Starting phenix.real_space_refine
on Sat May 17 19:46:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yaq_39104/05_2025/8yaq_39104.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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      5      4.86       5
     C   10142      2.51       5
     N    2627      2.21       5
     O    3022      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15860
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 7877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 984, 7877
          Classifications: {'peptide': 984}
          Link IDs: {'PTRANS': 33, 'TRANS': 950}
    Chain: "B"
      Number of atoms: 7887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7887
          Classifications: {'peptide': 985}
          Link IDs: {'PTRANS': 33, 'TRANS': 951}
    Chain: "D"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 56
          Unusual residues: {'BGC': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {'BGC': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   PHE A 295 " occ=0.90
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 295 " occ=0.90
    residue:
      pdb=" N   PHE B 295 " occ=0.95
      ... (9 atoms not shown)
      pdb=" CZ  PHE B 295 " occ=0.95
    residue:
      pdb=" C1  BGC D   2 " occ=0.68
      ... (9 atoms not shown)
      pdb=" O6  BGC D   2 " occ=0.68
    residue:
      pdb=" C1  BGC D   3 " occ=0.78
      ... (9 atoms not shown)
      pdb=" O6  BGC D   3 " occ=0.78
    residue:
      pdb=" C1  BGC D   4 " occ=0.64
      ... (9 atoms not shown)
      pdb=" O6  BGC D   4 " occ=0.64
    residue:
      pdb=" C1  BGC D   5 " occ=0.58
      ... (9 atoms not shown)
      pdb=" O6  BGC D   5 " occ=0.58
    residue:
      pdb=" C1  BGC C   2 " occ=0.36
      ... (9 atoms not shown)
      pdb=" O6  BGC C   2 " occ=0.36
    residue:
      pdb=" C1  BGC C   3 " occ=0.44
      ... (9 atoms not shown)
      pdb=" O6  BGC C   3 " occ=0.44
  Time building chain proxies: 10.48, per 1000 atoms: 0.66
  Number of scatterers: 15860
  At special positions: 0
  Unit cell: (92.13, 112.88, 146.91, 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      5     17.00
     S      64     16.00
     O    3022      8.00
     N    2627      7.00
     C   10142      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " BGC C   1 " - " BGC C   2 "
      " BGC C   2 " - " BGC C   3 "
      " BGC D   1 " - " BGC D   2 "
      " BGC D   2 " - " BGC D   3 "
      " BGC D   3 " - " BGC D   4 "
      " BGC D   4 " - " BGC D   5 "
  Time building additional restraints: 4.60
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3690

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 24 sheets defined
      35.4% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 23
    Processing helix  chain 'A' and resid 55 through 63
      removed outlier: 3.588A  pdb=" N   VAL A  59 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 72
      removed outlier: 3.775A  pdb=" N   GLN A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 113
    Processing helix  chain 'A' and resid 155 through 160
    Processing helix  chain 'A' and resid 291 through 297
      removed outlier: 4.171A  pdb=" N   PHE A 295 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 327 through 330
    Processing helix  chain 'A' and resid 355 through 361
    Processing helix  chain 'A' and resid 418 through 433
      removed outlier: 3.585A  pdb=" N   MET A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 453
      removed outlier: 4.180A  pdb=" N   VAL A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 472
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 4.221A  pdb=" N   ALA A 508 " --> pdb=" O   GLN A 504 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 509 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TYR A 511 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   TYR A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 531
    Processing helix  chain 'A' and resid 555 through 572
      removed outlier: 3.899A  pdb=" N   TRP A 559 " --> pdb=" O   ASP A 555 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LEU A 560 " --> pdb=" O   ASP A 556 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLN A 562 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 563 " --> pdb=" O   TRP A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 578
      removed outlier: 3.880A  pdb=" N   VAL A 576 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 606
      removed outlier: 3.585A  pdb=" N   SER A 604 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 650
    Processing helix  chain 'A' and resid 665 through 685
    Processing helix  chain 'A' and resid 687 through 709
    Processing helix  chain 'A' and resid 749 through 759
      removed outlier: 3.902A  pdb=" N   PHE A 753 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 777
