Starting phenix.real_space_refine
on Tue Nov 18 17:50:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yaq_39104/11_2025/8yaq_39104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yaq_39104/11_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yaq_39104/11_2025/8yaq_39104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yaq_39104/11_2025/8yaq_39104.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yaq_39104/11_2025/8yaq_39104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yaq_39104/11_2025/8yaq_39104.map"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 3.77, per 1000 atoms: 0.24
  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: 1.44
  Conformation dependent library (CDL) restraints added in 758.6 milliseconds
  

  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: 0.81
  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: 3.77

  Time building geometry restraints manager: 1.88 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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.250
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.390
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.000   ARG B 909 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.010   0.001   TRP A 755 
 HIS   0.003   0.000   HIS B 450 

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

*********************** 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  : 0.677 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.8362
  time to fit residues: 62.2237
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  : 0.652 
-------------------------------------------------------------------------------
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 98 optimal weight:    5.9990
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0050
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.060187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2390 r_free = 0.2390 target = 0.042971 restraints weight = 32817.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2432 rms_B_bonded: 2.91
r_work: 0.2281 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2156 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2156
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2169 r_free = 0.2169    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 = 0.2169 r_free = 0.2169    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
moved from start:          0.0544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16213  Z= 0.130
  Angle     :  0.470   7.100  21953  Z= 0.255
  Chirality :  0.041   0.143   2425
  Planarity :  0.003   0.046   2826
  Dihedral  :  6.184 115.157   2304
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.95 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  5.87 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.19), residues: 1965
  helix:  1.98 (0.21), residues: 628
  sheet:  1.32 (0.29), residues: 338
  loop : -0.26 (0.19), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 909 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.011   0.001   TRP A 755 
 HIS   0.002   0.000   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (16207)
  covalent geometry    : angle       0.46733 (21935)
  hydrogen bonds       : bond        0.04205 (  707)
  hydrogen bonds       : angle       4.73395 ( 2103)
  link_BETA1-4         : bond        0.00428 (    6)
  link_BETA1-4         : angle       1.83835 (   18)

*********************** 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
  79 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.639 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 77
  average time/residue: 0.7625
  time to fit residues: 64.6316
Evaluate side-chains
  68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 125 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 143 optimal weight:    2.9990
   chunk 140 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 175 optimal weight:    4.9990
   chunk 178 optimal weight:    0.7980
   chunk 184 optimal weight:    0.9990
   chunk 138 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.2762 r_free = 0.2762 target = 0.059490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2369 r_free = 0.2369 target = 0.042190 restraints weight = 33396.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.2376 rms_B_bonded: 2.93
r_work: 0.2220 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2091 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2145 r_free = 0.2145    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2145 r_free = 0.2145    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.0695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16213  Z= 0.153
  Angle     :  0.471   7.426  21953  Z= 0.254
  Chirality :  0.041   0.138   2425
  Planarity :  0.003   0.043   2826
  Dihedral  :  5.942 114.151   2301
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.00 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  5.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.19), residues: 1965
  helix:  2.07 (0.21), residues: 628
  sheet:  1.38 (0.29), residues: 338
  loop : -0.30 (0.19), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 909 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.014   0.001   TRP A 755 
 HIS   0.003   0.001   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (16207)
  covalent geometry    : angle       0.46878 (21935)
  hydrogen bonds       : bond        0.04079 (  707)
  hydrogen bonds       : angle       4.54708 ( 2103)
  link_BETA1-4         : bond        0.00520 (    6)
  link_BETA1-4         : angle       1.82550 (   18)

