Starting phenix.real_space_refine
on Fri Aug 22 22:04:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fpl_29368/08_2025/8fpl_29368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fpl_29368/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fpl_29368/08_2025/8fpl_29368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fpl_29368/08_2025/8fpl_29368.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fpl_29368/08_2025/8fpl_29368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fpl_29368/08_2025/8fpl_29368.map"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.98, per 1000 atoms: 0.36
  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: 0.81
  Conformation dependent library (CDL) restraints added in 454.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.18
  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: 0.85

  Time building geometry restraints manager: 1.05 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: 0.00
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 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 902))
  selection = (chain 'C' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ 
ugh 902))
  selection = (chain 'D' and (resid 393 through 434 or resid 436 through 763 or resid 765 thro \ 
ugh 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:             3.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.800
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:7.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.110
-------------------------------------------------------------------------------
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 : 7.29
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.007   0.001   ARG B 453 
 TYR   0.018   0.001   TYR A 647 
 PHE   0.008   0.002   PHE D 495 
 TRP   0.007   0.001   TRP C 766 
 HIS   0.003   0.001   HIS A 412 

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

*********************** 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  : 0.398 
Fit side-chains
REVERT: B  685 THR cc_start: 0.8330 (m) cc_final: 0.7944 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 114
  average time/residue: 0.7184
  time to fit residues: 86.1118
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  : 0.334 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7390

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.108300 restraints weight = 29647.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 4.11
r_work: 0.2959 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.0809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8348  Z= 0.113
  Angle     :  0.470   6.275  11280  Z= 0.248
  Chirality :  0.042   0.132   1240
  Planarity :  0.003   0.043   1390
  Dihedral  : 11.494 106.229   1274
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.14 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.26), residues: 1016
  helix:  1.41 (0.26), residues: 456
  sheet: -1.19 (0.41), residues: 140
  loop : -0.42 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 661 
 TYR   0.012   0.001   TYR D 673 
 PHE   0.008   0.002   PHE B 495 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.004   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8344)
  covalent geometry    : angle       0.47027 (11272)
  SS BOND              : bond        0.00111 (    4)
  SS BOND              : angle       0.50665 (    8)
  hydrogen bonds       : bond        0.03774 (  351)
  hydrogen bonds       : angle       4.79537 ( 1011)

*********************** 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
  145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  643 THR cc_start: 0.8055 (p) cc_final: 0.7783 (t)
REVERT: B  685 THR cc_start: 0.8203 (m) cc_final: 0.7772 (p)
REVERT: B  695 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6965 (tmmt)
REVERT: B  760 ASP cc_start: 0.8349 (m-30) cc_final: 0.7761 (m-30)
REVERT: C  662 SER cc_start: 0.7827 (t) cc_final: 0.7384 (p)
REVERT: A  503 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8820 (ttm)
REVERT: A  660 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.6983 (ttp80)
REVERT: D  458 LYS cc_start: 0.8241 (mppt) cc_final: 0.8035 (mppt)
REVERT: D  760 ASP cc_start: 0.8251 (m-30) cc_final: 0.8049 (m-30)
  outliers start: 17
  outliers final: 8
  residues processed: 138
  average time/residue: 0.7142
  time to fit residues: 103.4015
Evaluate side-chains
  116 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 32 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.3664

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.133888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.104069 restraints weight = 18483.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.64
r_work: 0.2999 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8348  Z= 0.154
  Angle     :  0.518   7.224  11280  Z= 0.269
  Chirality :  0.044   0.130   1240
  Planarity :  0.004   0.045   1390
  Dihedral  : 11.491 104.407   1274
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.61 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.26), residues: 1016
  helix:  1.22 (0.25), residues: 456
  sheet: -1.17 (0.41), residues: 140
  loop : -0.52 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 661 
 TYR   0.015   0.001   TYR D 673 
 PHE   0.011   0.002   PHE A 438 
 TRP   0.010   0.001   TRP C 766 
 HIS   0.004   0.002   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8344)
  covalent geometry    : angle       0.51795 (11272)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       0.99203 (    8)
  hydrogen bonds       : bond        0.04219 (  351)
  hydrogen bonds       : angle       4.77302 ( 1011)

