Starting phenix.real_space_refine
on Fri Jun  6 22:05:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fpl_29368/06_2025/8fpl_29368.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     Cl      4      4.86       5
     C    5204      2.51       5
     N    1354      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8178
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1998
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "C"
      Number of atoms: 2009
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 256, 1994
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
      Conformer: "B"
        Number of residues, atoms: 256, 1994
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
          bond proxies already assigned to first conformer: 2012
    Chain: "A"
      Number of atoms: 1998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1998
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "D"
      Number of atoms: 2009
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 256, 1994
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
      Conformer: "B"
        Number of residues, atoms: 256, 1994
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
          bond proxies already assigned to first conformer: 2012
    Chain: "B"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'CYZ': 1, 'Y4Y': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'CYZ': 1, 'Y4Y': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'CYZ': 1, 'Y4Y': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {'CYZ': 1, 'Y4Y': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS C 435 " occ=0.80
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 435 " occ=0.20
    residue:
      pdb=" N  AHIS D 435 " occ=0.80
      ... (18 atoms not shown)
      pdb=" NE2BHIS D 435 " occ=0.20
  Time building chain proxies: 8.06, per 1000 atoms: 0.99
  Number of scatterers: 8178
  At special positions: 0
  Unit cell: (120.467, 99.1595, 73.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      64     16.00
     O    1552      8.00
     N    1354      7.00
     C    5204      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 718 " - pdb=" SG  CYS B 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 718 " - pdb=" SG  CYS C 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 718 " - pdb=" SG  CYS A 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 718 " - pdb=" SG  CYS D 773 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.02
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1880

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 19 sheets defined
      44.8% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'B' and resid 416 through 419
      removed outlier: 4.001A  pdb=" N   GLU B 419 " --> pdb=" O   GLU B 416 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 416 through 419'
    Processing helix  chain 'B' and resid 423 through 437
    Processing helix  chain 'B' and resid 461 through 469
    Processing helix  chain 'B' and resid 482 through 489
    Processing helix  chain 'B' and resid 635 through 642
    Processing helix  chain 'B' and resid 653 through 661
    Processing helix  chain 'B' and resid 664 through 676
    Processing helix  chain 'B' and resid 685 through 696
    Processing helix  chain 'B' and resid 706 through 714
    Processing helix  chain 'B' and resid 742 through 756
    Processing helix  chain 'B' and resid 757 through 768
    Processing helix  chain 'C' and resid 416 through 419
      removed outlier: 3.989A  pdb=" N   GLU C 419 " --> pdb=" O   GLU C 416 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 416 through 419'
    Processing helix  chain 'C' and resid 423 through 437
    Processing helix  chain 'C' and resid 461 through 469
    Processing helix  chain 'C' and resid 482 through 487
    Processing helix  chain 'C' and resid 635 through 642
      removed outlier: 3.584A  pdb=" N   LEU C 639 " --> pdb=" O   SER C 635 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN C 642 " --> pdb=" O   ASP C 638 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 653 through 662
    Processing helix  chain 'C' and resid 664 through 676
    Processing helix  chain 'C' and resid 685 through 696
    Processing helix  chain 'C' and resid 706 through 714
    Processing helix  chain 'C' and resid 742 through 756
    Processing helix  chain 'C' and resid 757 through 768
    Processing helix  chain 'A' and resid 411 through 415
    Processing helix  chain 'A' and resid 416 through 419
    Processing helix  chain 'A' and resid 423 through 437
    Processing helix  chain 'A' and resid 461 through 469
    Processing helix  chain 'A' and resid 482 through 487
    Processing helix  chain 'A' and resid 635 through 642
    Processing helix  chain 'A' and resid 653 through 661
    Processing helix  chain 'A' and resid 664 through 676
    Processing helix  chain 'A' and resid 685 through 696
    Processing helix  chain 'A' and resid 706 through 714
    Processing helix  chain 'A' and resid 742 through 756
    Processing helix  chain 'A' and resid 757 through 768
