781
  time to fit residues: 27.3436
Evaluate side-chains
  97 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  654 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    0.2980
   chunk 42 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.113557 restraints weight = 11675.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.116746 restraints weight = 7508.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.118944 restraints weight = 5534.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8271  Z= 0.125
  Angle     :  0.537   5.901  11224  Z= 0.289
  Chirality :  0.043   0.159   1279
  Planarity :  0.004   0.058   1460
  Dihedral  :  4.817  40.255   1120
  Min Nonbonded Distance : 1.733

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 30.26 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.25), residues: 1031
  helix: -1.56 (0.44), residues: 112
  sheet: -0.01 (0.31), residues: 282
  loop : -2.22 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 
 PHE   0.015   0.002   PHE A 487 
 TYR   0.017   0.001   TYR A 697 
 ARG   0.002   0.000   ARG B 394 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03368 (  214)
  hydrogen bonds       : angle       5.04995 (  618)
  covalent geometry    : bond        0.00302 ( 8271)
  covalent geometry    : angle       0.53722 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  660 MET cc_start: 0.7542 (tpp) cc_final: 0.7320 (tpp)
REVERT: B  251 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7148 (pm20)
REVERT: B  537 ASP cc_start: 0.8153 (m-30) cc_final: 0.7383 (t0)
REVERT: B  595 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5757 (mm)
REVERT: B  627 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8361 (t0)
  outliers start: 33
  outliers final: 19
  residues processed: 120
  average time/residue: 0.1798
  time to fit residues: 30.7277
Evaluate side-chains
  107 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  591 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  710 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 59 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0020
   overall best weight:    0.7790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.148446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124863 restraints weight = 11606.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128159 restraints weight = 7358.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130407 restraints weight = 5368.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8271  Z= 0.120
  Angle     :  0.521   6.077  11224  Z= 0.278
  Chirality :  0.043   0.156   1279
  Planarity :  0.003   0.047   1460
  Dihedral  :  4.665  40.184   1119
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.93 %
    Favored  : 66.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.25), residues: 1031
  helix: -1.24 (0.45), residues: 126
  sheet: -0.00 (0.32), residues: 282
  loop : -2.14 (0.23), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 
 PHE   0.014   0.002   PHE A 281 
 TYR   0.012   0.001   TYR B 297 
 ARG   0.003   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03114 (  214)
  hydrogen bonds       : angle       4.74076 (  618)
  covalent geometry    : bond        0.00289 ( 8271)
  covalent geometry    : angle       0.52070 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 86
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6430 (ptm160)
REVERT: A  412 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7716 (tt)
REVERT: B  537 ASP cc_start: 0.8207 (m-30) cc_final: 0.7446 (t0)
REVERT: B  627 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8009 (t0)
REVERT: B  699 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8217 (m)
  outliers start: 37
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1747
  time to fit residues: 29.5580
Evaluate side-chains
  105 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  699 VAL
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0980
   chunk 20 optimal weight:    0.2980
   chunk 75 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 682 ASN
B 392 ASN
B 428 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127785 restraints weight = 11377.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130961 restraints weight = 7235.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.133217 restraints weight = 5281.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8271  Z= 0.092
  Angle     :  0.494   5.891  11224  Z= 0.263
  Chirality :  0.043   0.151   1279
  Planarity :  0.003   0.040   1460
  Dihedral  :  4.458  40.772   1119
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 29.93 %
    Favored  : 65.18 %
  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: -1.87 (0.26), residues: 1031
  helix: -0.72 (0.49), residues: 115
  sheet:  0.06 (0.32), residues: 283
  loop : -2.08 (0.23), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 
 PHE   0.010   0.001   PHE A 711 
 TYR   0.011   0.001   TYR A 697 
 ARG   0.003   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02684 (  214)
  hydrogen bonds       : angle       4.48853 (  618)
  covalent geometry    : bond        0.00227 ( 8271)
  covalent geometry    : angle       0.49376 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 91
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLU cc_start: 0.7486 (pm20) cc_final: 0.7174 (pm20)