*********************** 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
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B  434 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7959 (ttpt)
REVERT: B  637 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7299 (mt-10)
REVERT: B  685 THR cc_start: 0.8231 (m) cc_final: 0.7805 (p)
REVERT: B  695 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6823 (tmmt)
REVERT: C  503 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8828 (ttm)
REVERT: C  661 ARG cc_start: 0.7276 (ptp-110) cc_final: 0.6980 (ptp90)
REVERT: C  662 SER cc_start: 0.7814 (t) cc_final: 0.7391 (p)
REVERT: A  503 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8796 (ttm)
REVERT: A  657 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6832 (mp0)
  outliers start: 22
  outliers final: 10
  residues processed: 123
  average time/residue: 0.7563
  time to fit residues: 97.4594
Evaluate side-chains
  128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  637 GLU
Chi-restraints excluded: chain B residue  695 LYS
Chi-restraints excluded: chain B residue  736 THR
Chi-restraints excluded: chain C residue  503 MET
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  503 MET
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.1186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.106208 restraints weight = 27778.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 3.80
r_work: 0.2937 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8348  Z= 0.133
  Angle     :  0.495   8.326  11280  Z= 0.255
  Chirality :  0.043   0.129   1240
  Planarity :  0.003   0.045   1390
  Dihedral  : 11.179 101.915   1274
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1016
  helix:  1.26 (0.25), residues: 456
  sheet: -1.17 (0.41), residues: 140
  loop : -0.55 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 661 
 TYR   0.015   0.001   TYR D 673 
 PHE   0.010   0.002   PHE A 438 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8344)
  covalent geometry    : angle       0.49471 (11272)
  SS BOND              : bond        0.00110 (    4)
  SS BOND              : angle       0.74526 (    8)
  hydrogen bonds       : bond        0.03778 (  351)
  hydrogen bonds       : angle       4.62139 ( 1011)

*********************** 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
  144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.265 
Fit side-chains
REVERT: B  434 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7968 (ttpt)
REVERT: B  685 THR cc_start: 0.8109 (m) cc_final: 0.7713 (p)
REVERT: B  695 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6906 (tmmt)
REVERT: C  503 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8909 (ttm)
REVERT: C  661 ARG cc_start: 0.7330 (ptp-110) cc_final: 0.7075 (ptp90)
REVERT: C  662 SER cc_start: 0.7774 (t) cc_final: 0.7324 (p)
REVERT: C  688 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7014 (tm-30)
REVERT: A  503 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8849 (ttm)
REVERT: D  760 ASP cc_start: 0.8351 (m-30) cc_final: 0.8093 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 132
  average time/residue: 0.7107
  time to fit residues: 98.5234
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  736 THR
Chi-restraints excluded: chain C residue  503 MET
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  688 GLU
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  503 MET
Chi-restraints excluded: chain A residue  655 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 21 optimal weight:    0.2980
   chunk 18 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0000
   chunk 92 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.8590

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.132130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.103446 restraints weight = 31959.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 4.27
r_work: 0.2882 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    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 = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1476

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= 0.192
  Angle     :  0.562   8.904  11280  Z= 0.288
  Chirality :  0.045   0.131   1240
  Planarity :  0.004   0.046   1390
  Dihedral  : 11.243 101.198   1274
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.30 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.26), residues: 1016
  helix:  1.04 (0.25), residues: 456
  sheet: -1.17 (0.42), residues: 140
  loop : -0.64 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 661 
 TYR   0.018   0.002   TYR D 673 
 PHE   0.014   0.002   PHE A 438 
 TRP   0.011   0.001   TRP A 766 
 HIS   0.007   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 8344)
  covalent geometry    : angle       0.56097 (11272)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       1.14714 (    8)
  hydrogen bonds       : bond        0.04524 (  351)
  hydrogen bonds       : angle       4.75758 ( 1011)

*********************** 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
  136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8093 (ttpt)
REVERT: B  685 THR cc_start: 0.8304 (m) cc_final: 0.7881 (p)
REVERT: B  695 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7296 (tmmt)
REVERT: B  705 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7950 (mp0)
REVERT: C  503 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8904 (ttm)
REVERT: C  662 SER cc_start: 0.7804 (t) cc_final: 0.7372 (p)
REVERT: A  503 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8897 (ttm)
REVERT: A  705 GLU cc_start: 0.8148 (mp0) cc_final: 0.7721 (mp0)
REVERT: D  684 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (ttm110)
  outliers start: 23
  outliers final: 14
  residues processed: 125
  average time/residue: 0.7257
  time to fit residues: 95.1350
Evaluate side-chains
  123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  503 MET
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  503 MET
Chi-restraints excluded: chain A residue  655 THR
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  746 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
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 26 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.134225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.106075 restraints weight = 35023.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 4.70
r_work: 0.2887 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8348  Z= 0.137
  Angle     :  0.509   9.882  11280  Z= 0.260
  Chirality :  0.043   0.128   1240
  Planarity :  0.003   0.047   1390
  Dihedral  : 10.840  99.000   1274
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.53 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.26), residues: 1016
  helix:  1.21 (0.25), residues: 456
  sheet: -1.19 (0.42), residues: 140
  loop : -0.63 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 453 
 TYR   0.016   0.001   TYR D 673 
 PHE   0.011   0.002   PHE D 658 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.006   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8344)
  covalent geometry    : angle       0.50842 (11272)
  SS BOND              : bond        0.00119 (    4)
  SS BOND              : angle       0.63418 (    8)
  hydrogen bonds       : bond        0.03783 (  351)
  hydrogen bonds       : angle       4.60751 ( 1011)