    Processing helix  chain 'D' and resid 416 through 419
      removed outlier: 3.872A  pdb=" N   GLU D 419 " --> pdb=" O   GLU D 416 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 416 through 419'
    Processing helix  chain 'D' and resid 423 through 437
    Processing helix  chain 'D' and resid 461 through 469
    Processing helix  chain 'D' and resid 482 through 489
    Processing helix  chain 'D' and resid 635 through 642
    Processing helix  chain 'D' and resid 653 through 662
    Processing helix  chain 'D' and resid 664 through 676
    Processing helix  chain 'D' and resid 685 through 696
    Processing helix  chain 'D' and resid 706 through 714
    Processing helix  chain 'D' and resid 742 through 756
    Processing helix  chain 'D' and resid 757 through 768
    Processing sheet with id=AA1, first strand: chain 'B' and resid 440 through 444
      removed outlier: 6.477A  pdb=" N   VAL B 395 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   THR B 443 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   VAL B 397 " --> pdb=" O   THR B 443 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 407 through 408
    Processing sheet with id=AA3, first strand: chain 'B' and resid 490 through 491
    Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 498
      removed outlier: 3.804A  pdb=" N   MET B 496 " --> pdb=" O   TYR B 732 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 648
      removed outlier: 6.521A  pdb=" N   ALA B 646 " --> pdb=" O   ALA B 701 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   LEU B 703 " --> pdb=" O   ALA B 646 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   GLY B 648 " --> pdb=" O   LEU B 703 " (cutoff:3.500A)
      removed outlier: 9.193A  pdb=" N   GLU B 705 " --> pdb=" O   GLY B 648 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   TYR B 700 " --> pdb=" O   LYS B 505 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   LYS B 505 " --> pdb=" O   TYR B 700 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ILE B 502 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 440 through 444
      removed outlier: 6.656A  pdb=" N   VAL C 395 " --> pdb=" O   LYS C 441 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   THR C 443 " --> pdb=" O   VAL C 395 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   VAL C 397 " --> pdb=" O   THR C 443 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 407 through 408
    Processing sheet with id=AA8, first strand: chain 'C' and resid 489 through 491
    Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 498
      removed outlier: 3.669A  pdb=" N   MET C 496 " --> pdb=" O   TYR C 732 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 646 through 648
      removed outlier: 6.467A  pdb=" N   ALA C 646 " --> pdb=" O   ALA C 701 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   LEU C 703 " --> pdb=" O   ALA C 646 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLY C 648 " --> pdb=" O   LEU C 703 " (cutoff:3.500A)
      removed outlier: 9.583A  pdb=" N   GLU C 705 " --> pdb=" O   GLY C 648 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   TYR C 700 " --> pdb=" O   LYS C 505 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   LYS C 505 " --> pdb=" O   TYR C 700 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ILE C 502 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 440 through 444
      removed outlier: 6.623A  pdb=" N   VAL A 395 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   THR A 443 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL A 397 " --> pdb=" O   THR A 443 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 476 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   ALA A 477 " --> pdb=" O   GLY A 733 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   GLY A 733 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LEU A 479 " --> pdb=" O   GLY A 731 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLY A 731 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 444
      removed outlier: 6.623A  pdb=" N   VAL A 395 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   THR A 443 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL A 397 " --> pdb=" O   THR A 443 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 476 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   ALA A 477 " --> pdb=" O   GLY A 733 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   GLY A 733 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LEU A 479 " --> pdb=" O   GLY A 731 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLY A 731 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET A 496 " --> pdb=" O   TYR A 732 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408
    Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 648
