Starting phenix.real_space_refine
on Wed Sep 17 11:43:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mdi_48171/09_2025/9mdi_48171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mdi_48171/09_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_48171/09_2025/9mdi_48171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mdi_48171/09_2025/9mdi_48171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mdi_48171/09_2025/9mdi_48171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mdi_48171/09_2025/9mdi_48171.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.085
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.31, per 1000 atoms: 0.28
  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: 0.65
  Conformation dependent library (CDL) restraints added in 431.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.36
  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: 1.29

  Time building geometry restraints manager: 0.88 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 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:             3.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.550
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG B 607 
 TYR   0.041   0.001   TYR B 261 
 PHE   0.018   0.002   PHE A 281 
 TRP   0.016   0.002   TRP A 503 
 HIS   0.000   0.000   HIS B 359 

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

*********************** 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  : 0.355 
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: 0.0843
  time to fit residues: 13.0034
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  : 0.345 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0270
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.0644

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.145492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.121172 restraints weight = 11818.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124694 restraints weight = 7264.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.127152 restraints weight = 5208.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.128732 restraints weight = 4116.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129884 restraints weight = 3496.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8271  Z= 0.150
  Angle     :  0.566   6.138  11224  Z= 0.304
  Chirality :  0.044   0.163   1279
  Planarity :  0.004   0.059   1460
  Dihedral  :  4.961  39.766   1120
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 30.37 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.25), residues: 1031
  helix: -1.79 (0.41), residues: 124
  sheet: -0.05 (0.31), residues: 282
  loop : -2.22 (0.23), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 528 
 TYR   0.017   0.001   TYR A 697 
 PHE   0.017   0.002   PHE A 281 
 TRP   0.015   0.002   TRP A 503 
 HIS   0.001   0.000   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8271)
  covalent geometry    : angle       0.56587 (11224)
  hydrogen bonds       : bond        0.03606 (  214)
  hydrogen bonds       : angle       5.10041 (  618)

*********************** 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
  131 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  251 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7191 (pm20)
REVERT: B  537 ASP cc_start: 0.8217 (m-30) cc_final: 0.7373 (t0)
REVERT: B  595 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5596 (mm)
REVERT: B  627 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8369 (t0)
  outliers start: 37
  outliers final: 20
  residues processed: 124
  average time/residue: 0.0800
  time to fit residues: 14.3211
Evaluate side-chains
  111 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  260 ASN
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 42 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.142007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.117923 restraints weight = 11657.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.121444 restraints weight = 6898.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.123915 restraints weight = 4858.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.125546 restraints weight = 3804.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.126585 restraints weight = 3203.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8271  Z= 0.203
  Angle     :  0.625   6.631  11224  Z= 0.336
  Chirality :  0.046   0.168   1279
  Planarity :  0.004   0.050   1460
  Dihedral  :  5.295  37.154   1119
  Min Nonbonded Distance : 1.716

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.12 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 29.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.25), residues: 1031
  helix: -1.54 (0.42), residues: 125
  sheet: -0.20 (0.32), residues: 282
  loop : -2.24 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.020   0.002   TYR A 395 
 PHE   0.020   0.002   PHE A 281 
 TRP   0.019   0.002   TRP A 503 
 HIS   0.001   0.000   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 8271)
  covalent geometry    : angle       0.62533 (11224)
  hydrogen bonds       : bond        0.03996 (  214)
  hydrogen bonds       : angle       5.18063 (  618)

*********************** 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
  145 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6992 (ptm160)
REVERT: B  297 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.5632 (p90)
REVERT: B  537 ASP cc_start: 0.8406 (m-30) cc_final: 0.7489 (t0)
REVERT: B  595 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5495 (mm)
REVERT: B  627 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8040 (t0)
  outliers start: 52
  outliers final: 27
  residues processed: 134
  average time/residue: 0.0801
  time to fit residues: 15.6640
Evaluate side-chains
  117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  281 PHE
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  417 ASP
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  744 THR
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  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  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
Chi-restraints excluded: chain B residue  744 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0070
   chunk 47 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.146795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.123329 restraints weight = 11715.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126651 restraints weight = 7382.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128908 restraints weight = 5344.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.130459 restraints weight = 4272.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.131538 restraints weight = 3645.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
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   0.036   8271  Z= 0.109
  Angle     :  0.530   6.211  11224  Z= 0.283
  Chirality :  0.044   0.157   1279
  Planarity :  0.003   0.041   1460
  Dihedral  :  4.791  39.301   1119
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.83 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.05 (0.25), residues: 1031
  helix: -1.13 (0.45), residues: 126
  sheet: -0.03 (0.32), residues: 283
  loop : -2.17 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 290 
 TYR   0.013   0.001   TYR A 464 
 PHE   0.012   0.002   PHE A 281 
 TRP   0.009   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8271)
  covalent geometry    : angle       0.52951 (11224)
  hydrogen bonds       : bond        0.02961 (  214)
  hydrogen bonds       : angle       4.76177 (  618)