    Processing helix  chain 'A' and resid 816 through 831
    Processing helix  chain 'A' and resid 835 through 852
      removed outlier: 3.685A  pdb=" N   LEU A 852 " --> pdb=" O   PHE A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 860
      removed outlier: 5.902A  pdb=" N   TYR A 856 " --> pdb=" O   VAL A 853 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 859 " --> pdb=" O   TYR A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 866
    Processing helix  chain 'A' and resid 890 through 904
    Processing helix  chain 'B' and resid 13 through 23
    Processing helix  chain 'B' and resid 55 through 63
    Processing helix  chain 'B' and resid 63 through 71
    Processing helix  chain 'B' and resid 101 through 112
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 297 through 304
      removed outlier: 3.687A  pdb=" N   THR B 301 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 330
    Processing helix  chain 'B' and resid 355 through 361
    Processing helix  chain 'B' and resid 418 through 433
      removed outlier: 3.653A  pdb=" N   MET B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 453
      removed outlier: 4.374A  pdb=" N   VAL B 439 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLU B 440 " --> pdb=" O   SER B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 472
    Processing helix  chain 'B' and resid 472 through 485
    Processing helix  chain 'B' and resid 501 through 504
    Processing helix  chain 'B' and resid 505 through 515
      removed outlier: 5.472A  pdb=" N   TYR B 511 " --> pdb=" O   PHE B 507 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   TYR B 512 " --> pdb=" O   ALA B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 531
    Processing helix  chain 'B' and resid 558 through 572
      removed outlier: 4.133A  pdb=" N   GLN B 562 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 578
    Processing helix  chain 'B' and resid 593 through 606
      removed outlier: 3.553A  pdb=" N   SER B 604 " --> pdb=" O   ILE B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 650
    Processing helix  chain 'B' and resid 665 through 685
    Processing helix  chain 'B' and resid 687 through 709
    Processing helix  chain 'B' and resid 749 through 759
      removed outlier: 3.984A  pdb=" N   PHE B 753 " --> pdb=" O   PHE B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 763 through 777
    Processing helix  chain 'B' and resid 791 through 795
    Processing helix  chain 'B' and resid 799 through 803
    Processing helix  chain 'B' and resid 816 through 831
    Processing helix  chain 'B' and resid 835 through 852
      removed outlier: 3.634A  pdb=" N   LEU B 852 " --> pdb=" O   PHE B 848 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 853 through 860
      removed outlier: 5.867A  pdb=" N   TYR B 856 " --> pdb=" O   VAL B 853 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU B 859 " --> pdb=" O   TYR B 856 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 866
    Processing helix  chain 'B' and resid 889 through 903
      removed outlier: 4.580A  pdb=" N   THR B 893 " --> pdb=" O   SER B 889 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 6.440A  pdb=" N   GLN B 306 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA B 308 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE B 320 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU B 310 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B 318 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET B 338 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ARG B 334 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   TYR B 324 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
      removed outlier: 9.150A  pdb=" N   ASP B 332 " --> pdb=" O   TYR B 324 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU B 242 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLU B 222 " --> pdb=" O   LYS B 237 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6
      removed outlier: 6.440A  pdb=" N   GLN B 306 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA B 308 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE B 320 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU B 310 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B 318 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET B 338 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   ARG B 334 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   TYR B 324 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
      removed outlier: 9.150A  pdb=" N   ASP B 332 " --> pdb=" O   TYR B 324 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU B 345 " --> pdb=" O   ASN B 342 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36
