Starting phenix.real_space_refine
on Wed Mar 12 15:29:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5njg_3654/03_2025/5njg_3654.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5234      2.51       5
     N    1288      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8038
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2249
          Classifications: {'peptide': 286}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 277}
    Chain: "B"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2249
          Classifications: {'peptide': 286}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 277}
    Chain: "C"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 928
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "D"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 814
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 928
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "F"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 814
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100}
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.93, per 1000 atoms: 0.61
  Number of scatterers: 8038
  At special positions: 0
  Unit cell: (82.081, 94.549, 107.017, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1466      8.00
     N    1288      7.00
     C    5234      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS B 603 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG G   1 " - " ASN A 596 "
      " NAG H   1 " - " ASN B 596 "
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      47.1% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 373 through 391
      removed outlier: 3.616A  pdb=" N   LEU A 377 " --> pdb=" O   PHE A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 413
      removed outlier: 4.023A  pdb=" N   SER A 395 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 422 through 441
      removed outlier: 3.526A  pdb=" N   GLY A 428 " --> pdb=" O   GLN A 424 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 435 " --> pdb=" O   PHE A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 450
      removed outlier: 3.739A  pdb=" N   LEU A 447 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 448 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   VAL A 450 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 461
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 502 through 529
    Processing helix  chain 'A' and resid 533 through 550
      removed outlier: 4.282A  pdb=" N   ALA A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 557
      removed outlier: 4.324A  pdb=" N   VAL A 556 " --> pdb=" O   SER A 552 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASN A 557 " --> pdb=" O   GLY A 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 552 through 557'
    Processing helix  chain 'A' and resid 558 through 561
      removed outlier: 3.777A  pdb=" N   ILE A 561 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 558 through 561'
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.507A  pdb=" N   LEU A 568 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 569 " --> pdb=" O   SER A 566 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR A 570 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 582
      removed outlier: 3.899A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.582A  pdb=" N   PHE A 586 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 587 " --> pdb=" O   HIS A 583 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 582 through 587'
    Processing helix  chain 'A' and resid 610 through 618
    Processing helix  chain 'A' and resid 623 through 652
      removed outlier: 3.773A  pdb=" N   TRP A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 391
      removed outlier: 3.615A  pdb=" N   LEU B 377 " --> pdb=" O   PHE B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 413
      removed outlier: 4.023A  pdb=" N   SER B 395 " --> pdb=" O   ASN B 391 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 421
      No H-bonds generated for 'chain 'B' and resid 419 through 421'
    Processing helix  chain 'B' and resid 422 through 441
      removed outlier: 3.525A  pdb=" N   GLY B 428 " --> pdb=" O   GLN B 424 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR B 435 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 450
      removed outlier: 3.739A  pdb=" N   LEU B 447 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE B 448 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   VAL B 450 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 461
