Starting phenix.real_space_refine
on Mon Apr 28 20:49:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5njg_3654/04_2025/5njg_3654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5njg_3654/04_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_3654/04_2025/5njg_3654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5njg_3654/04_2025/5njg_3654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5njg_3654/04_2025/5njg_3654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5njg_3654/04_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-5669/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: 5.09, per 1000 atoms: 0.63
  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.95
  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: 2.40

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.19 -     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:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.220
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.610
-------------------------------------------------------------------------------
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   8253  Z= 0.591
  Angle     :  1.334  13.153  11222  Z= 0.691
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01234 (    2)
  link_NAG-ASN         : angle       9.49000 (    6)
  link_BETA1-4         : bond        0.00456 (    2)
  link_BETA1-4         : angle       4.37014 (    6)
  hydrogen bonds       : bond        0.14370 (  414)
  hydrogen bonds       : angle       9.64209 ( 1170)
  SS BOND              : bond        0.01072 (    7)
  SS BOND              : angle       1.68298 (   14)
  covalent geometry    : bond        0.01388 ( 8242)
  covalent geometry    : angle       1.31222 (11196)

*********************** 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  : 0.949 
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: 0.2069
  time to fit residues: 72.3545
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  : 0.839 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.9582

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.125743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.103744 restraints weight = 13360.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106494 restraints weight = 7912.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108199 restraints weight = 5629.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8253  Z= 0.163
  Angle     :  0.788   9.277  11222  Z= 0.395
  Chirality :  0.046   0.230   1284
  Planarity :  0.006   0.059   1370
  Dihedral  :  8.141  65.978   1185
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.77 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.21 %
    Favored  : 84.85 %
  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: -1.75 (0.25), residues: 1008
  helix: -0.43 (0.23), residues: 392
  sheet: -1.20 (0.32), residues: 212
  loop : -1.74 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 624 
 HIS   0.002   0.001   HIS B 583 
 PHE   0.022   0.002   PHE D  62 
 TYR   0.028   0.002   TYR B 645 
 ARG   0.004   0.001   ARG B 383 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (    2)
  link_NAG-ASN         : angle       5.46706 (    6)
  link_BETA1-4         : bond        0.00474 (    2)
  link_BETA1-4         : angle       2.45177 (    6)
  hydrogen bonds       : bond        0.04302 (  414)
  hydrogen bonds       : angle       5.80785 ( 1170)
  SS BOND              : bond        0.00476 (    7)
  SS BOND              : angle       1.57398 (   14)
  covalent geometry    : bond        0.00367 ( 8242)
  covalent geometry    : angle       0.77480 (11196)