*********************** 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
  133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 94
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7074 (t70) cc_final: 0.6783 (t0)
REVERT: A  263 GLU cc_start: 0.7520 (pm20) cc_final: 0.7292 (pm20)
REVERT: A  394 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7241 (ptm160)
REVERT: B  251 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7112 (pm20)
REVERT: B  537 ASP cc_start: 0.8185 (m-30) cc_final: 0.7454 (t0)
REVERT: B  573 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7822 (pp20)
REVERT: B  627 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.7954 (t0)
  outliers start: 39
  outliers final: 22
  residues processed: 129
  average time/residue: 0.0868
  time to fit residues: 16.0043
Evaluate side-chains
  109 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  310 SER
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  457 SER
Chi-restraints excluded: chain B residue  462 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  573 GLU
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  739 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0770
   chunk 12 optimal weight:    0.0020
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0870
   chunk 51 optimal weight:    9.9990
   overall best weight:    0.3524

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 ASN
B 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125081 restraints weight = 11606.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.128390 restraints weight = 7306.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130667 restraints weight = 5296.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132213 restraints weight = 4221.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.133072 restraints weight = 3601.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1715

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     :  0.510   6.615  11224  Z= 0.271
  Chirality :  0.043   0.155   1279
  Planarity :  0.003   0.037   1460
  Dihedral  :  4.529  37.485   1119
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 30.48 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.26), residues: 1031
  helix: -0.57 (0.50), residues: 114
  sheet:  0.09 (0.32), residues: 281
  loop : -2.08 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.014   0.001   TYR A 395 
 PHE   0.017   0.001   PHE B 281 
 TRP   0.007   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8271)
  covalent geometry    : angle       0.51043 (11224)
  hydrogen bonds       : bond        0.02691 (  214)
  hydrogen bonds       : angle       4.52776 (  618)

*********************** 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
  136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 95
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7097 (t70) cc_final: 0.6725 (t0)
REVERT: A  263 GLU cc_start: 0.7498 (pm20) cc_final: 0.7214 (pm20)
REVERT: A  376 ASN cc_start: 0.8299 (t0) cc_final: 0.8086 (t0)
REVERT: A  394 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7196 (ptm160)
REVERT: B  251 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7131 (pm20)
REVERT: B  537 ASP cc_start: 0.8098 (m-30) cc_final: 0.7396 (t0)
  outliers start: 41
  outliers final: 24
  residues processed: 130
  average time/residue: 0.0820
  time to fit residues: 15.2840
Evaluate side-chains
  113 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  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  514 SER
Chi-restraints excluded: chain B residue  573 GLU
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  739 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.7298

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.144876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.121424 restraints weight = 11547.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.124607 restraints weight = 7349.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126799 restraints weight = 5384.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.128341 restraints weight = 4323.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.129344 restraints weight = 3700.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8271  Z= 0.118
  Angle     :  0.532   6.046  11224  Z= 0.282
  Chirality :  0.044   0.156   1279
  Planarity :  0.003   0.036   1460
  Dihedral  :  4.445  22.814   1117
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.26), residues: 1031
  helix: -0.83 (0.46), residues: 127
  sheet:  0.05 (0.32), residues: 284
  loop : -2.07 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.015   0.001   TYR A 395 
 PHE   0.022   0.002   PHE B 281 
 TRP   0.010   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8271)
  covalent geometry    : angle       0.53215 (11224)
  hydrogen bonds       : bond        0.02933 (  214)
  hydrogen bonds       : angle       4.54153 (  618)