*********************** 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
  77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  689 GLN cc_start: 0.8739 (pp30) cc_final: 0.8455 (tm-30)
REVERT: A  692 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8302 (tm-30)
REVERT: A  949 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (mtm)
  outliers start: 12
  outliers final: 4
  residues processed: 74
  average time/residue: 0.8602
  time to fit residues: 69.9124
Evaluate side-chains
  69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  949 MET
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 41 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 177 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 179 optimal weight:    2.9990
   chunk 161 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.059408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2369 r_free = 0.2369 target = 0.042180 restraints weight = 32935.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2414 rms_B_bonded: 2.91
r_work: 0.2262 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2136 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2148 r_free = 0.2148    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 = 0.2148 r_free = 0.2148    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16213  Z= 0.152
  Angle     :  0.467   7.628  21953  Z= 0.252
  Chirality :  0.041   0.137   2425
  Planarity :  0.003   0.052   2826
  Dihedral  :  5.896 113.191   2301
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.95 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.19), residues: 1965
  helix:  2.10 (0.21), residues: 627
  sheet:  1.37 (0.29), residues: 338
  loop : -0.31 (0.19), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 909 
 TYR   0.012   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.015   0.001   TRP B 755 
 HIS   0.003   0.001   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (16207)
  covalent geometry    : angle       0.46411 (21935)
  hydrogen bonds       : bond        0.03933 (  707)
  hydrogen bonds       : angle       4.46916 ( 2103)
  link_BETA1-4         : bond        0.00521 (    6)
  link_BETA1-4         : angle       1.83766 (   18)

*********************** 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: 8
    poor density    : 64
  time to evaluate  : 0.605 
Fit side-chains
REVERT: B  798 ASP cc_start: 0.8933 (t70) cc_final: 0.8684 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 70
  average time/residue: 0.7887
  time to fit residues: 60.6252
Evaluate side-chains
  68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 178 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0040
   chunk 41 optimal weight:    0.7980
   chunk 176 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 195 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 169 optimal weight:    4.9990
   chunk 188 optimal weight:    3.9990
   chunk 165 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.9194

-------------------------------------------------------------------------------
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 = 0.2774 r_free = 0.2774 target = 0.060002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2389 r_free = 0.2389 target = 0.042994 restraints weight = 32909.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.2434 rms_B_bonded: 2.89
r_work: 0.2284 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2157 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2168 r_free = 0.2168    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 = 0.2168 r_free = 0.2168    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.0842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16213  Z= 0.117
  Angle     :  0.452   7.817  21953  Z= 0.244
  Chirality :  0.041   0.135   2425
  Planarity :  0.003   0.048   2826
  Dihedral  :  5.799 112.174   2301
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.90 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.75 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.19), residues: 1965
  helix:  2.09 (0.21), residues: 630
  sheet:  1.41 (0.29), residues: 334
  loop : -0.27 (0.19), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 909 
 TYR   0.011   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.014   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (16207)
  covalent geometry    : angle       0.44928 (21935)
  hydrogen bonds       : bond        0.03645 (  707)
  hydrogen bonds       : angle       4.39819 ( 2103)
  link_BETA1-4         : bond        0.00549 (    6)
  link_BETA1-4         : angle       1.76506 (   18)

*********************** 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
  72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  689 GLN cc_start: 0.8684 (pp30) cc_final: 0.8402 (tm-30)
REVERT: B  798 ASP cc_start: 0.8917 (t70) cc_final: 0.8676 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 71
  average time/residue: 0.7873
  time to fit residues: 61.6395
Evaluate side-chains
  68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  619 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0670
   chunk 67 optimal weight:    2.9990
   chunk 170 optimal weight:    4.9990
   chunk 186 optimal weight:    5.9990
   chunk 120 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 145 optimal weight:    2.9990
   chunk 181 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    3.0126

-------------------------------------------------------------------------------
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 = 0.2711 r_free = 0.2711 target = 0.057082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2306 r_free = 0.2306 target = 0.039774 restraints weight = 33535.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.2351 rms_B_bonded: 2.90
r_work: 0.2198 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2072 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2086 r_free = 0.2086    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 = 0.2086 r_free = 0.2086    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8989
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  16213  Z= 0.320
  Angle     :  0.560   7.636  21953  Z= 0.300
  Chirality :  0.045   0.154   2425
  Planarity :  0.004   0.047   2826
  Dihedral  :  6.136 114.104   2301
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.21 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.81 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.19), residues: 1965
  helix:  2.01 (0.21), residues: 617
  sheet:  1.27 (0.28), residues: 341
  loop : -0.41 (0.19), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 909 
 TYR   0.017   0.001   TYR A 236 
 PHE   0.017   0.001   PHE B 476 
 TRP   0.016   0.002   TRP B 755 
 HIS   0.005   0.001   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00760 (16207)
  covalent geometry    : angle       0.55678 (21935)
  hydrogen bonds       : bond        0.04870 (  707)
  hydrogen bonds       : angle       4.60922 ( 2103)
  link_BETA1-4         : bond        0.00592 (    6)
  link_BETA1-4         : angle       2.08046 (   18)