    Processing helix  chain 'B' and resid 465 through 477
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 483 through 494
    Processing helix  chain 'B' and resid 502 through 529
    Processing helix  chain 'B' and resid 533 through 550
      removed outlier: 4.281A  pdb=" N   ALA B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 557
      removed outlier: 4.323A  pdb=" N   VAL B 556 " --> pdb=" O   SER B 552 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASN B 557 " --> pdb=" O   GLY B 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 552 through 557'
    Processing helix  chain 'B' and resid 558 through 561
      removed outlier: 3.777A  pdb=" N   ILE B 561 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 558 through 561'
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.507A  pdb=" N   LEU B 568 " --> pdb=" O   LEU B 565 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN B 569 " --> pdb=" O   SER B 566 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR B 570 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 582
      removed outlier: 3.899A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 587
      removed outlier: 3.582A  pdb=" N   PHE B 586 " --> pdb=" O   GLN B 582 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU B 587 " --> pdb=" O   HIS B 583 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 582 through 587'
    Processing helix  chain 'B' and resid 610 through 618
    Processing helix  chain 'B' and resid 623 through 652
      removed outlier: 3.774A  pdb=" N   TRP B 627 " --> pdb=" O   PRO B 623 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'E' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.608A  pdb=" N   THR C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE C  79 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.222A  pdb=" N   ARG C  39 " --> pdb=" O   TRP C  48 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   TRP C  48 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.501A  pdb=" N   TYR C 108 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.140A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG D  45 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.608A  pdb=" N   THR E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE E  79 " --> pdb=" O   CYS E  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.222A  pdb=" N   ARG E  39 " --> pdb=" O   TRP E  48 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   TRP E  48 " --> pdb=" O   ARG E  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.501A  pdb=" N   TYR E 108 " --> pdb=" O   THR E  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 6
    Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.140A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG F  45 " --> pdb=" O   GLN F  37 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1170 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1319
        1.32 -     1.44: 2395
        1.44 -     1.57: 4452
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8242
  Sorted by residual:
  bond pdb=" CB  GLN A 569 "
       pdb=" CG  GLN A 569 "
    ideal  model  delta    sigma   weight residual
    1.520  1.435  0.085 3.00e-02 1.11e+03 7.94e+00
  bond pdb=" CB  GLN B 569 "
       pdb=" CG  GLN B 569 "
    ideal  model  delta    sigma   weight residual
    1.520  1.437  0.083 3.00e-02 1.11e+03 7.71e+00
  bond pdb=" C   ASN A 601 "
       pdb=" N   PRO A 602 "
    ideal  model  delta    sigma   weight residual
    1.334  1.396 -0.062 2.34e-02 1.83e+03 7.02e+00
  bond pdb=" C   ASN B 601 "
       pdb=" N   PRO B 602 "
    ideal  model  delta    sigma   weight residual
    1.334  1.395 -0.061 2.34e-02 1.83e+03 6.83e+00
  bond pdb=" C   ASN F  42 "
       pdb=" N   ALA F  43 "
    ideal  model  delta    sigma   weight residual
    1.340  1.195  0.146 5.87e-02 2.90e+02 6.15e+00
  ... (remaining 8237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 10553
        2.50 -     5.00: 523
        5.00 -     7.49: 95
        7.49 -     9.99: 19
        9.99 -    12.49: 6
  Bond angle restraints: 11196
  Sorted by residual:
  angle pdb=" C   PRO A 602 "
        pdb=" N   CYS A 603 "
        pdb=" CA  CYS A 603 "
      ideal   model   delta    sigma   weight residual
     122.17  113.86    8.31 1.62e+00 3.81e-01 2.63e+01
  angle pdb=" C   PRO B 602 "
        pdb=" N   CYS B 603 "
        pdb=" CA  CYS B 603 "
      ideal   model   delta    sigma   weight residual
     122.17  113.88    8.29 1.62e+00 3.81e-01 2.62e+01