*********************** 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
  130 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 87
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7275 (t70) cc_final: 0.6791 (t0)
REVERT: A  394 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6700 (ptm160)
REVERT: A  522 GLU cc_start: 0.7441 (pm20) cc_final: 0.7238 (pm20)
REVERT: B  251 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7158 (pm20)
REVERT: B  297 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.5717 (p90)
REVERT: B  310 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8735 (t)
REVERT: B  537 ASP cc_start: 0.8119 (m-30) cc_final: 0.7429 (t0)
REVERT: B  595 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5808 (mm)
REVERT: B  612 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8394 (tp)
  outliers start: 43
  outliers final: 24
  residues processed: 124
  average time/residue: 0.0778
  time to fit residues: 14.0495
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  : 0.336 
-------------------------------------------------------------------------------
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  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  297 TYR
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
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  514 SER
Chi-restraints excluded: chain B residue  595 LEU
Chi-restraints excluded: chain B residue  612 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  689 LYS
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 90 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0470
   chunk 83 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.9482

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.142090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.118561 restraints weight = 11842.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.121760 restraints weight = 7540.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.123923 restraints weight = 5515.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.125455 restraints weight = 4432.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.126425 restraints weight = 3794.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8271  Z= 0.137
  Angle     :  0.563   6.438  11224  Z= 0.298
  Chirality :  0.045   0.158   1279
  Planarity :  0.003   0.034   1460
  Dihedral  :  4.596  23.700   1117
  Min Nonbonded Distance : 1.787

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 30.37 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.26), residues: 1031
  helix: -0.73 (0.46), residues: 124
  sheet:  0.03 (0.32), residues: 287
  loop : -2.11 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 528 
 TYR   0.022   0.001   TYR A 395 
 PHE   0.022   0.002   PHE B 281 
 TRP   0.012   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8271)
  covalent geometry    : angle       0.56283 (11224)
  hydrogen bonds       : bond        0.03104 (  214)
  hydrogen bonds       : angle       4.62654 (  618)

*********************** 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
  133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 91
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7504 (t70) cc_final: 0.7024 (t0)
REVERT: A  369 ASP cc_start: 0.7985 (t0) cc_final: 0.7664 (t0)
REVERT: A  394 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6599 (ptm160)
REVERT: B  251 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7125 (pm20)
REVERT: B  297 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.5807 (p90)
REVERT: B  310 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8792 (t)
REVERT: B  537 ASP cc_start: 0.8189 (m-30) cc_final: 0.7478 (t0)
REVERT: B  595 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5821 (mm)
REVERT: B  612 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (tp)
  outliers start: 42
  outliers final: 28
  residues processed: 125
  average time/residue: 0.0812
  time to fit residues: 14.6938
Evaluate side-chains
  118 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  332 THR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  297 TYR
Chi-restraints excluded: chain B residue  302 VAL
Chi-restraints excluded: chain B residue  310 SER
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  457 SER
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  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 10 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0470
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.123917 restraints weight = 11534.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.127136 restraints weight = 7307.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.129370 restraints weight = 5329.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.130930 restraints weight = 4262.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131902 restraints weight = 3635.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1970

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= 0.106
  Angle     :  0.539   7.067  11224  Z= 0.285
  Chirality :  0.043   0.155   1279
  Planarity :  0.003   0.034   1460
  Dihedral  :  4.418  23.004   1117
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 30.48 %
    Favored  : 65.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.26), residues: 1031
  helix: -0.70 (0.47), residues: 127
  sheet:  0.10 (0.32), residues: 283
  loop : -2.03 (0.24), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.017   0.001   TYR A 274 
 PHE   0.018   0.002   PHE B 281 
 TRP   0.009   0.001   TRP A 503 
 HIS   0.007   0.002   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8271)
  covalent geometry    : angle       0.53903 (11224)
  hydrogen bonds       : bond        0.02746 (  214)
  hydrogen bonds       : angle       4.45837 (  618)

*********************** 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: 38
    poor density    : 88
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7378 (t70) cc_final: 0.6961 (t0)
REVERT: A  376 ASN cc_start: 0.8296 (t0) cc_final: 0.8055 (t0)
REVERT: A  394 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6521 (ptm160)
REVERT: A  725 LEU cc_start: 0.7724 (pp) cc_final: 0.7477 (pp)
REVERT: B  251 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7128 (pm20)
REVERT: B  310 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8669 (t)
REVERT: B  537 ASP cc_start: 0.8142 (m-30) cc_final: 0.7471 (t0)
REVERT: B  595 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5783 (mm)
  outliers start: 38
  outliers final: 26
  residues processed: 122
  average time/residue: 0.0804
  time to fit residues: 14.2120
Evaluate side-chains
  113 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  394 ARG
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  389 ILE
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  457 SER
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  689 LYS
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 66 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0670
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 79 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.147833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.124312 restraints weight = 11525.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127576 restraints weight = 7328.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.129820 restraints weight = 5355.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.131306 restraints weight = 4295.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.132419 restraints weight = 3680.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1980