*********************** 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
  73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  154 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8861 (mmmt)
REVERT: A  689 GLN cc_start: 0.8844 (pp30) cc_final: 0.8539 (tm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 0.7894
  time to fit residues: 62.3083
Evaluate side-chains
  70 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LYS
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  619 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 156 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 168 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 180 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.2767 r_free = 0.2767 target = 0.059785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2378 r_free = 0.2378 target = 0.042570 restraints weight = 32807.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2424 rms_B_bonded: 2.90
r_work: 0.2274 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2147 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2158 r_free = 0.2158    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 = 0.2158 r_free = 0.2158    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.0954

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= 0.112
  Angle     :  0.463   8.106  21953  Z= 0.251
  Chirality :  0.041   0.176   2425
  Planarity :  0.003   0.048   2826
  Dihedral  :  5.852 111.108   2301
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.95 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.58 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.19), residues: 1965
  helix:  2.10 (0.21), residues: 622
  sheet:  1.39 (0.29), residues: 337
  loop : -0.30 (0.19), residues: 1006

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 909 
 TYR   0.011   0.001   TYR A 236 
 PHE   0.012   0.001   PHE A 927 
 TRP   0.015   0.001   TRP A 755 
 HIS   0.002   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (16207)
  covalent geometry    : angle       0.46026 (21935)
  hydrogen bonds       : bond        0.03627 (  707)
  hydrogen bonds       : angle       4.43679 ( 2103)
  link_BETA1-4         : bond        0.00636 (    6)
  link_BETA1-4         : angle       1.81708 (   18)

*********************** 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
  81 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8989 (tt0)
REVERT: B  116 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9013 (mppt)
  outliers start: 15
  outliers final: 5
  residues processed: 78
  average time/residue: 0.7945
  time to fit residues: 68.6908
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  : 0.675 
-------------------------------------------------------------------------------
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  529 TRP
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 65 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 144 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 155 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 181 optimal weight:    0.0870
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.2787 r_free = 0.2787 target = 0.060836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2403 r_free = 0.2403 target = 0.043623 restraints weight = 32891.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2445 rms_B_bonded: 2.92
r_work: 0.2296 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2170 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2183 r_free = 0.2183    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2183 r_free = 0.2183    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8928
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  16213  Z= 0.100
  Angle     :  0.460   8.183  21953  Z= 0.246
  Chirality :  0.040   0.152   2425
  Planarity :  0.003   0.043   2826
  Dihedral  :  5.699 110.278   2301
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.90 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.75 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.19), residues: 1965
  helix:  2.10 (0.21), residues: 631
  sheet:  1.34 (0.28), residues: 335
  loop : -0.26 (0.19), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 909 
 TYR   0.010   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.015   0.001   TRP A 755 
 HIS   0.002   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (16207)
  covalent geometry    : angle       0.45735 (21935)
  hydrogen bonds       : bond        0.03421 (  707)
  hydrogen bonds       : angle       4.30996 ( 2103)
  link_BETA1-4         : bond        0.00607 (    6)
  link_BETA1-4         : angle       1.71888 (   18)

*********************** 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
  78 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8948 (tt0)
REVERT: B  116 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.9009 (mppt)
REVERT: B  484 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8138 (mpp)
  outliers start: 12
  outliers final: 2
  residues processed: 77
  average time/residue: 0.8073
  time to fit residues: 68.1440
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  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  864 GLN
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  484 MET
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 148 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 174 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0870
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.2791 r_free = 0.2791 target = 0.061038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2408 r_free = 0.2408 target = 0.043798 restraints weight = 32841.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2414 rms_B_bonded: 2.92
r_work: 0.2261 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2131 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2184 r_free = 0.2184    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2184 r_free = 0.2184    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.1021

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     :  0.459   8.162  21953  Z= 0.246
  Chirality :  0.040   0.155   2425
  Planarity :  0.003   0.044   2826
  Dihedral  :  5.575 109.834   2299
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.75 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  7.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.19), residues: 1965
  helix:  2.15 (0.21), residues: 631
  sheet:  1.34 (0.28), residues: 336
  loop : -0.22 (0.19), residues: 998