      removed outlier: 6.608A  pdb=" N   ALA A 646 " --> pdb=" O   ALA A 701 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LEU A 703 " --> pdb=" O   ALA A 646 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY A 648 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   GLU A 705 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   TYR A 700 " --> pdb=" O   LYS A 505 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   LYS A 505 " --> pdb=" O   TYR A 700 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 440 through 444
    Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408
    Processing sheet with id=AB8, first strand: chain 'D' and resid 490 through 491
    Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498
      removed outlier: 3.842A  pdb=" N   MET D 496 " --> pdb=" O   TYR D 732 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648
      removed outlier: 6.588A  pdb=" N   ALA D 646 " --> pdb=" O   ALA D 701 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   LEU D 703 " --> pdb=" O   ALA D 646 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLY D 648 " --> pdb=" O   LEU D 703 " (cutoff:3.500A)
      removed outlier: 9.336A  pdb=" N   GLU D 705 " --> pdb=" O   GLY D 648 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   TYR D 700 " --> pdb=" O   LYS D 505 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   LYS D 505 " --> pdb=" O   TYR D 700 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE D 502 " --> pdb=" O   VAL D 723 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    1011 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: 2.33

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2550
        1.35 -     1.48: 2055
        1.48 -     1.60: 3595
        1.60 -     1.73: 40
        1.73 -     1.85: 104
  Bond restraints: 8344
  Sorted by residual:
  bond pdb=" C3  CYZ D 902 "
       pdb=" C4  CYZ D 902 "
    ideal  model  delta    sigma   weight residual
    1.334  1.578 -0.244 2.00e-02 2.50e+03 1.49e+02
  bond pdb=" C3  CYZ C 902 "
       pdb=" C4  CYZ C 902 "
    ideal  model  delta    sigma   weight residual
    1.334  1.578 -0.244 2.00e-02 2.50e+03 1.49e+02
  bond pdb=" C3  CYZ A 902 "
       pdb=" C4  CYZ A 902 "
    ideal  model  delta    sigma   weight residual
    1.334  1.578 -0.244 2.00e-02 2.50e+03 1.48e+02
  bond pdb=" C3  CYZ B 902 "
       pdb=" C4  CYZ B 902 "
    ideal  model  delta    sigma   weight residual
    1.334  1.578 -0.244 2.00e-02 2.50e+03 1.48e+02
  bond pdb=" C2  Y4Y D 901 "
       pdb=" O2  Y4Y D 901 "
    ideal  model  delta    sigma   weight residual
    1.208  1.447 -0.239 2.00e-02 2.50e+03 1.43e+02
  ... (remaining 8339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 11041
        2.15 -     4.30: 143
        4.30 -     6.45: 55
        6.45 -     8.60: 23
        8.60 -    10.75: 10
  Bond angle restraints: 11272
  Sorted by residual:
  angle pdb=" CB  MET C 408 "
        pdb=" CG  MET C 408 "
        pdb=" SD  MET C 408 "
      ideal   model   delta    sigma   weight residual
     112.70  123.45  -10.75 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" C9  CYZ A 902 "
        pdb=" S1  CYZ A 902 "
        pdb=" N1  CYZ A 902 "
      ideal   model   delta    sigma   weight residual
     101.75  111.71   -9.96 3.00e+00 1.11e-01 1.10e+01
  angle pdb=" C9  CYZ C 902 "
        pdb=" S1  CYZ C 902 "
        pdb=" N1  CYZ C 902 "
      ideal   model   delta    sigma   weight residual
     101.75  111.61   -9.86 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" CB  MET A 408 "
        pdb=" CG  MET A 408 "
        pdb=" SD  MET A 408 "
      ideal   model   delta    sigma   weight residual
     112.70  122.55   -9.85 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" C9  CYZ D 902 "
        pdb=" S1  CYZ D 902 "
        pdb=" N1  CYZ D 902 "
      ideal   model   delta    sigma   weight residual
     101.75  111.56   -9.81 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 11267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.64: 4630
       22.64 -    45.29: 381
       45.29 -    67.93: 75
       67.93 -    90.58: 15
       90.58 -   113.22: 11
  Dihedral angle restraints: 5112
    sinusoidal: 2156
      harmonic: 2956
  Sorted by residual:
  dihedral pdb=" N2  CYZ A 902 "
           pdb=" C8  CYZ A 902 "
           pdb=" N1  CYZ A 902 "
           pdb=" S1  CYZ A 902 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.73  -57.49  113.22     1      3.00e+01 1.11e-03 1.49e+01
  dihedral pdb=" N2  CYZ C 902 "
           pdb=" C8  CYZ C 902 "
           pdb=" N1  CYZ C 902 "
           pdb=" S1  CYZ C 902 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.73  -57.38  113.11     1      3.00e+01 1.11e-03 1.49e+01
  dihedral pdb=" N2  CYZ D 902 "
           pdb=" C8  CYZ D 902 "
           pdb=" N1  CYZ D 902 "
           pdb=" S1  CYZ D 902 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.73  -57.07  112.80     1      3.00e+01 1.11e-03 1.48e+01
  ... (remaining 5109 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1134
       0.086 -    0.172: 90
       0.172 -    0.258: 0
       0.258 -    0.344: 0
       0.344 -    0.430: 16
  Chirality restraints: 1240
  Sorted by residual:
  chirality pdb=" C8  CYZ A 902 "
            pdb=" C1  CYZ A 902 "
            pdb=" N1  CYZ A 902 "