*********************** 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
  225 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 0.884 
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  379 TRP cc_start: 0.7334 (t-100) cc_final: 0.7064 (t60)
REVERT: B  373 PHE cc_start: 0.6466 (t80) cc_final: 0.6244 (t80)
REVERT: B  479 LEU cc_start: 0.8923 (mt) cc_final: 0.8512 (tp)
REVERT: B  512 THR cc_start: 0.9328 (m) cc_final: 0.9095 (p)
REVERT: D   81 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7551 (pt0)
REVERT: D   82 ASP cc_start: 0.8277 (m-30) cc_final: 0.8050 (m-30)
REVERT: D   90 GLN cc_start: 0.9130 (pp30) cc_final: 0.8522 (pp30)
REVERT: F   13 VAL cc_start: 0.7967 (m) cc_final: 0.7577 (p)
REVERT: F   36 TYR cc_start: 0.8844 (m-80) cc_final: 0.8531 (m-80)
REVERT: F   82 ASP cc_start: 0.8377 (m-30) cc_final: 0.8123 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 214
  average time/residue: 0.1535
  time to fit residues: 47.2582
Evaluate side-chains
  177 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
A 629 ASN
B 437 GLN
B 557 ASN
B 629 ASN
C  82 GLN
D   6 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105117 restraints weight = 13723.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107865 restraints weight = 8045.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.109603 restraints weight = 5734.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8253  Z= 0.137
  Angle     :  0.708   9.076  11222  Z= 0.355
  Chirality :  0.044   0.232   1284
  Planarity :  0.005   0.053   1370
  Dihedral  :  7.356  62.083   1184
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.76 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.51 %
    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: -0.76 (0.27), residues: 1008
  helix:  0.57 (0.26), residues: 396
  sheet: -0.68 (0.34), residues: 212
  loop : -1.42 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  35 
 HIS   0.001   0.000   HIS B 583 
 PHE   0.017   0.002   PHE A 373 
 TYR   0.031   0.002   TYR A 645 
 ARG   0.004   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00078 (    2)
  link_NAG-ASN         : angle       4.87422 (    6)
  link_BETA1-4         : bond        0.00261 (    2)
  link_BETA1-4         : angle       2.24599 (    6)
  hydrogen bonds       : bond        0.03741 (  414)
  hydrogen bonds       : angle       5.30405 ( 1170)
  SS BOND              : bond        0.00431 (    7)
  SS BOND              : angle       1.18811 (   14)
  covalent geometry    : bond        0.00306 ( 8242)
  covalent geometry    : angle       0.69639 (11196)

*********************** 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
  226 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.887 
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  511 PHE cc_start: 0.8809 (t80) cc_final: 0.8419 (t80)
REVERT: B  373 PHE cc_start: 0.6576 (t80) cc_final: 0.6337 (t80)
REVERT: B  479 LEU cc_start: 0.8967 (mt) cc_final: 0.8541 (tp)
REVERT: B  511 PHE cc_start: 0.8630 (t80) cc_final: 0.8008 (t80)
REVERT: B  512 THR cc_start: 0.9335 (m) cc_final: 0.9132 (p)
REVERT: B  541 MET cc_start: 0.7729 (mmm) cc_final: 0.7032 (mmm)
REVERT: B  620 ASP cc_start: 0.8417 (t0) cc_final: 0.8210 (t0)
REVERT: C  100 TYR cc_start: 0.7188 (t80) cc_final: 0.6944 (t80)
REVERT: D   13 VAL cc_start: 0.7635 (m) cc_final: 0.7206 (p)
REVERT: D   18 ARG cc_start: 0.6692 (ttp80) cc_final: 0.6372 (ttp80)
REVERT: D   31 ASN cc_start: 0.8844 (m-40) cc_final: 0.8507 (m110)
REVERT: D   81 GLU cc_start: 0.7884 (pt0) cc_final: 0.7516 (pt0)
REVERT: D   82 ASP cc_start: 0.8221 (m-30) cc_final: 0.7986 (m-30)
REVERT: D   90 GLN cc_start: 0.9187 (pp30) cc_final: 0.8463 (pp30)
REVERT: F   13 VAL cc_start: 0.7931 (m) cc_final: 0.7563 (p)
REVERT: F   36 TYR cc_start: 0.8846 (m-80) cc_final: 0.8318 (m-80)
REVERT: F   82 ASP cc_start: 0.8368 (m-30) cc_final: 0.8157 (m-30)
  outliers start: 23
  outliers final: 10
  residues processed: 213
  average time/residue: 0.1716
  time to fit residues: 52.3646
Evaluate side-chains
  187 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
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 E residue   18 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   81 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0970
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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
B 437 GLN
C  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.128667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.107967 restraints weight = 13783.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.110453 restraints weight = 8515.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112018 restraints weight = 6283.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8253  Z= 0.131
  Angle     :  0.681   8.778  11222  Z= 0.342
  Chirality :  0.043   0.224   1284
  Planarity :  0.005   0.054   1370
  Dihedral  :  6.916  58.186   1184
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.66 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.79 %
    Favored  : 78.13 %
  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: -0.29 (0.27), residues: 1008
  helix:  1.00 (0.26), residues: 398
  sheet: -0.38 (0.36), residues: 212
  loop : -1.26 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  35 
 HIS   0.001   0.000   HIS B 583 
 PHE   0.014   0.001   PHE B 448 
 TYR   0.027   0.002   TYR A 645 
 ARG   0.002   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00071 (    2)
  link_NAG-ASN         : angle       4.52334 (    6)
  link_BETA1-4         : bond        0.00266 (    2)
  link_BETA1-4         : angle       2.10206 (    6)
  hydrogen bonds       : bond        0.03621 (  414)
  hydrogen bonds       : angle       5.09251 ( 1170)
  SS BOND              : bond        0.00769 (    7)
  SS BOND              : angle       1.24226 (   14)
  covalent geometry    : bond        0.00298 ( 8242)
  covalent geometry    : angle       0.67077 (11196)