      removed outlier: 3.787A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ASP A  33 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ALA A  48 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   VAL A  35 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   GLY A  46 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   GLU A  83 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 9.596A  pdb=" N   LEU A  50 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122
      removed outlier: 3.537A  pdb=" N   GLU A 222 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122
      removed outlier: 3.537A  pdb=" N   GLU A 222 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 9.123A  pdb=" N   ASP A 332 " --> pdb=" O   TYR A 324 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   TYR A 324 " --> pdb=" O   ASP A 332 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ARG A 334 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A 318 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU A 310 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ILE A 320 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ALA A 308 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   GLN A 306 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 147
    Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 212
      removed outlier: 6.485A  pdb=" N   LEU A 203 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   TYR A 212 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   PHE A 201 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 200 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 457 through 459
      removed outlier: 6.581A  pdb=" N   SER A 935 " --> pdb=" O   HIS A 977 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   VAL A 979 " --> pdb=" O   SER A 935 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   LYS A 937 " --> pdb=" O   VAL A 979 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   LEU A 981 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   SER A 939 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   PHE A 983 " --> pdb=" O   SER A 939 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   THR A 941 " --> pdb=" O   PHE A 983 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLU A 953 " --> pdb=" O   LYS A 984 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 499
      removed outlier: 6.449A  pdb=" N   ASN A 540 " --> pdb=" O   PRO A 550 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN A 542 " --> pdb=" O   LYS A 548 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 582
    Processing sheet with id=AB2, first strand: chain 'A' and resid 663 through 664
    Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 780
    Processing sheet with id=AB4, first strand: chain 'A' and resid 814 through 815
    Processing sheet with id=AB5, first strand: chain 'A' and resid 907 through 908
    Processing sheet with id=AB6, first strand: chain 'B' and resid 32 through 36
      removed outlier: 5.879A  pdb=" N   GLU B  83 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 144 through 147
    Processing sheet with id=AB8, first strand: chain 'B' and resid 208 through 212
      removed outlier: 6.505A  pdb=" N   LEU B 203 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   TYR B 212 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   PHE B 201 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLN B 200 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 459
      removed outlier: 6.598A  pdb=" N   SER B 935 " --> pdb=" O   HIS B 977 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL B 979 " --> pdb=" O   SER B 935 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   LYS B 937 " --> pdb=" O   VAL B 979 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   LEU B 981 " --> pdb=" O   LYS B 937 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   SER B 939 " --> pdb=" O   LEU B 981 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   PHE B 983 " --> pdb=" O   SER B 939 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   THR B 941 " --> pdb=" O   PHE B 983 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLU B 953 " --> pdb=" O   LYS B 984 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   LEU B 956 " --> pdb=" O   ILE B 963 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 498 through 499
      removed outlier: 6.437A  pdb=" N   ASN B 540 " --> pdb=" O   PRO B 550 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN B 542 " --> pdb=" O   LYS B 548 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 580 through 582
    Processing sheet with id=AC3, first strand: chain 'B' and resid 663 through 664
    Processing sheet with id=AC4, first strand: chain 'B' and resid 779 through 780
    Processing sheet with id=AC5, first strand: chain 'B' and resid 814 through 815
    Processing sheet with id=AC6, first strand: chain 'B' and resid 907 through 908

    761 hydrogen bonds defined for protein.