REVERT: A  394 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6971 (ptm160)
REVERT: A  412 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7688 (tt)
REVERT: A  522 GLU cc_start: 0.7333 (pm20) cc_final: 0.7125 (pm20)
REVERT: B  251 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7170 (pm20)
REVERT: B  537 ASP cc_start: 0.8098 (m-30) cc_final: 0.7415 (t0)
REVERT: B  595 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5833 (mm)
REVERT: B  627 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.7900 (t0)
  outliers start: 45
  outliers final: 25
  residues processed: 130
  average time/residue: 0.1846
  time to fit residues: 34.3802
Evaluate side-chains
  115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  689 LYS
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0370
   chunk 47 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
B 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.149205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126474 restraints weight = 11345.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.129693 restraints weight = 7254.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.131886 restraints weight = 5297.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8271  Z= 0.106
  Angle     :  0.504   5.995  11224  Z= 0.267
  Chirality :  0.043   0.158   1279
  Planarity :  0.003   0.037   1460
  Dihedral  :  4.475  39.713   1119
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 29.93 %
    Favored  : 64.75 %
  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: -1.85 (0.26), residues: 1031
  helix: -0.53 (0.50), residues: 114
  sheet:  0.02 (0.32), residues: 285
  loop : -2.07 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 
 PHE   0.013   0.001   PHE A 281 
 TYR   0.012   0.001   TYR A 261 
 ARG   0.002   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02742 (  214)
  hydrogen bonds       : angle       4.43968 (  618)
  covalent geometry    : bond        0.00259 ( 8271)
  covalent geometry    : angle       0.50357 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 92
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 ASN cc_start: 0.8260 (t0) cc_final: 0.8008 (t0)
REVERT: A  394 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6738 (ptm160)
REVERT: A  412 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7691 (tt)
REVERT: B  251 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7105 (pm20)
REVERT: B  537 ASP cc_start: 0.8035 (m-30) cc_final: 0.7352 (t0)
REVERT: B  595 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5836 (mm)
REVERT: B  627 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.7922 (t0)
  outliers start: 49
  outliers final: 29
  residues processed: 132
  average time/residue: 0.1835
  time to fit residues: 34.6276
Evaluate side-chains
  120 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 86
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  689 LYS
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    0.3980
   chunk 94 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0050
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0270
   overall best weight:    0.4252

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

Flipped N/Q/H residues before XYZ refinement:
B 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.150626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127550 restraints weight = 11368.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.130838 restraints weight = 7133.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.133123 restraints weight = 5167.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8271  Z= 0.094
  Angle     :  0.499   5.834  11224  Z= 0.263
  Chirality :  0.043   0.151   1279
  Planarity :  0.003   0.034   1460
  Dihedral  :  4.391  39.993   1119
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.83 %
    Favored  : 65.18 %
  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: -1.78 (0.26), residues: 1031
  helix: -0.40 (0.50), residues: 116
  sheet:  0.06 (0.32), residues: 285
  loop : -2.05 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 503 
 HIS   0.000   0.000   HIS A 359 
 PHE   0.010   0.001   PHE A 711 
 TYR   0.032   0.001   TYR A 261 
 ARG   0.002   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02573 (  214)
  hydrogen bonds       : angle       4.32125 (  618)
  covalent geometry    : bond        0.00234 ( 8271)
  covalent geometry    : angle       0.49884 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 93
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6650 (ptm160)
REVERT: A  412 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7610 (tt)
REVERT: A  479 GLU cc_start: 0.7876 (pp20) cc_final: 0.7359 (pp20)
REVERT: B  251 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7139 (pm20)
REVERT: B  310 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (t)
REVERT: B  437 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7497 (t0)
REVERT: B  537 ASP cc_start: 0.8149 (m-30) cc_final: 0.7429 (t0)
REVERT: B  595 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5901 (mm)
REVERT: B  612 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (tp)
REVERT: B  627 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.7873 (t0)
  outliers start: 46
  outliers final: 28
  residues processed: 132
  average time/residue: 0.1682
  time to fit residues: 32.0698