            pdb=" N2  CYZ A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.63   -0.43 2.00e-01 2.50e+01 4.63e+00
  chirality pdb=" C8  CYZ C 902 "
            pdb=" C1  CYZ C 902 "
            pdb=" N1  CYZ C 902 "
            pdb=" N2  CYZ C 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.63   -0.43 2.00e-01 2.50e+01 4.58e+00
  chirality pdb=" C8  CYZ B 902 "
            pdb=" C1  CYZ B 902 "
            pdb=" N1  CYZ B 902 "
            pdb=" N2  CYZ B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.63   -0.42 2.00e-01 2.50e+01 4.50e+00
  ... (remaining 1237 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 736 "    0.026 5.00e-02 4.00e+02   3.89e-02 2.43e+00
        pdb=" N   PRO C 737 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 737 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 737 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 736 "   -0.023 5.00e-02 4.00e+02   3.50e-02 1.96e+00
        pdb=" N   PRO D 737 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO D 737 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 737 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 728 "   -0.005 2.00e-02 2.50e+03   1.09e-02 1.18e+00
        pdb=" CG  ASP A 728 "    0.019 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 728 "   -0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 728 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 326
        2.72 -     3.27: 7833
        3.27 -     3.81: 13785
        3.81 -     4.36: 17480
        4.36 -     4.90: 29098
  Nonbonded interactions: 68522
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 413 "
            pdb=" OE1 GLU C 413 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" N   GLU A 413 "
            pdb=" OE1 GLU A 413 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG  SER A 497 "
            pdb=" O2  CYZ A 902 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG  SER C 497 "
            pdb=" O2  CYZ C 902 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE1 GLU A 402 "
            pdb=" OH  TYR A 450 "
     model   vdw
     2.288 3.040
  ... (remaining 68517 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: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ 
r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ 
 or resid 440 through 763 or resid 765 through 773 or resid 901 through 902))
  selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ 
r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ 
 or resid 440 through 763 or resid 765 through 773 or resid 901 through 902))
  selection = (chain 'C' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ 
ugh 773 or resid 901 through 902))
  selection = (chain 'D' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ 
ugh 773 or resid 901 through 902))
}

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=0.18 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.510
  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:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.640
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.050
  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:12.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
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      :  0.018   0.244   8348  Z= 0.884
  Angle     :  0.786  10.747  11280  Z= 0.328
  Chirality :  0.062   0.430   1240
  Planarity :  0.003   0.039   1390
  Dihedral  : 17.839 113.224   3220
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 21.23 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1016
  helix:  1.31 (0.25), residues: 452
  sheet: -1.06 (0.40), residues: 152
  loop : -0.61 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 766 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.008   0.002   PHE D 495 
 TYR   0.018   0.001   TYR A 647 
 ARG   0.007   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16951 (  351)
  hydrogen bonds       : angle       6.19531 ( 1011)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.41844 (    8)
  covalent geometry    : bond        0.01773 ( 8344)
  covalent geometry    : angle       0.78589 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 1.186 
Fit side-chains
REVERT: B  685 THR cc_start: 0.8330 (m) cc_final: 0.7944 (p)
REVERT: A  657 GLU cc_start: 0.7168 (mp0) cc_final: 0.6897 (mp0)
  outliers start: 3
  outliers final: 2
  residues processed: 114
  average time/residue: 1.7816
  time to fit residues: 213.9258
Evaluate side-chains
  117 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0970
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
C 709 ASN
D 756 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.134120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.105694 restraints weight = 33766.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 4.54
r_work: 0.2897 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8348  Z= 0.155
  Angle     :  0.517   6.740  11280  Z= 0.271
  Chirality :  0.044   0.133   1240
  Planarity :  0.004   0.043   1390
  Dihedral  : 11.673 106.377   1274