  angle pdb=" N   PRO A 602 "
        pdb=" CA  PRO A 602 "
        pdb=" C   PRO A 602 "
      ideal   model   delta    sigma   weight residual
     112.47  122.52  -10.05 2.06e+00 2.36e-01 2.38e+01
  angle pdb=" N   PRO B 602 "
        pdb=" CA  PRO B 602 "
        pdb=" C   PRO B 602 "
      ideal   model   delta    sigma   weight residual
     112.47  122.48  -10.01 2.06e+00 2.36e-01 2.36e+01
  angle pdb=" C   TYR B 605 "
        pdb=" CA  TYR B 605 "
        pdb=" CB  TYR B 605 "
      ideal   model   delta    sigma   weight residual
     111.48  103.98    7.50 1.59e+00 3.96e-01 2.23e+01
  ... (remaining 11191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.45: 4384
       14.45 -    28.89: 338
       28.89 -    43.34: 79
       43.34 -    57.79: 31
       57.79 -    72.23: 5
  Dihedral angle restraints: 4837
    sinusoidal: 1899
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CA  ASN A 601 "
           pdb=" C   ASN A 601 "
           pdb=" N   PRO A 602 "
           pdb=" CA  PRO A 602 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -124.15  -55.85     0      5.00e+00 4.00e-02 1.25e+02
  dihedral pdb=" CA  ASN B 601 "
           pdb=" C   ASN B 601 "
           pdb=" N   PRO B 602 "
           pdb=" CA  PRO B 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.17  -55.83     0      5.00e+00 4.00e-02 1.25e+02
  dihedral pdb=" CA  PRO A 602 "
           pdb=" C   PRO A 602 "
           pdb=" N   CYS A 603 "
           pdb=" CA  CYS A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.89   42.11     0      5.00e+00 4.00e-02 7.09e+01
  ... (remaining 4834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1084
       0.094 -    0.188: 186
       0.188 -    0.282: 6
       0.282 -    0.376: 4
       0.376 -    0.470: 4
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A 596 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.52e+00
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN B 596 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.96   -0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" CB  ILE A 573 "
            pdb=" CA  ILE A 573 "
            pdb=" CG1 ILE A 573 "
            pdb=" CG2 ILE A 573 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 601 "   -0.046 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO A 602 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 602 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 602 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 601 "    0.046 5.00e-02 4.00e+02   6.98e-02 7.80e+00
        pdb=" N   PRO B 602 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 602 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 602 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 576 "    0.019 2.00e-02 2.50e+03   1.82e-02 6.62e+00
        pdb=" CG  TYR B 576 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 576 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 576 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 576 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 576 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 576 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 576 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 848
        2.73 -     3.27: 7957
        3.27 -     3.81: 13432
        3.81 -     4.36: 16003
        4.36 -     4.90: 27840
  Nonbonded interactions: 66080
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 575 "
            pdb=" OG1 THR B 579 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" O   ARG A 575 "
            pdb=" OG1 THR A 579 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   VAL A 508 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   VAL B 508 "
            pdb=" OG1 THR B 512 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   CYS A 438 "
            pdb=" OG  SER A 441 "
     model   vdw
     2.273 3.040
  ... (remaining 66075 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  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:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.880
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
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      :  0.014   0.146   8242  Z= 0.880
  Angle     :  1.312  12.489  11196  Z= 0.687
  Chirality :  0.071   0.470   1284
  Planarity :  0.009   0.070   1370
  Dihedral  : 11.637  70.998   2944
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.94 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  3.42 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.61 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.21), residues: 1008