    2103 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: 8.48

  Time building geometry restraints manager: 5.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5123
        1.34 -     1.46: 3883
        1.46 -     1.58: 7095
        1.58 -     1.70: 0
        1.70 -     1.82: 106
  Bond restraints: 16207
  Sorted by residual:
  bond pdb=" CB  GLN B  86 "
       pdb=" CG  GLN B  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.72e+00
  bond pdb=" CB  GLN A 689 "
       pdb=" CG  GLN A 689 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" CB  GLN A 692 "
       pdb=" CG  GLN A 692 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.38e+00
  bond pdb=" CB  PRO B  75 "
       pdb=" CG  PRO B  75 "
    ideal  model  delta    sigma   weight residual
    1.492  1.546 -0.054 5.00e-02 4.00e+02 1.19e+00
  bond pdb=" C   ILE B 516 "
       pdb=" O   ILE B 516 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.012 1.19e-02 7.06e+03 9.62e-01
  ... (remaining 16202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 21666
        1.63 -     3.26: 220
        3.26 -     4.89: 35
        4.89 -     6.52: 9
        6.52 -     8.15: 5
  Bond angle restraints: 21935
  Sorted by residual:
  angle pdb=" CA  GLN A 689 "
        pdb=" CB  GLN A 689 "
        pdb=" CG  GLN A 689 "
      ideal   model   delta    sigma   weight residual
     114.10  121.80   -7.70 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CA  GLN B  86 "
        pdb=" CB  GLN B  86 "
        pdb=" CG  GLN B  86 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" N   VAL A 853 "
        pdb=" CA  VAL A 853 "
        pdb=" C   VAL A 853 "
      ideal   model   delta    sigma   weight residual
     113.53  110.25    3.28 9.80e-01 1.04e+00 1.12e+01
  angle pdb=" CA  GLN A 692 "
        pdb=" CB  GLN A 692 "
        pdb=" CG  GLN A 692 "
      ideal   model   delta    sigma   weight residual
     114.10  120.68   -6.58 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" CB  GLN A 689 "
        pdb=" CG  GLN A 689 "
        pdb=" CD  GLN A 689 "
      ideal   model   delta    sigma   weight residual
     112.60  117.84   -5.24 1.70e+00 3.46e-01 9.49e+00
  ... (remaining 21930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.75: 9478
       24.75 -    49.50: 250
       49.50 -    74.24: 26
       74.24 -    98.99: 5
       98.99 -   123.74: 2
  Dihedral angle restraints: 9761
    sinusoidal: 4006
      harmonic: 5755
  Sorted by residual:
  dihedral pdb=" CA  VAL A  74 "
           pdb=" C   VAL A  74 "
           pdb=" N   PRO A  75 "
           pdb=" CA  PRO A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.17   22.83     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" C2  BGC D   5 "
           pdb=" C1  BGC D   5 "
           pdb=" O5  BGC D   5 "
           pdb=" C5  BGC D   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -65.02   58.72 -123.74     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" CA  ALA B 620 "
           pdb=" C   ALA B 620 "
           pdb=" N   ASP B 621 "
           pdb=" CA  ASP B 621 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.86   19.14     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 9758 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1489
       0.029 -    0.058: 628
       0.058 -    0.087: 162
       0.087 -    0.116: 120
       0.116 -    0.145: 26
  Chirality restraints: 2425
  Sorted by residual:
  chirality pdb=" CB  VAL A  74 "
            pdb=" CA  VAL A  74 "
            pdb=" CG1 VAL A  74 "
            pdb=" CG2 VAL A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  ILE B 339 "
            pdb=" N   ILE B 339 "
            pdb=" C   ILE B 339 "
            pdb=" CB  ILE B 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  VAL B 164 "
            pdb=" N   VAL B 164 "
            pdb=" C   VAL B 164 "
            pdb=" CB  VAL B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 2422 not shown)

  Planarity restraints: 2826
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  74 "   -0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO B  75 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B  75 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  75 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 565 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   TYR A 565 "    0.030 2.00e-02 2.50e+03
        pdb=" O   TYR A 565 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG A 566 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 446 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" C   ILE B 446 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE B 446 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 447 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2823 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 4002
        2.79 -     3.32: 14583
        3.32 -     3.85: 26514
        3.85 -     4.37: 33071
        4.37 -     4.90: 56187
  Nonbonded interactions: 134357
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 780 "
            pdb=" O   GLY B 783 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" N   GLU A 415 "
            pdb=" OE1 GLU A 415 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OD2 ASP B 621 "
            pdb=" NH1 ARG B 717 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   GLU A 124 "
            pdb=" OG  SER A 468 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   THR A 156 "
            pdb=" OG1 THR A 160 "
     model   vdw
     2.310 3.040
  ... (remaining 134352 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'