*********************** 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
  225 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 198
  time to evaluate  : 0.834 
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  482 ARG cc_start: 0.8662 (mmp80) cc_final: 0.7850 (mmt180)
REVERT: A  511 PHE cc_start: 0.8771 (t80) cc_final: 0.8397 (t80)
REVERT: B  373 PHE cc_start: 0.6579 (t80) cc_final: 0.6359 (t80)
REVERT: B  479 LEU cc_start: 0.8975 (mt) cc_final: 0.8568 (tp)
REVERT: B  509 MET cc_start: 0.8622 (ttt) cc_final: 0.8254 (ttt)
REVERT: B  511 PHE cc_start: 0.8606 (t80) cc_final: 0.8087 (t80)
REVERT: D   13 VAL cc_start: 0.7601 (m) cc_final: 0.7242 (p)
REVERT: D   18 ARG cc_start: 0.6672 (ttp80) cc_final: 0.6393 (ttp80)
REVERT: D   31 ASN cc_start: 0.8739 (m-40) cc_final: 0.8407 (m110)
REVERT: D   81 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7371 (pt0)
REVERT: D   82 ASP cc_start: 0.8142 (m-30) cc_final: 0.7900 (m-30)
REVERT: D   90 GLN cc_start: 0.9200 (pp30) cc_final: 0.8498 (pp30)
REVERT: D  107 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5871 (tpt90)
REVERT: F   13 VAL cc_start: 0.7815 (m) cc_final: 0.7537 (p)
REVERT: F   36 TYR cc_start: 0.8776 (m-80) cc_final: 0.8327 (m-80)
REVERT: F   82 ASP cc_start: 0.8232 (m-30) cc_final: 0.7979 (m-30)
  outliers start: 27
  outliers final: 17
  residues processed: 210
  average time/residue: 0.1691
  time to fit residues: 50.8457
Evaluate side-chains
  202 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  548 MET
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   19 VAL
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:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 92 optimal weight:    0.0010
   overall best weight:    1.1190

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

Flipped N/Q/H residues before XYZ refinement:
C  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106418 restraints weight = 13700.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.108861 restraints weight = 8556.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110434 restraints weight = 6365.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8253  Z= 0.151
  Angle     :  0.682  11.881  11222  Z= 0.342
  Chirality :  0.044   0.254   1284
  Planarity :  0.005   0.054   1370
  Dihedral  :  6.529  54.308   1184
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.46 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.13 %
    Favored  : 77.22 %
  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: -0.10 (0.27), residues: 1008
  helix:  1.28 (0.26), residues: 402
  sheet: -0.35 (0.36), residues: 210
  loop : -1.28 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  35 
 HIS   0.004   0.001   HIS B 630 
 PHE   0.015   0.002   PHE B 545 
 TYR   0.028   0.002   TYR A 645 
 ARG   0.003   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00110 (    2)
  link_NAG-ASN         : angle       4.18693 (    6)
  link_BETA1-4         : bond        0.00241 (    2)
  link_BETA1-4         : angle       1.98790 (    6)
  hydrogen bonds       : bond        0.03530 (  414)
  hydrogen bonds       : angle       4.87955 ( 1170)
  SS BOND              : bond        0.00884 (    7)
  SS BOND              : angle       0.88145 (   14)
  covalent geometry    : bond        0.00347 ( 8242)
  covalent geometry    : angle       0.67342 (11196)