  helix: -3.07 (0.15), residues: 382
  sheet: -1.95 (0.28), residues: 226
  loop : -2.70 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP C 109 
 HIS   0.004   0.002   HIS A 457 
 PHE   0.041   0.005   PHE D  98 
 TYR   0.044   0.005   TYR B 576 
 ARG   0.013   0.002   ARG B 426 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 259
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  379 TRP cc_start: 0.7422 (t-100) cc_final: 0.6817 (t60)
REVERT: A  396 ILE cc_start: 0.8793 (mt) cc_final: 0.8500 (mp)
REVERT: A  488 ILE cc_start: 0.8833 (mt) cc_final: 0.8591 (mt)
REVERT: A  492 ILE cc_start: 0.8281 (pt) cc_final: 0.7780 (pt)
REVERT: A  548 MET cc_start: 0.8118 (mtm) cc_final: 0.7614 (mtt)
REVERT: A  624 TRP cc_start: 0.8288 (t60) cc_final: 0.7982 (t60)
REVERT: B  373 PHE cc_start: 0.6804 (t80) cc_final: 0.6512 (t80)
REVERT: B  379 TRP cc_start: 0.7367 (t-100) cc_final: 0.6686 (t60)
REVERT: B  479 LEU cc_start: 0.8692 (mt) cc_final: 0.8320 (tp)
REVERT: B  488 ILE cc_start: 0.8756 (mt) cc_final: 0.8452 (mt)
REVERT: B  617 GLN cc_start: 0.8253 (tp-100) cc_final: 0.8026 (mm-40)
REVERT: D   90 GLN cc_start: 0.8991 (pp30) cc_final: 0.8382 (pp30)
REVERT: E  103 LYS cc_start: 0.8851 (tttt) cc_final: 0.8349 (tttp)
  outliers start: 6
  outliers final: 1
  residues processed: 263
  average time/residue: 0.2114
  time to fit residues: 73.7466
Evaluate side-chains
  171 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  546 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
A 557 ASN
A 601 ASN
B 424 GLN
C  40 GLN
C  82 GLN
D  38 GLN
E  82 GLN
F  38 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103076 restraints weight = 13370.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.105878 restraints weight = 7695.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107682 restraints weight = 5435.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8242  Z= 0.246
  Angle     :  0.781   9.221  11196  Z= 0.395
  Chirality :  0.046   0.232   1284
  Planarity :  0.006   0.058   1370
  Dihedral  :  8.169  66.081   1185
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.87 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.10 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.25), residues: 1008
  helix: -0.46 (0.23), residues: 392
  sheet: -1.23 (0.32), residues: 212
  loop : -1.75 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 624 
 HIS   0.002   0.001   HIS A 630 
 PHE   0.022   0.002   PHE D  62 
 TYR   0.028   0.002   TYR B 645 
 ARG   0.004   0.001   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 PHE cc_start: 0.6474 (t80) cc_final: 0.6273 (t80)
REVERT: A  379 TRP cc_start: 0.7334 (t-100) cc_final: 0.7063 (t60)
REVERT: B  373 PHE cc_start: 0.6473 (t80) cc_final: 0.6252 (t80)
REVERT: B  479 LEU cc_start: 0.8836 (mt) cc_final: 0.8414 (tp)
REVERT: B  512 THR cc_start: 0.9332 (m) cc_final: 0.9100 (p)
REVERT: D   36 TYR cc_start: 0.8802 (m-80) cc_final: 0.8591 (m-80)
REVERT: D   81 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7563 (pt0)
REVERT: D   82 ASP cc_start: 0.8297 (m-30) cc_final: 0.8062 (m-30)
REVERT: D   90 GLN cc_start: 0.9142 (pp30) cc_final: 0.8418 (pp30)
REVERT: F   13 VAL cc_start: 0.7986 (m) cc_final: 0.7591 (p)
REVERT: F   36 TYR cc_start: 0.8842 (m-80) cc_final: 0.8534 (m-80)
REVERT: F   82 ASP cc_start: 0.8398 (m-30) cc_final: 0.8101 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 210
  average time/residue: 0.1629
  time to fit residues: 49.2562
Evaluate side-chains
  179 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 172
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain F residue   81 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 76 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 71 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
A 601 ASN
A 629 ASN
B 437 GLN
B 557 ASN
B 629 ASN
C  82 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.104151 restraints weight = 13707.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.107019 restraints weight = 7753.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108807 restraints weight = 5431.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8242  Z= 0.213
  Angle     :  0.704   9.025  11196  Z= 0.358
  Chirality :  0.044   0.230   1284
  Planarity :  0.005   0.053   1370
  Dihedral  :  7.371  61.617   1184