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= 0.104
  Angle     :  0.529   7.400  11224  Z= 0.280
  Chirality :  0.043   0.146   1279
  Planarity :  0.003   0.060   1460
  Dihedral  :  4.364  23.026   1117
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 30.80 %
    Favored  : 65.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.26), residues: 1031
  helix: -0.30 (0.50), residues: 115
  sheet:  0.14 (0.32), residues: 282
  loop : -1.99 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 290 
 TYR   0.018   0.001   TYR A 388 
 PHE   0.012   0.001   PHE A 281 
 TRP   0.009   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8271)
  covalent geometry    : angle       0.52923 (11224)
  hydrogen bonds       : bond        0.02657 (  214)
  hydrogen bonds       : angle       4.38582 (  618)

*********************** 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
  122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 87
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ASP cc_start: 0.7443 (t70) cc_final: 0.7023 (t0)
REVERT: A  376 ASN cc_start: 0.8285 (t0) cc_final: 0.8041 (t0)
REVERT: A  394 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6503 (ptm160)
REVERT: A  725 LEU cc_start: 0.7731 (pp) cc_final: 0.7503 (pp)
REVERT: B  251 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7103 (pm20)
REVERT: B  310 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8602 (t)
REVERT: B  537 ASP cc_start: 0.8140 (m-30) cc_final: 0.7476 (t0)
  outliers start: 35
  outliers final: 25
  residues processed: 117
  average time/residue: 0.0760
  time to fit residues: 12.8679
Evaluate side-chains
  109 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  332 THR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  457 SER
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  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  739 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 75 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0040
   chunk 37 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 ASN
B 427 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.124943 restraints weight = 11546.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128144 restraints weight = 7301.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130376 restraints weight = 5347.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131844 restraints weight = 4286.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132942 restraints weight = 3677.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8271  Z= 0.110
  Angle     :  0.538   7.514  11224  Z= 0.285
  Chirality :  0.044   0.168   1279
  Planarity :  0.003   0.055   1460
  Dihedral  :  4.360  23.215   1117
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 31.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.26), residues: 1031
  helix: -0.29 (0.50), residues: 115
  sheet:  0.14 (0.32), residues: 282
  loop : -1.97 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 528 
 TYR   0.017   0.001   TYR A 395 
 PHE   0.013   0.001   PHE A 281 
 TRP   0.009   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8271)
  covalent geometry    : angle       0.53815 (11224)
  hydrogen bonds       : bond        0.02698 (  214)
  hydrogen bonds       : angle       4.37124 (  618)

********************** 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
  112 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  376 ASN cc_start: 0.8245 (t0) cc_final: 0.7981 (t0)
REVERT: A  394 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6431 (ptm160)
REVERT: A  725 LEU cc_start: 0.7706 (pp) cc_final: 0.7465 (pp)
REVERT: B  251 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7090 (pm20)
REVERT: B  310 SER cc_start: 0.8846 (m) cc_final: 0.8616 (t)
REVERT: B  537 ASP cc_start: 0.8134 (m-30) cc_final: 0.7473 (t0)
REVERT: B  595 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5807 (mm)
  outliers start: 31
  outliers final: 25
  residues processed: 110
  average time/residue: 0.0755
  time to fit residues: 12.1341
Evaluate side-chains
  108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  332 THR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  394 ARG
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  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  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  689 LYS
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 6 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 329 ASN
** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119004 restraints weight = 11748.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.122416 restraints weight = 7180.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124715 restraints weight = 5141.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.126358 restraints weight = 4084.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127462 restraints weight = 3450.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8271  Z= 0.152
  Angle     :  0.580   7.527  11224  Z= 0.308
  Chirality :  0.045   0.171   1279
  Planarity :  0.003   0.056   1460
  Dihedral  :  4.659  25.283   1117
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 31.45 %
    Favored  : 65.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.26), residues: 1031
  helix: -0.55 (0.48), residues: 120
  sheet:  0.06 (0.32), residues: 286
  loop : -2.02 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 290 
 TYR   0.025   0.001   TYR A 395 
 PHE   0.017   0.002   PHE A 281 
 TRP   0.012   0.001   TRP A 503 
 HIS   0.001   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8271)
  covalent geometry    : angle       0.58025 (11224)
  hydrogen bonds       : bond        0.03171 (  214)
  hydrogen bonds       : angle       4.61336 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1383.50 seconds
wall clock time: 24 minutes 47.64 seconds (1487.64 seconds total)