*********************** 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
  215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.851 
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: 0.7314 (pt0) cc_final: 0.6875 (pt0)
REVERT: A  482 ARG cc_start: 0.8681 (mmp80) cc_final: 0.7996 (mmt180)
REVERT: A  511 PHE cc_start: 0.8769 (t80) cc_final: 0.8507 (t80)
REVERT: B  479 LEU cc_start: 0.8991 (mt) cc_final: 0.8530 (tp)
REVERT: B  511 PHE cc_start: 0.8644 (t80) cc_final: 0.8123 (t80)
REVERT: D   13 VAL cc_start: 0.7509 (m) cc_final: 0.7181 (p)
REVERT: D   31 ASN cc_start: 0.8549 (m-40) cc_final: 0.8313 (m-40)
REVERT: D   81 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7447 (pt0)
REVERT: D   90 GLN cc_start: 0.9307 (pp30) cc_final: 0.8527 (pp30)
REVERT: F   13 VAL cc_start: 0.7743 (m) cc_final: 0.7445 (p)
REVERT: F   36 TYR cc_start: 0.8799 (m-80) cc_final: 0.8288 (m-80)
  outliers start: 32
  outliers final: 23
  residues processed: 199
  average time/residue: 0.1710
  time to fit residues: 48.2470
Evaluate side-chains
  192 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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  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 B residue  377 LEU
Chi-restraints excluded: chain B residue  379 TRP
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  111 GLN
Chi-restraints excluded: chain D residue   81 GLU
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  111 GLN
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   17 ASP
Chi-restraints excluded: chain F residue   53 SER
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:    8.9990
   chunk 63 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0020
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
C  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.128530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108032 restraints weight = 13672.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.110537 restraints weight = 8467.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112098 restraints weight = 6225.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8253  Z= 0.129
  Angle     :  0.679  11.891  11222  Z= 0.338
  Chirality :  0.043   0.206   1284
  Planarity :  0.005   0.052   1370
  Dihedral  :  6.266  51.713   1184
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.37 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.05 %
    Favored  : 76.65 %
  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: -0.06 (0.27), residues: 1008
  helix:  1.32 (0.26), residues: 408
  sheet: -0.35 (0.35), residues: 210
  loop : -1.29 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  35 
 HIS   0.002   0.001   HIS B 630 
 PHE   0.012   0.001   PHE F  62 
 TYR   0.028   0.002   TYR B 645 
 ARG   0.007   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00187 (    2)
  link_NAG-ASN         : angle       3.99011 (    6)
  link_BETA1-4         : bond        0.00337 (    2)
  link_BETA1-4         : angle       1.95971 (    6)
  hydrogen bonds       : bond        0.03375 (  414)
  hydrogen bonds       : angle       4.81675 ( 1170)
  SS BOND              : bond        0.00649 (    7)
  SS BOND              : angle       1.45582 (   14)
  covalent geometry    : bond        0.00296 ( 8242)
  covalent geometry    : angle       0.66947 (11196)