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.96 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.40 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.26), residues: 1008
  helix:  0.55 (0.25), residues: 398
  sheet: -0.70 (0.34), residues: 212
  loop : -1.44 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  35 
 HIS   0.002   0.000   HIS B 583 
 PHE   0.015   0.002   PHE E  79 
 TYR   0.031   0.002   TYR A 645 
 ARG   0.003   0.000   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8667 (mmp80) cc_final: 0.7866 (mmt180)
REVERT: A  511 PHE cc_start: 0.8828 (t80) cc_final: 0.8443 (t80)
REVERT: B  373 PHE cc_start: 0.6609 (t80) cc_final: 0.6375 (t80)
REVERT: B  479 LEU cc_start: 0.8969 (mt) cc_final: 0.8533 (tp)
REVERT: B  511 PHE cc_start: 0.8648 (t80) cc_final: 0.8032 (t80)
REVERT: B  512 THR cc_start: 0.9346 (m) cc_final: 0.9137 (p)
REVERT: B  620 ASP cc_start: 0.8404 (t0) cc_final: 0.8197 (t0)
REVERT: C  100 TYR cc_start: 0.7242 (t80) cc_final: 0.6988 (t80)
REVERT: D   13 VAL cc_start: 0.7648 (m) cc_final: 0.7224 (p)
REVERT: D   18 ARG cc_start: 0.6713 (ttp80) cc_final: 0.6379 (ttp80)
REVERT: D   31 ASN cc_start: 0.8847 (m-40) cc_final: 0.8490 (m110)
REVERT: D   81 GLU cc_start: 0.7910 (pt0) cc_final: 0.7523 (pt0)
REVERT: D   82 ASP cc_start: 0.8230 (m-30) cc_final: 0.7995 (m-30)
REVERT: D   90 GLN cc_start: 0.9211 (pp30) cc_final: 0.8494 (pp30)
REVERT: D  107 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5898 (tpt90)
REVERT: F   13 VAL cc_start: 0.7936 (m) cc_final: 0.7590 (p)
REVERT: F   36 TYR cc_start: 0.8858 (m-80) cc_final: 0.8335 (m-80)
  outliers start: 24
  outliers final: 10
  residues processed: 215
  average time/residue: 0.1673
  time to fit residues: 50.9290
Evaluate side-chains
  182 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue  107 ARG
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue    3 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 87 optimal weight:    0.2980
   chunk 85 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 437 GLN
C  82 GLN
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109387 restraints weight = 13719.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111900 restraints weight = 8437.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113491 restraints weight = 6231.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8242  Z= 0.168
  Angle     :  0.655   8.355  11196  Z= 0.332
  Chirality :  0.042   0.231   1284
  Planarity :  0.005   0.057   1370
  Dihedral  :  6.728  57.213   1184
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.66 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.79 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.27), residues: 1008
  helix:  1.09 (0.26), residues: 398
  sheet: -0.36 (0.36), residues: 212
  loop : -1.22 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  35 
 HIS   0.001   0.000   HIS A 630 
 PHE   0.015   0.001   PHE F  62 
 TYR   0.028   0.001   TYR A 645 
 ARG   0.002   0.000   ARG A 378 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7276 (pt0) cc_final: 0.6827 (pt0)
REVERT: A  482 ARG cc_start: 0.8675 (mmp80) cc_final: 0.7996 (mmt180)
REVERT: A  511 PHE cc_start: 0.8748 (t80) cc_final: 0.8358 (t80)
REVERT: B  373 PHE cc_start: 0.6711 (t80) cc_final: 0.6497 (t80)
REVERT: B  479 LEU cc_start: 0.8984 (mt) cc_final: 0.8615 (tp)
REVERT: B  509 MET cc_start: 0.8602 (ttt) cc_final: 0.8263 (ttt)
REVERT: B  511 PHE cc_start: 0.8592 (t80) cc_final: 0.8081 (t80)
REVERT: B  512 THR cc_start: 0.9357 (m) cc_final: 0.9154 (p)
REVERT: C   11 LEU cc_start: 0.8350 (tp) cc_final: 0.7661 (mp)
REVERT: D   13 VAL cc_start: 0.7618 (m) cc_final: 0.7289 (p)
REVERT: D   18 ARG cc_start: 0.6671 (ttp80) cc_final: 0.6390 (ttp80)
REVERT: D   31 ASN cc_start: 0.8664 (m-40) cc_final: 0.8338 (m110)
REVERT: D   36 TYR cc_start: 0.8720 (m-80) cc_final: 0.8392 (m-80)
REVERT: D   81 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7390 (pt0)
REVERT: D   82 ASP cc_start: 0.8154 (m-30) cc_final: 0.7937 (m-30)
REVERT: D   90 GLN cc_start: 0.9171 (pp30) cc_final: 0.8451 (pp30)
REVERT: D  107 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5803 (tpt90)
REVERT: F   13 VAL cc_start: 0.7848 (m) cc_final: 0.7561 (p)
REVERT: F   36 TYR cc_start: 0.8734 (m-80) cc_final: 0.8223 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 211
  average time/residue: 0.1670
  time to fit residues: 50.9608
Evaluate side-chains
  192 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  635 CYS
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain D residue   81 GLU
Chi-restraints excluded: chain D residue  107 ARG