*********************** 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
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8011 (ttpt)
REVERT: B  685 THR cc_start: 0.8112 (m) cc_final: 0.7725 (p)
REVERT: B  695 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6985 (tmmt)
REVERT: C  503 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8927 (ttm)
REVERT: C  662 SER cc_start: 0.7814 (t) cc_final: 0.7410 (p)
REVERT: A  503 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8906 (ttm)
REVERT: D  684 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7693 (ttm110)
  outliers start: 22
  outliers final: 15
  residues processed: 121
  average time/residue: 0.7159
  time to fit residues: 90.9058
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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  736 THR
Chi-restraints excluded: chain C residue  503 MET
Chi-restraints excluded: chain C residue  666 VAL
Chi-restraints excluded: chain C residue  683 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  503 MET
Chi-restraints excluded: chain A residue  655 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3539 r_free = 0.3539 target = 0.134124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.105948 restraints weight = 29653.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 4.07
r_work: 0.2922 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8348  Z= 0.133
  Angle     :  0.515  10.966  11280  Z= 0.262
  Chirality :  0.043   0.130   1240
  Planarity :  0.003   0.047   1390
  Dihedral  : 10.531  98.193   1274
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.26), residues: 1016
  helix:  1.24 (0.25), residues: 456
  sheet: -1.18 (0.42), residues: 140
  loop : -0.63 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 453 
 TYR   0.016   0.001   TYR D 673 
 PHE   0.011   0.002   PHE D 658 
 TRP   0.012   0.001   TRP C 766 
 HIS   0.006   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8344)
  covalent geometry    : angle       0.51511 (11272)
  SS BOND              : bond        0.00091 (    4)
  SS BOND              : angle       0.62676 (    8)
  hydrogen bonds       : bond        0.03712 (  351)
  hydrogen bonds       : angle       4.56531 ( 1011)

*********************** 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
  139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7985 (ttpt)
REVERT: B  684 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7279 (mtm110)
REVERT: B  685 THR cc_start: 0.8091 (m) cc_final: 0.7705 (p)
REVERT: B  695 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7229 (tmmt)
REVERT: B  705 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: C  662 SER cc_start: 0.7803 (t) cc_final: 0.7422 (p)
REVERT: A  503 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8861 (ttm)
REVERT: A  705 GLU cc_start: 0.8091 (mp0) cc_final: 0.7644 (mp0)
REVERT: D  454 ASP cc_start: 0.6957 (t0) cc_final: 0.6385 (t70)
REVERT: D  684 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7654 (ttm110)
REVERT: D  705 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7928 (mp0)
  outliers start: 25
  outliers final: 16
  residues processed: 129
  average time/residue: 0.6947
  time to fit residues: 94.0987
Evaluate side-chains
  128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  723 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  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
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 57 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0980
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.133355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.105264 restraints weight = 27753.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 3.82
r_work: 0.2925 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
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 = 0.21   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 = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8348  Z= 0.152
  Angle     :  0.542  12.516  11280  Z= 0.273
  Chirality :  0.044   0.136   1240
  Planarity :  0.004   0.047   1390
  Dihedral  : 10.602  97.635   1274
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.26), residues: 1016
  helix:  1.18 (0.25), residues: 456
  sheet: -1.33 (0.41), residues: 148
  loop : -0.71 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 453 
 TYR   0.017   0.001   TYR D 673 
 PHE   0.011   0.002   PHE A 438 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.006   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8344)
  covalent geometry    : angle       0.54217 (11272)
  SS BOND              : bond        0.00126 (    4)
  SS BOND              : angle       0.82745 (    8)
  hydrogen bonds       : bond        0.03961 (  351)
  hydrogen bonds       : angle       4.61697 ( 1011)

*********************** 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
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7980 (ttpt)
REVERT: B  685 THR cc_start: 0.8104 (m) cc_final: 0.7724 (p)
REVERT: B  695 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7225 (tmmt)
REVERT: B  705 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: C  662 SER cc_start: 0.7832 (t) cc_final: 0.7456 (p)
REVERT: A  503 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (ttm)
REVERT: D  454 ASP cc_start: 0.6975 (t0) cc_final: 0.6386 (t0)
REVERT: D  684 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7575 (ttm110)
REVERT: D  705 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7917 (mp0)
  outliers start: 23
  outliers final: 17
  residues processed: 121
  average time/residue: 0.7384
  time to fit residues: 93.5930
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
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  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  723 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  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
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 83 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3508 r_free = 0.3508 target = 0.131549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.103347 restraints weight = 27780.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 3.78
r_work: 0.2910 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8348  Z= 0.200
  Angle     :  0.591  13.944  11280  Z= 0.299
  Chirality :  0.046   0.150   1240
  Planarity :  0.004   0.047   1390
  Dihedral  : 10.928 101.698   1274
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.77 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1016
  helix:  1.02 (0.25), residues: 456
  sheet: -1.32 (0.41), residues: 148
  loop : -0.76 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 453 
 TYR   0.020   0.002   TYR D 673 
 PHE   0.014   0.002   PHE A 438 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.006   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8344)
  covalent geometry    : angle       0.59033 (11272)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       1.09255 (    8)
  hydrogen bonds       : bond        0.04543 (  351)
  hydrogen bonds       : angle       4.73965 ( 1011)