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.91 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1016
  helix:  1.24 (0.25), residues: 456
  sheet: -1.17 (0.41), residues: 140
  loop : -0.48 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 766 
 HIS   0.005   0.002   HIS C 412 
 PHE   0.011   0.002   PHE A 438 
 TYR   0.014   0.002   TYR D 673 
 ARG   0.006   0.001   ARG C 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (  351)
  hydrogen bonds       : angle       4.89894 ( 1011)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.92713 (    8)
  covalent geometry    : bond        0.00368 ( 8344)
  covalent geometry    : angle       0.51647 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8050 (ttpt)
REVERT: B  643 THR cc_start: 0.8087 (p) cc_final: 0.7832 (t)
REVERT: B  685 THR cc_start: 0.8255 (m) cc_final: 0.7821 (p)
REVERT: B  695 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7069 (tmmt)
REVERT: C  661 ARG cc_start: 0.7138 (ptp-110) cc_final: 0.6927 (ptp90)
REVERT: C  662 SER cc_start: 0.7889 (t) cc_final: 0.7427 (p)
REVERT: A  503 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8899 (ttm)
REVERT: A  660 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.7051 (ttp80)
REVERT: A  705 GLU cc_start: 0.8144 (mp0) cc_final: 0.7724 (mp0)
REVERT: D  458 LYS cc_start: 0.8245 (mppt) cc_final: 0.7992 (mppt)
  outliers start: 21
  outliers final: 9
  residues processed: 137
  average time/residue: 1.5589
  time to fit residues: 225.1631
Evaluate side-chains
  120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  503 MET
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain D residue  447 ASP
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    0.1980
   chunk 4 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0370
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.137345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.109369 restraints weight = 26446.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.70
r_work: 0.2988 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8348  Z= 0.096
  Angle     :  0.441   6.336  11280  Z= 0.232
  Chirality :  0.041   0.126   1240
  Planarity :  0.003   0.044   1390
  Dihedral  : 11.088 102.648   1274
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.42 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1016
  helix:  1.43 (0.26), residues: 456
  sheet: -1.20 (0.41), residues: 140
  loop : -0.48 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 766 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.008   0.001   PHE D 658 
 TYR   0.013   0.001   TYR D 673 
 ARG   0.004   0.000   ARG D 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  351)
  hydrogen bonds       : angle       4.56213 ( 1011)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.36746 (    8)
  covalent geometry    : bond        0.00212 ( 8344)
  covalent geometry    : angle       0.44110 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.832 
Fit side-chains
REVERT: B  685 THR cc_start: 0.8044 (m) cc_final: 0.7649 (p)
REVERT: B  695 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6976 (tmmt)
REVERT: B  760 ASP cc_start: 0.8315 (m-30) cc_final: 0.7674 (m-30)
REVERT: C  662 SER cc_start: 0.7786 (t) cc_final: 0.7367 (p)
REVERT: A  660 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6956 (ttp80)
REVERT: D  411 ASN cc_start: 0.7860 (p0) cc_final: 0.7619 (p0)
REVERT: D  458 LYS cc_start: 0.8284 (mppt) cc_final: 0.8029 (mppt)
  outliers start: 20
  outliers final: 9
  residues processed: 130
  average time/residue: 1.4366
  time to fit residues: 196.6805
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  723 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN
C 709 ASN
A 709 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.131932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.103740 restraints weight = 26129.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 3.70
r_work: 0.2916 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8348  Z= 0.211
  Angle     :  0.578   8.895  11280  Z= 0.297
  Chirality :  0.046   0.133   1240
  Planarity :  0.004   0.046   1390
  Dihedral  : 11.437 102.415   1274
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.95 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1016
  helix:  1.01 (0.25), residues: 456
  sheet: -1.15 (0.42), residues: 140
  loop : -0.68 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 766 
 HIS   0.003   0.001   HIS D 412 
 PHE   0.015   0.003   PHE A 438 
 TYR   0.018   0.002   TYR D 673 
 ARG   0.005   0.001   ARG D 692 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  351)
  hydrogen bonds       : angle       4.81767 ( 1011)
  SS BOND              : bond        0.00218 (    4)
  SS BOND              : angle       1.34222 (    8)
  covalent geometry    : bond        0.00511 ( 8344)
  covalent geometry    : angle       0.57691 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8094 (ttpt)
REVERT: B  685 THR cc_start: 0.8292 (m) cc_final: 0.7879 (p)
REVERT: B  695 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7219 (tmmt)