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 909 
 TYR   0.009   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.015   0.001   TRP B 755 
 HIS   0.002   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (16207)
  covalent geometry    : angle       0.45631 (21935)
  hydrogen bonds       : bond        0.03368 (  707)
  hydrogen bonds       : angle       4.27090 ( 2103)
  link_BETA1-4         : bond        0.00541 (    6)
  link_BETA1-4         : angle       1.68957 (   18)

*********************** 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
  73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8930 (tt0)
REVERT: B  116 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.9022 (mppt)
REVERT: B  339 ILE cc_start: 0.8841 (mt) cc_final: 0.8584 (tt)
REVERT: B  484 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8132 (mpp)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 0.8450
  time to fit residues: 66.6706
Evaluate side-chains
  72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  484 MET
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 168 optimal weight:    5.9990
   chunk 174 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    0.3980
   chunk 162 optimal weight:    0.9980
   chunk 136 optimal weight:    0.0770
   chunk 187 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 180 optimal weight:    0.7980
   chunk 188 optimal weight:    2.9990
   overall best weight:    0.8540

-------------------------------------------------------------------------------
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 = 0.2786 r_free = 0.2786 target = 0.060581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2401 r_free = 0.2401 target = 0.043370 restraints weight = 32919.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.2445 rms_B_bonded: 2.92
r_work: 0.2296 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2170 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2184 r_free = 0.2184    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2184 r_free = 0.2184    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16213  Z= 0.114
  Angle     :  0.468   8.284  21953  Z= 0.250
  Chirality :  0.040   0.151   2425
  Planarity :  0.003   0.041   2826
  Dihedral  :  5.568 109.609   2299
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.90 %
    Favored  : 97.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.19), residues: 1965
  helix:  2.19 (0.21), residues: 625
  sheet:  1.37 (0.28), residues: 335
  loop : -0.22 (0.19), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 909 
 TYR   0.010   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.015   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (16207)
  covalent geometry    : angle       0.46520 (21935)
  hydrogen bonds       : bond        0.03452 (  707)
  hydrogen bonds       : angle       4.26507 ( 2103)
  link_BETA1-4         : bond        0.00549 (    6)
  link_BETA1-4         : angle       1.70865 (   18)

********************** 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
  74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  864 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8930 (tt0)
REVERT: B   96 GLN cc_start: 0.8606 (mt0) cc_final: 0.8351 (mt0)
REVERT: B  116 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9023 (mppt)
REVERT: B  339 ILE cc_start: 0.8851 (mt) cc_final: 0.8591 (tt)
REVERT: B  484 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8153 (mpp)
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.8231
  time to fit residues: 65.7887
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  : 0.665 
-------------------------------------------------------------------------------
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  484 MET
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  850 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 175 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 190 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 99 optimal weight:    0.0670
   chunk 68 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0370
   overall best weight:    1.0200

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

Flipped N/Q/H residues before XYZ refinement:
B 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.060145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2390 r_free = 0.2390 target = 0.042915 restraints weight = 32697.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.2397 rms_B_bonded: 2.91
r_work: 0.2243 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2114 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2167 r_free = 0.2167    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 = 0.2167 r_free = 0.2167    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8931
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16213  Z= 0.128
  Angle     :  0.477   8.430  21953  Z= 0.255
  Chirality :  0.041   0.153   2425
  Planarity :  0.003   0.042   2826
  Dihedral  :  5.592 109.517   2299
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.00 %
    Favored  : 96.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.19), residues: 1965
  helix:  2.19 (0.21), residues: 623
  sheet:  1.39 (0.28), residues: 337
  loop : -0.27 (0.19), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 909 
 TYR   0.011   0.001   TYR A 236 
 PHE   0.011   0.001   PHE A 927 
 TRP   0.015   0.001   TRP B 755 
 HIS   0.003   0.000   HIS B 450 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (16207)
  covalent geometry    : angle       0.47469 (21935)
  hydrogen bonds       : bond        0.03571 (  707)
  hydrogen bonds       : angle       4.28139 ( 2103)
  link_BETA1-4         : bond        0.00540 (    6)
  link_BETA1-4         : angle       1.74116 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6145.02 seconds
wall clock time: 105 minutes 34.98 seconds (6334.98 seconds total)