*********************** 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
  208 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7243 (pt0) cc_final: 0.6826 (pt0)
REVERT: A  482 ARG cc_start: 0.8683 (mmp80) cc_final: 0.7989 (mmt180)
REVERT: B  479 LEU cc_start: 0.8903 (mt) cc_final: 0.8447 (tp)
REVERT: B  511 PHE cc_start: 0.8668 (t80) cc_final: 0.8290 (t80)
REVERT: C   11 LEU cc_start: 0.8312 (tp) cc_final: 0.7694 (mp)
REVERT: D   13 VAL cc_start: 0.7632 (m) cc_final: 0.7407 (p)
REVERT: D   90 GLN cc_start: 0.9292 (pp30) cc_final: 0.8544 (pp30)
REVERT: F   13 VAL cc_start: 0.7446 (m) cc_final: 0.6667 (p)
REVERT: F   36 TYR cc_start: 0.8777 (m-80) cc_final: 0.8232 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 190
  average time/residue: 0.1738
  time to fit residues: 47.5607
Evaluate side-chains
  195 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  405 LEU
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  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  111 GLN
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 E residue   96 CYS
Chi-restraints excluded: chain F residue    3 VAL
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:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0970
   chunk 85 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
B 617 GLN
D  31 ASN
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.129191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108424 restraints weight = 13589.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.110889 restraints weight = 8506.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.112484 restraints weight = 6310.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8253  Z= 0.126
  Angle     :  0.671  10.202  11222  Z= 0.336
  Chirality :  0.043   0.209   1284
  Planarity :  0.005   0.052   1370
  Dihedral  :  6.028  46.317   1184
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.62 %
    Favored  : 76.20 %
  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:  0.05 (0.27), residues: 1008
  helix:  1.42 (0.26), residues: 408
  sheet: -0.30 (0.35), residues: 210
  loop : -1.23 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  35 
 HIS   0.003   0.001   HIS B 630 
 PHE   0.032   0.002   PHE A 511 
 TYR   0.025   0.001   TYR A 645 
 ARG   0.005   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    2)
  link_NAG-ASN         : angle       3.83565 (    6)
  link_BETA1-4         : bond        0.00437 (    2)
  link_BETA1-4         : angle       1.97241 (    6)
  hydrogen bonds       : bond        0.03318 (  414)
  hydrogen bonds       : angle       4.74126 ( 1170)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       1.54851 (   14)
  covalent geometry    : bond        0.00294 ( 8242)
  covalent geometry    : angle       0.66250 (11196)

*********************** 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
  215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7274 (pt0) cc_final: 0.6853 (pt0)
REVERT: A  482 ARG cc_start: 0.8729 (mmp80) cc_final: 0.8045 (mmt180)
REVERT: B  479 LEU cc_start: 0.9020 (mt) cc_final: 0.8613 (tp)
REVERT: B  511 PHE cc_start: 0.8674 (t80) cc_final: 0.8288 (t80)
REVERT: C   11 LEU cc_start: 0.8302 (tp) cc_final: 0.7718 (mp)
REVERT: C   80 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8223 (m-80)
REVERT: D   90 GLN cc_start: 0.9339 (pp30) cc_final: 0.8490 (pp30)
REVERT: F   36 TYR cc_start: 0.8801 (m-80) cc_final: 0.8240 (m-80)
  outliers start: 28
  outliers final: 23
  residues processed: 199
  average time/residue: 0.1524
  time to fit residues: 44.3426
Evaluate side-chains
  195 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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 B residue  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 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   65 THR
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain D residue   88 CYS
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   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.0784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107509 restraints weight = 13674.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.109881 restraints weight = 8622.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.111411 restraints weight = 6463.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8253  Z= 0.147
  Angle     :  0.684   9.111  11222  Z= 0.345
  Chirality :  0.044   0.210   1284
  Planarity :  0.005   0.050   1370
  Dihedral  :  5.920  46.268   1184
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.55 %
    Favored  : 74.15 %
  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:  0.13 (0.28), residues: 1008
  helix:  1.46 (0.27), residues: 408
  sheet: -0.23 (0.35), residues: 210
  loop : -1.18 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  35 
 HIS   0.002   0.001   HIS B 630 
 PHE   0.025   0.002   PHE B 373 
 TYR   0.025   0.002   TYR B 645 
 ARG   0.004   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00247 (    2)
  link_NAG-ASN         : angle       3.82220 (    6)
  link_BETA1-4         : bond        0.00242 (    2)
  link_BETA1-4         : angle       1.85894 (    6)
  hydrogen bonds       : bond        0.03498 (  414)
  hydrogen bonds       : angle       4.73836 ( 1170)
  SS BOND              : bond        0.00510 (    7)
  SS BOND              : angle       1.83320 (   14)
  covalent geometry    : bond        0.00345 ( 8242)
  covalent geometry    : angle       0.67461 (11196)