Evaluate side-chains
  121 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 85
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  437 ASP
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  689 LYS
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0670
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
B 329 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.125157 restraints weight = 11459.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.128299 restraints weight = 7203.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130527 restraints weight = 5269.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8271  Z= 0.112
  Angle     :  0.521   6.381  11224  Z= 0.276
  Chirality :  0.043   0.153   1279
  Planarity :  0.003   0.034   1460
  Dihedral  :  4.449  38.888   1119
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.83 %
    Favored  : 64.97 %
  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: -1.79 (0.26), residues: 1031
  helix: -0.61 (0.48), residues: 122
  sheet:  0.10 (0.32), residues: 285
  loop : -2.05 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 503 
 HIS   0.000   0.000   HIS A 314 
 PHE   0.013   0.001   PHE A 281 
 TYR   0.018   0.001   TYR A 261 
 ARG   0.001   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02777 (  214)
  hydrogen bonds       : angle       4.33269 (  618)
  covalent geometry    : bond        0.00274 ( 8271)
  covalent geometry    : angle       0.52099 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 86
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 ASN cc_start: 0.8305 (t0) cc_final: 0.8057 (t0)
REVERT: A  412 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7516 (tt)
REVERT: B  251 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7164 (pm20)
REVERT: B  297 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.5879 (p90)
REVERT: B  310 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8710 (t)
REVERT: B  403 MET cc_start: 0.8017 (tpp) cc_final: 0.7553 (tpt)
REVERT: B  437 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7502 (t0)
REVERT: B  537 ASP cc_start: 0.8208 (m-30) cc_final: 0.7491 (t0)
REVERT: B  595 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5748 (mm)
REVERT: B  627 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7888 (t0)
  outliers start: 48
  outliers final: 31
  residues processed: 127
  average time/residue: 0.1695
  time to fit residues: 31.5997
Evaluate side-chains
  122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 84
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  297 TYR
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  437 ASP
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  689 LYS
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0040
   chunk 83 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0170
   chunk 80 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5430

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

Flipped N/Q/H residues before XYZ refinement:
A 682 ASN
B 329 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.124256 restraints weight = 11470.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.127442 restraints weight = 7229.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.129622 restraints weight = 5263.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8271  Z= 0.102
  Angle     :  0.517   7.010  11224  Z= 0.272
  Chirality :  0.043   0.146   1279
  Planarity :  0.003   0.033   1460
  Dihedral  :  4.365  38.113   1119
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 30.48 %
    Favored  : 64.86 %
  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: -1.74 (0.26), residues: 1031
  helix: -0.28 (0.50), residues: 116
  sheet:  0.08 (0.32), residues: 284
  loop : -2.04 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 375 
 HIS   0.000   0.000   HIS A 359 
 PHE   0.011   0.001   PHE A 281 
 TYR   0.018   0.001   TYR A 261 
 ARG   0.001   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02604 (  214)
  hydrogen bonds       : angle       4.28216 (  618)
  covalent geometry    : bond        0.00253 ( 8271)
  covalent geometry    : angle       0.51737 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 83
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 ASN cc_start: 0.8292 (t0) cc_final: 0.8055 (t0)
REVERT: B  251 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7163 (pm20)
REVERT: B  310 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8690 (t)
REVERT: B  403 MET cc_start: 0.8109 (tpp) cc_final: 0.7549 (tpt)
REVERT: B  437 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7520 (t0)
REVERT: B  537 ASP cc_start: 0.8237 (m-30) cc_final: 0.7496 (t0)
REVERT: B  595 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5736 (mm)
REVERT: B  627 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7790 (t0)
  outliers start: 43
  outliers final: 29
  residues processed: 117
  average time/residue: 0.1612
  time to fit residues: 27.8138
Evaluate side-chains
  117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  437 ASP
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  627 ASN
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  689 LYS
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