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    0.1980
   chunk 56 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
D  38 GLN
E  40 GLN
F  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.124559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.103415 restraints weight = 13787.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.105861 restraints weight = 8687.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107380 restraints weight = 6472.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8242  Z= 0.292
  Angle     :  0.719  14.463  11196  Z= 0.364
  Chirality :  0.046   0.248   1284
  Planarity :  0.005   0.053   1370
  Dihedral  :  6.591  51.779   1184
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.16 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.70 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.27), residues: 1008
  helix:  1.14 (0.26), residues: 408
  sheet: -0.27 (0.36), residues: 224
  loop : -1.40 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 109 
 HIS   0.003   0.001   HIS B 583 
 PHE   0.015   0.002   PHE A 586 
 TYR   0.029   0.002   TYR A 645 
 ARG   0.003   0.000   ARG E  39 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7370 (pt0) cc_final: 0.6952 (pt0)
REVERT: A  482 ARG cc_start: 0.8716 (mmp80) cc_final: 0.8034 (mmt180)
REVERT: A  511 PHE cc_start: 0.8790 (t80) cc_final: 0.8517 (t80)
REVERT: B  373 PHE cc_start: 0.6808 (t80) cc_final: 0.6595 (t80)
REVERT: B  479 LEU cc_start: 0.8938 (mt) cc_final: 0.8634 (tp)
REVERT: B  511 PHE cc_start: 0.8659 (t80) cc_final: 0.8156 (t80)
REVERT: D   13 VAL cc_start: 0.7520 (m) cc_final: 0.7196 (p)
REVERT: D   31 ASN cc_start: 0.8612 (m-40) cc_final: 0.8385 (m-40)
REVERT: E   96 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5641 (p)
REVERT: F   13 VAL cc_start: 0.7828 (m) cc_final: 0.7517 (p)
REVERT: F   36 TYR cc_start: 0.8823 (m-80) cc_final: 0.8316 (m-80)
  outliers start: 30
  outliers final: 22
  residues processed: 192
  average time/residue: 0.2163
  time to fit residues: 57.8890
Evaluate side-chains
  186 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   65 THR
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.0370
   chunk 63 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0020
   overall best weight:    0.6066

-------------------------------------------------------------------------------
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 = 0.3648 r_free = 0.3648 target = 0.128742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108170 restraints weight = 13607.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110620 restraints weight = 8525.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112164 restraints weight = 6359.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8242  Z= 0.175
  Angle     :  0.677  11.856  11196  Z= 0.337
  Chirality :  0.043   0.203   1284
  Planarity :  0.005   0.053   1370
  Dihedral  :  6.279  51.987   1184
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.46 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.07 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.28), residues: 1008
  helix:  1.39 (0.26), residues: 406
  sheet: -0.23 (0.35), residues: 224
  loop : -1.23 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  35 
 HIS   0.001   0.000   HIS A 583 
 PHE   0.012   0.001   PHE B 551 
 TYR   0.026   0.001   TYR A 645 
 ARG   0.006   0.001   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7307 (pt0) cc_final: 0.6905 (pt0)
REVERT: A  482 ARG cc_start: 0.8701 (mmp80) cc_final: 0.8038 (mmt180)
REVERT: A  483 MET cc_start: 0.8026 (ttp) cc_final: 0.7819 (ttm)
REVERT: A  511 PHE cc_start: 0.8767 (t80) cc_final: 0.8545 (t80)
REVERT: B  373 PHE cc_start: 0.6715 (t80) cc_final: 0.6511 (t80)
REVERT: B  479 LEU cc_start: 0.8959 (mt) cc_final: 0.8500 (tp)
REVERT: B  511 PHE cc_start: 0.8657 (t80) cc_final: 0.8208 (t80)
REVERT: B  512 THR cc_start: 0.9391 (m) cc_final: 0.9179 (p)
REVERT: C   11 LEU cc_start: 0.8297 (tt) cc_final: 0.7779 (mp)
REVERT: D   13 VAL cc_start: 0.7803 (m) cc_final: 0.7536 (p)
REVERT: D   36 TYR cc_start: 0.8858 (m-80) cc_final: 0.8438 (m-80)
REVERT: D   90 GLN cc_start: 0.9297 (pp30) cc_final: 0.8512 (pp30)
REVERT: F   13 VAL cc_start: 0.7694 (m) cc_final: 0.7432 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 191
  average time/residue: 0.1607
  time to fit residues: 45.0946
Evaluate side-chains
  192 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  635 CYS
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C  40 GLN