*********************** 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
  205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7288 (pt0) cc_final: 0.6918 (pt0)
REVERT: A  482 ARG cc_start: 0.8719 (mmp80) cc_final: 0.8064 (mmt180)
REVERT: B  479 LEU cc_start: 0.8994 (mt) cc_final: 0.8488 (tp)
REVERT: B  511 PHE cc_start: 0.8668 (t80) cc_final: 0.8314 (t80)
REVERT: C   11 LEU cc_start: 0.8289 (tp) cc_final: 0.7710 (mp)
REVERT: C   80 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8232 (m-80)
REVERT: F   36 TYR cc_start: 0.8817 (m-80) cc_final: 0.8281 (m-80)
  outliers start: 29
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1952
  time to fit residues: 55.7000
Evaluate side-chains
  191 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
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  405 LEU
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 B residue  379 TRP
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   79 GLN
Chi-restraints excluded: chain D residue   88 CYS
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   85 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.128628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107422 restraints weight = 13839.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.109850 restraints weight = 8808.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111398 restraints weight = 6598.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8253  Z= 0.149
  Angle     :  0.685   8.891  11222  Z= 0.345
  Chirality :  0.044   0.213   1284
  Planarity :  0.004   0.047   1370
  Dihedral  :  5.893  46.226   1184
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.21 %
    Favored  : 74.37 %
  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:  0.24 (0.28), residues: 1008
  helix:  1.49 (0.27), residues: 408
  sheet: -0.08 (0.35), residues: 224
  loop : -1.15 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  35 
 HIS   0.003   0.001   HIS B 630 
 PHE   0.030   0.002   PHE A 511 
 TYR   0.025   0.002   TYR B 645 
 ARG   0.004   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    2)
  link_NAG-ASN         : angle       3.77407 (    6)
  link_BETA1-4         : bond        0.00176 (    2)
  link_BETA1-4         : angle       1.78209 (    6)
  hydrogen bonds       : bond        0.03418 (  414)
  hydrogen bonds       : angle       4.71981 ( 1170)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       2.26768 (   14)
  covalent geometry    : bond        0.00350 ( 8242)
  covalent geometry    : angle       0.67399 (11196)