*********************** 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
  144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8052 (ttpt)
REVERT: B  685 THR cc_start: 0.8212 (m) cc_final: 0.7789 (p)
REVERT: B  695 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7316 (tmmt)
REVERT: B  705 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7869 (mp0)
REVERT: C  662 SER cc_start: 0.7879 (t) cc_final: 0.7478 (p)
REVERT: A  503 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8870 (ttm)
REVERT: A  642 GLN cc_start: 0.7331 (pp30) cc_final: 0.6834 (pp30)
REVERT: A  705 GLU cc_start: 0.8112 (mp0) cc_final: 0.7676 (mp0)
REVERT: D  454 ASP cc_start: 0.6947 (t0) cc_final: 0.6339 (t0)
REVERT: D  684 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7628 (ttm110)
REVERT: D  705 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7902 (mp0)
  outliers start: 24
  outliers final: 14
  residues processed: 134
  average time/residue: 0.7134
  time to fit residues: 100.2028
Evaluate side-chains
  126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  503 MET
Chi-restraints excluded: chain A residue  655 THR
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
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 82 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0270
   chunk 20 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0970
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.5236

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.136308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.108728 restraints weight = 22405.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.72
r_work: 0.3032 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8348  Z= 0.100
  Angle     :  0.504  14.091  11280  Z= 0.252
  Chirality :  0.042   0.203   1240
  Planarity :  0.003   0.047   1390
  Dihedral  : 10.057  97.322   1274
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 21.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1016
  helix:  1.37 (0.25), residues: 456
  sheet: -1.13 (0.42), residues: 140
  loop : -0.61 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 453 
 TYR   0.015   0.001   TYR D 673 
 PHE   0.010   0.001   PHE B 658 
 TRP   0.011   0.001   TRP C 766 
 HIS   0.006   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8344)
  covalent geometry    : angle       0.50407 (11272)
  SS BOND              : bond        0.00113 (    4)
  SS BOND              : angle       0.19749 (    8)
  hydrogen bonds       : bond        0.02975 (  351)
  hydrogen bonds       : angle       4.48403 ( 1011)

********************** 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
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: B  434 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7990 (ttpt)
REVERT: B  695 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6959 (tmmt)
REVERT: C  419 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: C  662 SER cc_start: 0.7668 (t) cc_final: 0.7360 (p)
REVERT: D  454 ASP cc_start: 0.6965 (t0) cc_final: 0.6192 (t0)
REVERT: D  705 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7738 (mp0)
REVERT: D  760 ASP cc_start: 0.8258 (m-30) cc_final: 0.7989 (m-30)
  outliers start: 17
  outliers final: 9
  residues processed: 124
  average time/residue: 0.6895
  time to fit residues: 89.8427
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  : 0.340 
-------------------------------------------------------------------------------
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 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  746 VAL
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  488 VAL
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:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0050
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   chunk 65 optimal weight:    6.9990
   overall best weight:    0.7596

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.135416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107650 restraints weight = 31585.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 4.42
r_work: 0.2925 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    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 = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8348  Z= 0.114
  Angle     :  0.518  14.357  11280  Z= 0.260
  Chirality :  0.042   0.213   1240
  Planarity :  0.003   0.047   1390
  Dihedral  :  9.839  96.001   1274
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 22.85 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 42.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1016
  helix:  1.41 (0.25), residues: 456
  sheet: -1.07 (0.42), residues: 140
  loop : -0.61 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 453 
 TYR   0.014   0.001   TYR D 673 
 PHE   0.010   0.001   PHE D 658 
 TRP   0.013   0.001   TRP A 766 
 HIS   0.006   0.002   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8344)
  covalent geometry    : angle       0.51812 (11272)
  SS BOND              : bond        0.00108 (    4)
  SS BOND              : angle       0.49148 (    8)
  hydrogen bonds       : bond        0.03299 (  351)
  hydrogen bonds       : angle       4.47044 ( 1011)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3111.44 seconds
wall clock time: 53 minutes 53.06 seconds (3233.06 seconds total)