  selection = (chain 'B' and (resid 2 through 985 or resid 1002 through 1003))
}

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=0.36 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:             7.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     41.640
  Find NCS groups from input model:        0.920
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   63.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
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      :  0.003   0.054  16213  Z= 0.126
  Angle     :  0.465   8.148  21953  Z= 0.253
  Chirality :  0.040   0.145   2425
  Planarity :  0.003   0.048   2826
  Dihedral  : 11.192 123.737   6071
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.70 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.22 %
    Favored  : 93.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.19), residues: 1965
  helix:  1.45 (0.21), residues: 630
  sheet:  1.39 (0.28), residues: 338
  loop : -0.31 (0.19), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.011   0.001   PHE A 927 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00559 (    6)
  link_BETA1-4         : angle       1.22447 (   18)
  hydrogen bonds       : bond        0.14367 (  707)
  hydrogen bonds       : angle       6.23155 ( 2103)
  covalent geometry    : bond        0.00286 (16207)
  covalent geometry    : angle       0.46341 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.796 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 1.8781
  time to fit residues: 140.4792
Evaluate side-chains
  66 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  712 GLU
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 148 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 153 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 114 optimal weight:    1.9990
   chunk 177 optimal weight:    7.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.057327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2313 r_free = 0.2313 target = 0.040066 restraints weight = 33359.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.2358 rms_B_bonded: 2.90
r_work: 0.2205 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2079 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2088 r_free = 0.2088    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2088 r_free = 0.2088    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.0748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  16213  Z= 0.316
  Angle     :  0.564   7.153  21953  Z= 0.304
  Chirality :  0.046   0.148   2425
  Planarity :  0.004   0.048   2826
  Dihedral  :  6.456 115.743   2304
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.26 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.87 %
    Favored  : 93.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.19), residues: 1965
  helix:  1.78 (0.21), residues: 634
  sheet:  1.25 (0.29), residues: 341
  loop : -0.41 (0.19), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 755 
 HIS   0.005   0.001   HIS B 450 
 PHE   0.014   0.001   PHE B 476 
 TYR   0.016   0.001   TYR A 236 
 ARG   0.005   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00553 (    6)
  link_BETA1-4         : angle       2.11941 (   18)
  hydrogen bonds       : bond        0.05146 (  707)
  hydrogen bonds       : angle       4.82301 ( 2103)
  covalent geometry    : bond        0.00746 (16207)
  covalent geometry    : angle       0.56145 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 1.778 
Fit side-chains
  outliers start: 8
  outliers final: 3
  residues processed: 71
  average time/residue: 1.6181
  time to fit residues: 126.6812
Evaluate side-chains
  67 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 1.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 141 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9980
   chunk 126 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 139 optimal weight:    0.6980
   chunk 138 optimal weight:    2.9990
   chunk 169 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 195 optimal weight:    5.9990
   chunk 189 optimal weight:    0.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.059743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2374 r_free = 0.2374 target = 0.042496 restraints weight = 32784.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2419 rms_B_bonded: 2.91
r_work: 0.2268 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2142 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2156 r_free = 0.2156    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2156 r_free = 0.2156    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.0746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  16213  Z= 0.112
  Angle     :  0.461   7.419  21953  Z= 0.249
  Chirality :  0.041   0.138   2425
  Planarity :  0.003   0.047   2826
  Dihedral  :  6.037 114.004   2301
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.85 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  5.58 %
    Favored  : 93.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.19), residues: 1965
  helix:  2.02 (0.21), residues: 628
  sheet:  1.42 (0.29), residues: 335
  loop : -0.35 (0.19), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 755 
 HIS   0.002   0.000   HIS B 450 
 PHE   0.012   0.001   PHE A 927 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00439 (    6)
  link_BETA1-4         : angle       1.77641 (   18)
  hydrogen bonds       : bond        0.03907 (  707)
  hydrogen bonds       : angle       4.56964 ( 2103)
  covalent geometry    : bond        0.00249 (16207)
  covalent geometry    : angle       0.45788 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 1.816 