REVERT: B  705 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: C  662 SER cc_start: 0.7806 (t) cc_final: 0.7338 (p)
  outliers start: 24
  outliers final: 15
  residues processed: 124
  average time/residue: 1.5434
  time to fit residues: 200.8380
Evaluate side-chains
  123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  407 MET
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  723 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain D residue  447 ASP
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0030
   chunk 68 optimal weight:    0.0770
   chunk 18 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7150

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.107298 restraints weight = 25509.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.52
r_work: 0.2977 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8348  Z= 0.108
  Angle     :  0.468   6.947  11280  Z= 0.242
  Chirality :  0.042   0.127   1240
  Planarity :  0.003   0.047   1390
  Dihedral  : 10.813  98.699   1274
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.30 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1016
  helix:  1.32 (0.25), residues: 456
  sheet: -1.18 (0.41), residues: 140
  loop : -0.63 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 766 
 HIS   0.002   0.001   HIS A 412 
 PHE   0.010   0.001   PHE D 658 
 TYR   0.014   0.001   TYR D 673 
 ARG   0.004   0.000   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  351)
  hydrogen bonds       : angle       4.53048 ( 1011)
  SS BOND              : bond        0.00051 (    4)
  SS BOND              : angle       0.42048 (    8)
  covalent geometry    : bond        0.00249 ( 8344)
  covalent geometry    : angle       0.46797 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: B  684 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7337 (mtm110)
REVERT: B  685 THR cc_start: 0.8117 (m) cc_final: 0.7746 (p)
REVERT: B  695 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6886 (tmmt)
REVERT: B  760 ASP cc_start: 0.8351 (m-30) cc_final: 0.7697 (m-30)
REVERT: C  419 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: C  662 SER cc_start: 0.7753 (t) cc_final: 0.7367 (p)
REVERT: D  684 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7556 (ttm110)
  outliers start: 22
  outliers final: 15
  residues processed: 126
  average time/residue: 1.3757
  time to fit residues: 182.6126
Evaluate side-chains
  124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  723 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain D residue  447 ASP
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 82 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 69 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN
C 709 ASN
A 709 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.131396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.103173 restraints weight = 23197.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.92
r_work: 0.2953 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8348  Z= 0.213
  Angle     :  0.584   9.427  11280  Z= 0.298
  Chirality :  0.046   0.137   1240
  Planarity :  0.004   0.046   1390
  Dihedral  : 11.075  99.943   1274
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.65 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1016
  helix:  1.01 (0.25), residues: 456
  sheet: -1.17 (0.42), residues: 140
  loop : -0.74 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 766 
 HIS   0.008   0.002   HIS C 412 
 PHE   0.015   0.003   PHE A 438 
 TYR   0.020   0.002   TYR D 673 
 ARG   0.004   0.001   ARG D 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  351)
  hydrogen bonds       : angle       4.76323 ( 1011)
  SS BOND              : bond        0.00205 (    4)
  SS BOND              : angle       1.24759 (    8)
  covalent geometry    : bond        0.00515 ( 8344)
  covalent geometry    : angle       0.58280 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (ttpt)
REVERT: B  685 THR cc_start: 0.8282 (m) cc_final: 0.7887 (p)
REVERT: B  695 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7252 (tmmt)
REVERT: B  705 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7797 (mp0)
REVERT: C  419 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: C  662 SER cc_start: 0.7804 (t) cc_final: 0.7397 (p)
REVERT: A  705 GLU cc_start: 0.7978 (mp0) cc_final: 0.7538 (mp0)
REVERT: D  684 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7523 (ttm110)
  outliers start: 24
  outliers final: 14
  residues processed: 121
  average time/residue: 1.4891
  time to fit residues: 189.4670
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.106782 restraints weight = 32864.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 4.56
r_work: 0.2907 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8348  Z= 0.110
  Angle     :  0.482   7.348  11280  Z= 0.248
  Chirality :  0.042   0.128   1240
  Planarity :  0.003   0.047   1390
  Dihedral  : 10.481  96.989   1274
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.77 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1016