*********************** 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
  208 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7316 (pt0) cc_final: 0.6926 (pt0)
REVERT: A  482 ARG cc_start: 0.8774 (mmp80) cc_final: 0.8155 (mmt180)
REVERT: B  479 LEU cc_start: 0.8974 (mt) cc_final: 0.8446 (tp)
REVERT: B  511 PHE cc_start: 0.8685 (t80) cc_final: 0.8334 (t80)
REVERT: C   11 LEU cc_start: 0.8262 (tp) cc_final: 0.7700 (mp)
REVERT: C   80 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8238 (m-80)
REVERT: E   11 LEU cc_start: 0.8327 (tp) cc_final: 0.7678 (mp)
REVERT: F   36 TYR cc_start: 0.8806 (m-80) cc_final: 0.8260 (m-80)
  outliers start: 30
  outliers final: 26
  residues processed: 194
  average time/residue: 0.1500
  time to fit residues: 43.2940
Evaluate side-chains
  198 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
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  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  489 PHE
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 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   65 THR
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 E residue   96 CYS
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   33 LEU
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:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.128576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107318 restraints weight = 13633.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.109715 restraints weight = 8739.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.111224 restraints weight = 6601.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8253  Z= 0.152
  Angle     :  0.691  10.353  11222  Z= 0.349
  Chirality :  0.044   0.204   1284
  Planarity :  0.004   0.047   1370
  Dihedral  :  5.838  46.458   1184
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 22.55 %
    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:  0.25 (0.28), residues: 1008
  helix:  1.50 (0.27), residues: 408
  sheet: -0.09 (0.35), residues: 224
  loop : -1.12 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  48 
 HIS   0.003   0.001   HIS B 630 
 PHE   0.027   0.002   PHE B 373 
 TYR   0.024   0.002   TYR A 645 
 ARG   0.004   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00201 (    2)
  link_NAG-ASN         : angle       3.75986 (    6)
  link_BETA1-4         : bond        0.00226 (    2)
  link_BETA1-4         : angle       1.73669 (    6)
  hydrogen bonds       : bond        0.03427 (  414)
  hydrogen bonds       : angle       4.70958 ( 1170)
  SS BOND              : bond        0.00494 (    7)
  SS BOND              : angle       2.06024 (   14)
  covalent geometry    : bond        0.00359 ( 8242)
  covalent geometry    : angle       0.68102 (11196)

********************** 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
  206 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 GLU cc_start: 0.7310 (pt0) cc_final: 0.6945 (pt0)
REVERT: A  482 ARG cc_start: 0.8680 (mmp80) cc_final: 0.8087 (mmt180)
REVERT: B  479 LEU cc_start: 0.8975 (mt) cc_final: 0.8478 (tp)
REVERT: B  511 PHE cc_start: 0.8697 (t80) cc_final: 0.8327 (t80)
REVERT: C   11 LEU cc_start: 0.8269 (tp) cc_final: 0.7734 (mp)
REVERT: C   80 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8224 (m-80)
REVERT: E   11 LEU cc_start: 0.8327 (tp) cc_final: 0.7673 (mp)
REVERT: F   36 TYR cc_start: 0.8805 (m-80) cc_final: 0.8254 (m-80)
  outliers start: 30
  outliers final: 26
  residues processed: 192
  average time/residue: 0.1505
  time to fit residues: 42.2956
Evaluate side-chains
  198 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  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  489 PHE
Chi-restraints excluded: chain B residue  491 CYS
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   80 PHE
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   65 THR
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   33 LEU
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:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0670
   chunk 33 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.128430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.106484 restraints weight = 13688.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109037 restraints weight = 8457.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.110660 restraints weight = 6252.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8253  Z= 0.129
  Angle     :  0.684  11.440  11222  Z= 0.343
  Chirality :  0.043   0.199   1284
  Planarity :  0.004   0.046   1370
  Dihedral  :  5.745  45.936   1184
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.55 %
    Favored  : 74.37 %
  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:  0.31 (0.28), residues: 1008
  helix:  1.53 (0.27), residues: 408
  sheet: -0.03 (0.34), residues: 224
  loop : -1.09 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E  48 
 HIS   0.003   0.001   HIS B 630 
 PHE   0.033   0.002   PHE A 511 
 TYR   0.024   0.002   TYR A 645 
 ARG   0.004   0.000   ARG D  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    2)
  link_NAG-ASN         : angle       3.63192 (    6)
  link_BETA1-4         : bond        0.00162 (    2)
  link_BETA1-4         : angle       1.71432 (    6)
  hydrogen bonds       : bond        0.03314 (  414)
  hydrogen bonds       : angle       4.64957 ( 1170)
  SS BOND              : bond        0.00446 (    7)
  SS BOND              : angle       1.86905 (   14)
  covalent geometry    : bond        0.00302 ( 8242)
  covalent geometry    : angle       0.67544 (11196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2715.78 seconds
wall clock time: 48 minutes 56.04 seconds (2936.04 seconds total)