Fit side-chains
REVERT: A  689 GLN cc_start: 0.8701 (pp30) cc_final: 0.8411 (tm-30)
  outliers start: 16
  outliers final: 4
  residues processed: 78
  average time/residue: 1.5670
  time to fit residues: 135.0700
Evaluate side-chains
  67 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 175 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 166 optimal weight:    3.9990
   chunk 174 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   chunk 147 optimal weight:    3.9990
   chunk 164 optimal weight:    0.5980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.059371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2374 r_free = 0.2374 target = 0.042366 restraints weight = 32761.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.2418 rms_B_bonded: 2.88
r_work: 0.2268 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2141 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2152 r_free = 0.2152    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2152 r_free = 0.2152    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.0828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  16213  Z= 0.134
  Angle     :  0.466   7.651  21953  Z= 0.252
  Chirality :  0.041   0.166   2425
  Planarity :  0.003   0.051   2826
  Dihedral  :  5.892 113.004   2301
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.95 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  6.28 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.19), residues: 1965
  helix:  2.09 (0.21), residues: 627
  sheet:  1.37 (0.29), residues: 338
  loop : -0.34 (0.19), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.011   0.001   PHE A 927 
 TYR   0.011   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00526 (    6)
  link_BETA1-4         : angle       1.81479 (   18)
  hydrogen bonds       : bond        0.03847 (  707)
  hydrogen bonds       : angle       4.45689 ( 2103)
  covalent geometry    : bond        0.00310 (16207)
  covalent geometry    : angle       0.46368 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.798 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 70
  average time/residue: 1.6459
  time to fit residues: 127.9377
Evaluate side-chains
  68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  529 TRP
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 155 optimal weight:    0.0970
   chunk 45 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.060230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2400 r_free = 0.2400 target = 0.043203 restraints weight = 32852.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2441 rms_B_bonded: 2.89
r_work: 0.2291 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2165 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2177 r_free = 0.2177    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2177 r_free = 0.2177    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  16213  Z= 0.103
  Angle     :  0.449   7.838  21953  Z= 0.242
  Chirality :  0.040   0.155   2425
  Planarity :  0.003   0.047   2826
  Dihedral  :  5.771 111.965   2301
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.85 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  6.40 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.19), residues: 1965
  helix:  2.11 (0.21), residues: 630
  sheet:  1.38 (0.29), residues: 335
  loop : -0.27 (0.19), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 755 
 HIS   0.002   0.000   HIS B 450 
 PHE   0.011   0.001   PHE A 927 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.008   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00546 (    6)
  link_BETA1-4         : angle       1.73299 (   18)
  hydrogen bonds       : bond        0.03514 (  707)
  hydrogen bonds       : angle       4.36678 ( 2103)
  covalent geometry    : bond        0.00231 (16207)
  covalent geometry    : angle       0.44662 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.712 
Fit side-chains
REVERT: A  692 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8334 (tm-30)
REVERT: A  864 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8990 (tt0)
REVERT: B   96 GLN cc_start: 0.8557 (mt0) cc_final: 0.8191 (mt0)
  outliers start: 10
  outliers final: 2
  residues processed: 71
  average time/residue: 1.7247
  time to fit residues: 134.8971
Evaluate side-chains
  66 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 181 optimal weight:    5.9990
   chunk 170 optimal weight:    5.9990
   overall best weight:    2.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.057505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2317 r_free = 0.2317 target = 0.040195 restraints weight = 33371.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.2325 rms_B_bonded: 2.91
r_work: 0.2167 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2037 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2092 r_free = 0.2092    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2092 r_free = 0.2092    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  16213  Z= 0.261
  Angle     :  0.536   7.663  21953  Z= 0.287
  Chirality :  0.044   0.157   2425
  Planarity :  0.003   0.048   2826
  Dihedral  :  6.053 113.703   2301
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.10 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.64 %
    Favored  : 92.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.19), residues: 1965
  helix:  2.11 (0.21), residues: 617
  sheet:  1.27 (0.28), residues: 341
  loop : -0.39 (0.19), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 755 
 HIS   0.005   0.001   HIS B 450 