D  31 ASN
D  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.128918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108344 restraints weight = 13564.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110787 restraints weight = 8487.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112197 restraints weight = 6334.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8242  Z= 0.191
  Angle     :  0.667  10.350  11196  Z= 0.335
  Chirality :  0.043   0.208   1284
  Planarity :  0.005   0.052   1370
  Dihedral  :  6.037  46.291   1184
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.53 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.28), residues: 1008
  helix:  1.46 (0.27), residues: 408
  sheet: -0.21 (0.34), residues: 224
  loop : -1.26 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  35 
 HIS   0.001   0.000   HIS B 583 
 PHE   0.012   0.001   PHE B 551 
 TYR   0.026   0.002   TYR B 645 
 ARG   0.005   0.000   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7307 (pt0) cc_final: 0.6912 (pt0)
REVERT: A  482 ARG cc_start: 0.8735 (mmp80) cc_final: 0.8136 (mmm-85)
REVERT: A  511 PHE cc_start: 0.8751 (t80) cc_final: 0.8483 (t80)
REVERT: B  479 LEU cc_start: 0.9023 (mt) cc_final: 0.8493 (tp)
REVERT: B  511 PHE cc_start: 0.8621 (t80) cc_final: 0.8150 (t80)
REVERT: B  512 THR cc_start: 0.9418 (m) cc_final: 0.9210 (p)
REVERT: C   11 LEU cc_start: 0.8267 (tt) cc_final: 0.7789 (mp)
REVERT: C   80 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8240 (m-80)
REVERT: D   90 GLN cc_start: 0.9302 (pp30) cc_final: 0.8517 (pp30)
REVERT: E   39 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8374 (ttm170)
REVERT: F   13 VAL cc_start: 0.7577 (m) cc_final: 0.6939 (p)
  outliers start: 29
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1613
  time to fit residues: 44.2053
Evaluate side-chains
  191 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   39 ARG
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.126383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.105579 restraints weight = 13679.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108005 restraints weight = 8528.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109556 restraints weight = 6354.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8242  Z= 0.263
  Angle     :  0.703   9.195  11196  Z= 0.354
  Chirality :  0.044   0.209   1284
  Planarity :  0.005   0.047   1370
  Dihedral  :  6.043  47.310   1184
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 22.78 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.28), residues: 1008
  helix:  1.40 (0.26), residues: 410
  sheet: -0.17 (0.34), residues: 224
  loop : -1.21 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  35 
 HIS   0.002   0.001   HIS A 583 
 PHE   0.022   0.002   PHE B 373 
 TYR   0.026   0.002   TYR A 645 
 ARG   0.004   0.000   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7337 (pt0) cc_final: 0.6957 (pt0)
REVERT: A  482 ARG cc_start: 0.8671 (mmp80) cc_final: 0.8061 (mmt180)
REVERT: A  511 PHE cc_start: 0.8805 (t80) cc_final: 0.8522 (t80)
REVERT: A  540 LEU cc_start: 0.9123 (tp) cc_final: 0.8900 (tt)
REVERT: B  479 LEU cc_start: 0.8982 (mt) cc_final: 0.8449 (tp)
REVERT: B  511 PHE cc_start: 0.8678 (t80) cc_final: 0.8257 (t80)
REVERT: C   11 LEU cc_start: 0.8374 (tt) cc_final: 0.7849 (mp)
REVERT: C   80 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8239 (m-80)
REVERT: D   36 TYR cc_start: 0.8928 (m-80) cc_final: 0.8317 (m-80)
REVERT: E   11 LEU cc_start: 0.8371 (tp) cc_final: 0.7715 (mp)
REVERT: F   36 TYR cc_start: 0.8827 (m-80) cc_final: 0.8274 (m-80)
  outliers start: 31
  outliers final: 26
  residues processed: 183
  average time/residue: 0.1627
  time to fit residues: 43.6304
Evaluate side-chains
  192 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  569 GLN
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.128595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.107853 restraints weight = 13761.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110351 restraints weight = 8584.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111943 restraints weight = 6372.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8242  Z= 0.194
  Angle     :  0.677   9.085  11196  Z= 0.339
  Chirality :  0.043   0.223   1284
  Planarity :  0.005   0.047   1370
  Dihedral  :  5.888  46.104   1184
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 22.44 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.28), residues: 1008