  helix:  1.29 (0.25), residues: 456
  sheet: -1.20 (0.41), residues: 140
  loop : -0.67 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 766 
 HIS   0.007   0.002   HIS C 412 
 PHE   0.010   0.002   PHE D 658 
 TYR   0.015   0.001   TYR D 673 
 ARG   0.004   0.000   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  351)
  hydrogen bonds       : angle       4.50338 ( 1011)
  SS BOND              : bond        0.00073 (    4)
  SS BOND              : angle       0.39966 (    8)
  covalent geometry    : bond        0.00252 ( 8344)
  covalent geometry    : angle       0.48191 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8078 (ttpt)
REVERT: B  685 THR cc_start: 0.8131 (m) cc_final: 0.7753 (p)
REVERT: B  695 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7019 (tmmt)
REVERT: C  419 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7875 (mm-30)
REVERT: C  662 SER cc_start: 0.7757 (t) cc_final: 0.7387 (p)
REVERT: A  503 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8886 (ttm)
REVERT: D  684 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7620 (ttm110)
REVERT: D  705 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 127
  average time/residue: 1.4408
  time to fit residues: 192.5886
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  503 MET
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  761 LYS
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Chi-restraints excluded: chain D residue  705 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN
C 709 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.102490 restraints weight = 30034.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 4.02
r_work: 0.2884 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8348  Z= 0.218
  Angle     :  0.596   9.873  11280  Z= 0.303
  Chirality :  0.046   0.133   1240
  Planarity :  0.004   0.046   1390
  Dihedral  : 10.792  98.241   1274
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.65 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.26), residues: 1016
  helix:  1.00 (0.25), residues: 456
  sheet: -1.38 (0.40), residues: 148
  loop : -0.82 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 766 
 HIS   0.007   0.002   HIS C 412 
 PHE   0.014   0.003   PHE A 438 
 TYR   0.021   0.002   TYR D 673 
 ARG   0.005   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04701 (  351)
  hydrogen bonds       : angle       4.73668 ( 1011)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       1.18635 (    8)
  covalent geometry    : bond        0.00528 ( 8344)
  covalent geometry    : angle       0.59508 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8120 (ttpt)
REVERT: B  685 THR cc_start: 0.8269 (m) cc_final: 0.7880 (p)
REVERT: B  695 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7351 (tmmt)
REVERT: C  419 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8016 (mm-30)
REVERT: C  458 LYS cc_start: 0.7473 (mmtm) cc_final: 0.7255 (mmtm)
REVERT: C  662 SER cc_start: 0.7841 (t) cc_final: 0.7432 (p)
REVERT: A  642 GLN cc_start: 0.7389 (pp30) cc_final: 0.6906 (pp30)
REVERT: D  454 ASP cc_start: 0.7038 (t0) cc_final: 0.6458 (t0)
REVERT: D  684 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7619 (ttm110)
REVERT: D  705 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8011 (mp0)
  outliers start: 22
  outliers final: 14
  residues processed: 133
  average time/residue: 1.8660
  time to fit residues: 260.9704
Evaluate side-chains
  122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  420 ARG
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Chi-restraints excluded: chain D residue  705 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 709 ASN
D 756 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.102710 restraints weight = 33663.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 4.42
r_work: 0.2861 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8348  Z= 0.200
  Angle     :  0.572   8.002  11280  Z= 0.293
  Chirality :  0.046   0.136   1240
  Planarity :  0.004   0.047   1390
  Dihedral  : 10.966  99.680   1274
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.23 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.26), residues: 1016
  helix:  0.97 (0.25), residues: 456
  sheet: -1.21 (0.42), residues: 140
  loop : -0.79 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 766 
 HIS   0.007   0.002   HIS C 412 
 PHE   0.014   0.002   PHE A 438 
 TYR   0.018   0.002   TYR D 673 
 ARG   0.005   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  351)
  hydrogen bonds       : angle       4.72059 ( 1011)
  SS BOND              : bond        0.00179 (    4)
  SS BOND              : angle       1.03748 (    8)
  covalent geometry    : bond        0.00483 ( 8344)
  covalent geometry    : angle       0.57133 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8039 (ttpt)
REVERT: B  684 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7354 (mtm110)
REVERT: B  685 THR cc_start: 0.8258 (m) cc_final: 0.7843 (p)
REVERT: B  695 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (tmmt)