 PHE   0.017   0.001   PHE B 476 
 TYR   0.015   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00612 (    6)
  link_BETA1-4         : angle       2.01170 (   18)
  hydrogen bonds       : bond        0.04623 (  707)
  hydrogen bonds       : angle       4.53938 ( 2103)
  covalent geometry    : bond        0.00617 (16207)
  covalent geometry    : angle       0.53282 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 2.095 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.9033 (tt0)
REVERT: B   96 GLN cc_start: 0.8507 (mt0) cc_final: 0.8170 (mt0)
REVERT: B  116 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9024 (mppt)
  outliers start: 12
  outliers final: 4
  residues processed: 76
  average time/residue: 1.5441
  time to fit residues: 130.2894
Evaluate side-chains
  69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 135 optimal weight:    4.9990
   chunk 181 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0010
   chunk 62 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.0988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.059231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2363 r_free = 0.2363 target = 0.041982 restraints weight = 32990.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2410 rms_B_bonded: 2.91
r_work: 0.2259 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2132 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2143 r_free = 0.2143    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2143 r_free = 0.2143    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.0964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16213  Z= 0.135
  Angle     :  0.472   7.912  21953  Z= 0.255
  Chirality :  0.041   0.151   2425
  Planarity :  0.003   0.048   2826
  Dihedral  :  5.890 111.843   2301
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.00 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.64 %
    Favored  : 92.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.19), residues: 1965
  helix:  2.13 (0.21), residues: 619
  sheet:  1.38 (0.28), residues: 337
  loop : -0.34 (0.19), residues: 1009

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.012   0.001   PHE A 927 
 TYR   0.011   0.001   TYR B 236 
 ARG   0.008   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00551 (    6)
  link_BETA1-4         : angle       1.81239 (   18)
  hydrogen bonds       : bond        0.03814 (  707)
  hydrogen bonds       : angle       4.43666 ( 2103)
  covalent geometry    : bond        0.00311 (16207)
  covalent geometry    : angle       0.46919 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 2.043 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8999 (tt0)
REVERT: B  116 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9005 (mppt)
  outliers start: 12
  outliers final: 4
  residues processed: 75
  average time/residue: 1.6083
  time to fit residues: 133.7355
Evaluate side-chains
  71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 1.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 149 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 195 optimal weight:    7.9990
   chunk 175 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 155 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9990
   chunk 126 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.057251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2314 r_free = 0.2314 target = 0.039994 restraints weight = 33177.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.2359 rms_B_bonded: 2.91
r_work: 0.2202 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2072 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2088 r_free = 0.2088    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2088 r_free = 0.2088    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  16213  Z= 0.276
  Angle     :  0.544   8.231  21953  Z= 0.292
  Chirality :  0.044   0.152   2425
  Planarity :  0.003   0.047   2826
  Dihedral  :  6.069 113.095   2301
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.16 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.75 %
    Favored  : 92.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.19), residues: 1965
  helix:  2.03 (0.21), residues: 617
  sheet:  1.23 (0.28), residues: 341
  loop : -0.42 (0.19), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 755 
 HIS   0.005   0.001   HIS A 450 
 PHE   0.016   0.001   PHE B 476 
 TYR   0.016   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00594 (    6)
  link_BETA1-4         : angle       2.02019 (   18)
  hydrogen bonds       : bond        0.04633 (  707)
  hydrogen bonds       : angle       4.55841 ( 2103)
  covalent geometry    : bond        0.00652 (16207)
  covalent geometry    : angle       0.54123 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.762 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9032 (tt0)
REVERT: B  116 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9012 (mppt)
  outliers start: 11
  outliers final: 6
  residues processed: 73
  average time/residue: 1.5411
  time to fit residues: 124.3712
Evaluate side-chains
  73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 1.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain B residue   73 PHE
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 177 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 44 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.059551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2381 r_free = 0.2381 target = 0.042646 restraints weight = 32885.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2428 rms_B_bonded: 2.89