  helix:  1.47 (0.27), residues: 410
  sheet: -0.11 (0.34), residues: 224
  loop : -1.11 (0.35), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  35 
 HIS   0.002   0.000   HIS A 583 
 PHE   0.014   0.001   PHE A 545 
 TYR   0.024   0.001   TYR A 645 
 ARG   0.004   0.000   ARG D  18 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 171
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7284 (pt0) cc_final: 0.6913 (pt0)
REVERT: A  482 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8110 (mmt180)
REVERT: A  511 PHE cc_start: 0.8765 (t80) cc_final: 0.8493 (t80)
REVERT: A  540 LEU cc_start: 0.9061 (tp) cc_final: 0.8857 (tt)
REVERT: B  479 LEU cc_start: 0.8928 (mt) cc_final: 0.8410 (tp)
REVERT: B  511 PHE cc_start: 0.8684 (t80) cc_final: 0.8271 (t80)
REVERT: C   11 LEU cc_start: 0.8354 (tt) cc_final: 0.7859 (mp)
REVERT: C   80 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8235 (m-80)
REVERT: D   36 TYR cc_start: 0.8928 (m-80) cc_final: 0.8328 (m-80)
REVERT: E   11 LEU cc_start: 0.8359 (tp) cc_final: 0.7729 (mp)
  outliers start: 31
  outliers final: 26
  residues processed: 185
  average time/residue: 0.1717
  time to fit residues: 45.6143
Evaluate side-chains
  194 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 TRP
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 ASP
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  635 CYS
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.128145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.107455 restraints weight = 13518.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.109868 restraints weight = 8442.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111396 restraints weight = 6307.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8242  Z= 0.213
  Angle     :  0.687  10.454  11196  Z= 0.344
  Chirality :  0.044   0.212   1284
  Planarity :  0.004   0.046   1370
  Dihedral  :  5.822  46.208   1184
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.89 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 1008
  helix:  1.46 (0.27), residues: 410
  sheet: -0.02 (0.34), residues: 224
  loop : -1.14 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  48 
 HIS   0.002   0.000   HIS A 583 
 PHE   0.024   0.002   PHE B 373 
 TYR   0.025   0.002   TYR A 645 
 ARG   0.005   0.000   ARG E  39 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7293 (pt0) cc_final: 0.6917 (pt0)
REVERT: A  463 TYR cc_start: 0.7821 (m-80) cc_final: 0.7578 (m-80)
REVERT: A  482 ARG cc_start: 0.8700 (mmp80) cc_final: 0.8087 (mmt180)
REVERT: A  511 PHE cc_start: 0.8756 (t80) cc_final: 0.8478 (t80)
REVERT: A  540 LEU cc_start: 0.9083 (tp) cc_final: 0.8880 (tt)
REVERT: B  479 LEU cc_start: 0.8908 (mt) cc_final: 0.8394 (tp)
REVERT: B  511 PHE cc_start: 0.8683 (t80) cc_final: 0.8250 (t80)
REVERT: C   11 LEU cc_start: 0.8379 (tt) cc_final: 0.7898 (mp)
REVERT: C   80 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8211 (m-80)
REVERT: D   36 TYR cc_start: 0.8928 (m-80) cc_final: 0.8332 (m-80)
REVERT: E   11 LEU cc_start: 0.8342 (tp) cc_final: 0.7732 (mp)
REVERT: F   36 TYR cc_start: 0.8806 (m-80) cc_final: 0.8249 (m-80)
  outliers start: 28
  outliers final: 23
  residues processed: 179
  average time/residue: 0.1607
  time to fit residues: 43.1582
Evaluate side-chains
  188 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain B residue  405 LEU
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  569 GLN
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0870
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.098866 restraints weight = 13995.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.101651 restraints weight = 8033.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103465 restraints weight = 5684.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8242  Z= 0.192
  Angle     :  0.674  11.549  11196  Z= 0.337
  Chirality :  0.043   0.195   1284
  Planarity :  0.004   0.046   1370
  Dihedral  :  5.701  45.773   1184
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.35 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.28), residues: 1008
  helix:  1.52 (0.27), residues: 410
  sheet:  0.03 (0.34), residues: 224
  loop : -1.11 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  48 
 HIS   0.001   0.000   HIS A 583 
 PHE   0.013   0.001   PHE C  79 
 TYR   0.025   0.001   TYR A 645 
 ARG   0.004   0.000   ARG D  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.75 seconds
wall clock time: 46 minutes 25.49 seconds (2785.49 seconds total)