REVERT: B  705 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7981 (mp0)
REVERT: C  458 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7241 (mmtm)
REVERT: C  662 SER cc_start: 0.7872 (t) cc_final: 0.7462 (p)
REVERT: A  642 GLN cc_start: 0.7397 (pp30) cc_final: 0.6898 (pp30)
REVERT: D  454 ASP cc_start: 0.7024 (t0) cc_final: 0.6224 (t0)
REVERT: D  684 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7496 (ttm110)
REVERT: D  705 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8001 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 124
  average time/residue: 1.5418
  time to fit residues: 201.0694
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  420 ARG
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Chi-restraints excluded: chain D residue  705 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0970
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN
D 756 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.133938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.105662 restraints weight = 33720.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 4.51
r_work: 0.2897 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8348  Z= 0.122
  Angle     :  0.509   9.563  11280  Z= 0.260
  Chirality :  0.043   0.177   1240
  Planarity :  0.004   0.046   1390
  Dihedral  : 10.482  98.639   1274
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.58 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1016
  helix:  1.22 (0.25), residues: 456
  sheet: -1.39 (0.40), residues: 148
  loop : -0.75 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 766 
 HIS   0.007   0.002   HIS C 412 
 PHE   0.010   0.002   PHE D 658 
 TYR   0.017   0.001   TYR D 673 
 ARG   0.008   0.001   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  351)
  hydrogen bonds       : angle       4.55706 ( 1011)
  SS BOND              : bond        0.00094 (    4)
  SS BOND              : angle       0.50812 (    8)
  covalent geometry    : bond        0.00281 ( 8344)
  covalent geometry    : angle       0.50872 (11272)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  420 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7278 (mtm180)
REVERT: B  434 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8089 (ttpt)
REVERT: B  685 THR cc_start: 0.8177 (m) cc_final: 0.7796 (p)
REVERT: B  695 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7231 (tmmt)
REVERT: B  705 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mp0)
REVERT: C  419 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: C  458 LYS cc_start: 0.7466 (mmtm) cc_final: 0.7246 (mmtm)
REVERT: C  662 SER cc_start: 0.7762 (t) cc_final: 0.7410 (p)
REVERT: D  454 ASP cc_start: 0.7038 (t0) cc_final: 0.6259 (t0)
REVERT: D  684 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7659 (ttm110)
REVERT: D  705 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7994 (mp0)
  outliers start: 20
  outliers final: 13
  residues processed: 134
  average time/residue: 1.3404
  time to fit residues: 189.4112
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  420 ARG
Chi-restraints excluded: chain B residue  434 LYS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 VAL
Chi-restraints excluded: chain C residue  744 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  657 GLU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  684 ARG
Chi-restraints excluded: chain D residue  705 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0030
   chunk 33 optimal weight:    0.0170
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0470
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.3326

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

Flipped N/Q/H residues before XYZ refinement:
B 756 GLN
C 709 ASN
** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.137313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.109761 restraints weight = 28828.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 4.00
r_work: 0.2985 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8348  Z= 0.091
  Angle     :  0.464   7.637  11280  Z= 0.238
  Chirality :  0.041   0.219   1240
  Planarity :  0.003   0.047   1390
  Dihedral  :  9.570  93.868   1274
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.62 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1016
  helix:  1.51 (0.25), residues: 456
  sheet: -1.12 (0.42), residues: 140
  loop : -0.58 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 766 
 HIS   0.007   0.001   HIS C 412 
 PHE   0.008   0.001   PHE B 658 
 TYR   0.013   0.001   TYR D 673 
 ARG   0.007   0.000   ARG B 453 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02698 (  351)
  hydrogen bonds       : angle       4.36461 ( 1011)
  SS BOND              : bond        0.00109 (    4)
  SS BOND              : angle       0.22803 (    8)
  covalent geometry    : bond        0.00196 ( 8344)
  covalent geometry    : angle       0.46424 (11272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6403.87 seconds
wall clock time: 111 minutes 34.78 seconds (6694.78 seconds total)