B 329 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.123190 restraints weight = 11688.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126441 restraints weight = 7355.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128683 restraints weight = 5332.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8271  Z= 0.131
  Angle     :  0.549   7.161  11224  Z= 0.290
  Chirality :  0.044   0.165   1279
  Planarity :  0.003   0.034   1460
  Dihedral  :  4.522  32.449   1119
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 31.02 %
    Favored  : 64.43 %
  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: -1.78 (0.26), residues: 1031
  helix: -0.43 (0.48), residues: 119
  sheet:  0.09 (0.32), residues: 287
  loop : -2.07 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 503 
 HIS   0.000   0.000   HIS A 314 
 PHE   0.014   0.002   PHE A 281 
 TYR   0.022   0.001   TYR A 261 
 ARG   0.001   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02924 (  214)
  hydrogen bonds       : angle       4.41504 (  618)
  covalent geometry    : bond        0.00321 ( 8271)
  covalent geometry    : angle       0.54871 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 85
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 ASN cc_start: 0.8316 (t0) cc_final: 0.8043 (t0)
REVERT: B  251 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7128 (pm20)
REVERT: B  537 ASP cc_start: 0.8252 (m-30) cc_final: 0.7510 (t0)
REVERT: B  595 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5788 (mm)
  outliers start: 42
  outliers final: 29
  residues processed: 121
  average time/residue: 0.1634
  time to fit residues: 29.1583
Evaluate side-chains
  114 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  260 ASN
Chi-restraints excluded: chain A residue  313 GLU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0070
   chunk 70 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   chunk 59 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0870
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
A 682 ASN
B 329 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.127814 restraints weight = 11343.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131113 restraints weight = 7084.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.133345 restraints weight = 5125.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8271  Z= 0.092
  Angle     :  0.513   7.486  11224  Z= 0.270
  Chirality :  0.043   0.153   1279
  Planarity :  0.003   0.032   1460
  Dihedral  :  4.161  21.171   1117
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 32.00 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.26), residues: 1031
  helix: -0.21 (0.51), residues: 117
  sheet:  0.12 (0.32), residues: 284
  loop : -1.98 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 
 PHE   0.011   0.001   PHE A 281 
 TYR   0.019   0.001   TYR A 261 
 ARG   0.002   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02481 (  214)
  hydrogen bonds       : angle       4.25003 (  618)
  covalent geometry    : bond        0.00229 ( 8271)
  covalent geometry    : angle       0.51293 (11224)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 89
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  725 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7510 (pp)
REVERT: B  251 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7159 (pm20)
REVERT: B  537 ASP cc_start: 0.8256 (m-30) cc_final: 0.7521 (t0)
REVERT: B  595 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5798 (mm)
  outliers start: 34
  outliers final: 26
  residues processed: 116
  average time/residue: 0.1567
  time to fit residues: 27.3038
Evaluate side-chains
  115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  599 LYS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain B residue  251 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  479 GLU
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  670 VAL
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain B residue  710 GLU
Chi-restraints excluded: chain B residue  739 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 233 ASN
B 329 ASN
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 363 ASN
B 392 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.113242 restraints weight = 12066.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.116599 restraints weight = 7279.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.118931 restraints weight = 5191.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   8271  Z= 0.339
  Angle     :  0.797  10.007  11224  Z= 0.425
  Chirality :  0.052   0.201   1279
  Planarity :  0.004   0.037   1460
  Dihedral  :  5.741  33.814   1117
  Min Nonbonded Distance : 1.613

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 31.89 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.25), residues: 1031
  helix: -1.09 (0.45), residues: 118
  sheet: -0.26 (0.32), residues: 277
  loop : -2.28 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP B 503 
 HIS   0.003   0.001   HIS A 314 
 PHE   0.026   0.003   PHE A 281 
 TYR   0.027   0.002   TYR A 261 
 ARG   0.003   0.001   ARG B 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04739 (  214)
  hydrogen bonds       : angle       5.41382 (  618)
  covalent geometry    : bond        0.00818 ( 8271)
  covalent geometry    : angle       0.79722 (11224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2594.30 seconds
wall clock time: 46 minutes 20.59 seconds (2780.59 seconds total)