r_work: 0.2272 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2143 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2157 r_free = 0.2157    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2157 r_free = 0.2157    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  16213  Z= 0.108
  Angle     :  0.474   8.823  21953  Z= 0.254
  Chirality :  0.041   0.148   2425
  Planarity :  0.003   0.046   2826
  Dihedral  :  5.825 110.668   2301
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.95 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.87 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.19), residues: 1965
  helix:  2.12 (0.21), residues: 620
  sheet:  1.38 (0.28), residues: 337
  loop : -0.34 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.012   0.001   PHE A 927 
 TYR   0.010   0.001   TYR B 236 
 ARG   0.008   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00567 (    6)
  link_BETA1-4         : angle       1.79216 (   18)
  hydrogen bonds       : bond        0.03590 (  707)
  hydrogen bonds       : angle       4.40379 ( 2103)
  covalent geometry    : bond        0.00244 (16207)
  covalent geometry    : angle       0.47097 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.785 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8987 (tt0)
REVERT: B  116 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.9010 (mppt)
  outliers start: 11
  outliers final: 5
  residues processed: 75
  average time/residue: 1.5526
  time to fit residues: 128.9354
Evaluate side-chains
  73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 1.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 189 optimal weight:    2.9990
   chunk 144 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 154 optimal weight:    0.7980
   chunk 55 optimal weight:    0.2980
   chunk 93 optimal weight:    6.9990
   chunk 142 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.059754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2378 r_free = 0.2378 target = 0.042519 restraints weight = 33124.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2424 rms_B_bonded: 2.92
r_work: 0.2274 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2147 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2159 r_free = 0.2159    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2159 r_free = 0.2159    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8943
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16213  Z= 0.120
  Angle     :  0.477   8.634  21953  Z= 0.255
  Chirality :  0.041   0.148   2425
  Planarity :  0.003   0.045   2826
  Dihedral  :  5.691 110.530   2299
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.90 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  7.22 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.19), residues: 1965
  helix:  2.14 (0.21), residues: 623
  sheet:  1.41 (0.28), residues: 336
  loop : -0.31 (0.19), residues: 1006

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.011   0.001   PHE A 927 
 TYR   0.010   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00560 (    6)
  link_BETA1-4         : angle       1.77858 (   18)
  hydrogen bonds       : bond        0.03645 (  707)
  hydrogen bonds       : angle       4.35496 ( 2103)
  covalent geometry    : bond        0.00276 (16207)
  covalent geometry    : angle       0.47411 (21935)

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

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

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3930 Ramachandran restraints generated.
    1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.983 
Fit side-chains
REVERT: B   96 GLN cc_start: 0.8552 (mt0) cc_final: 0.8188 (mt0)
REVERT: B  116 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.9006 (mppt)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 1.6149
  time to fit residues: 128.4719
Evaluate side-chains
  72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 146 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 154 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.059494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2372 r_free = 0.2372 target = 0.042285 restraints weight = 32971.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2379 rms_B_bonded: 2.91
r_work: 0.2225 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2095 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2149 r_free = 0.2149    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2149 r_free = 0.2149    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  16213  Z= 0.138
  Angle     :  0.482   8.128  21953  Z= 0.258
  Chirality :  0.041   0.147   2425
  Planarity :  0.003   0.043   2826
  Dihedral  :  5.697 110.347   2299
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.10 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  7.16 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.19), residues: 1965
  helix:  2.16 (0.21), residues: 621
  sheet:  1.36 (0.28), residues: 338
  loop : -0.32 (0.19), residues: 1006

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 
 PHE   0.011   0.001   PHE A 927 
 TYR   0.011   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 909 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00549 (    6)
  link_BETA1-4         : angle       1.79125 (   18)
  hydrogen bonds       : bond        0.03722 (  707)
  hydrogen bonds       : angle       4.35508 ( 2103)
  covalent geometry    : bond        0.00322 (16207)
  covalent geometry    : angle       0.47958 (21935)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11444.53 seconds
wall clock time: 198 minutes 33.59 seconds (11913.59 seconds total)