Starting phenix.real_space_refine
on Mon Jul 28 23:50:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x5f_38068/07_2025/8x5f_38068_neut_trim.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.084
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
     P      26      5.49       5
     S      40      5.16       5
     C    7212      2.51       5
     N    1669      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10843
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 5024
          Classifications: {'peptide': 616}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "B"
      Number of atoms: 5020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 5020
          Classifications: {'peptide': 616}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "A"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 399
          Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15}
          Classifications: {'undetermined': 21}
          Link IDs: {None: 20}
          Unresolved non-hydrogen bonds: 465
          Unresolved non-hydrogen angles: 564
          Unresolved non-hydrogen dihedrals: 416
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 10, 'POV:plan-1': 11}
          Unresolved non-hydrogen planarities: 91
    Chain: "B"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 396
          Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15}
          Classifications: {'undetermined': 21}
          Link IDs: {None: 20}
          Unresolved non-hydrogen bonds: 468
          Unresolved non-hydrogen angles: 567
          Unresolved non-hydrogen dihedrals: 419
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 9, 'POV:plan-1': 11}
          Unresolved non-hydrogen planarities: 89
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.05, per 1000 atoms: 0.65
  Number of scatterers: 10843
  At special positions: 0
  Unit cell: (111.35, 128.35, 102, 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)
     S      40     16.00
     P      26     15.00
     O    1896      8.00
     N    1669      7.00
     C    7212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      79.5% alpha, 0.0% 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 2 through 11
      removed outlier: 3.775A  pdb=" N   HIS A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 5.481A  pdb=" N   LYS A  17 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR A  19 " --> pdb=" O   ARG A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 35
      removed outlier: 3.514A  pdb=" N   PHE A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 50 through 52
      No H-bonds generated for 'chain 'A' and resid 50 through 52'
    Processing helix  chain 'A' and resid 53 through 103
      removed outlier: 3.525A  pdb=" N   LYS A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A  93 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU A 100 " --> pdb=" O   ASP A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 168
    Processing helix  chain 'A' and resid 170 through 179
      removed outlier: 3.633A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
      removed outlier: 3.728A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
      removed outlier: 3.572A  pdb=" N   ALA A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 259
      removed outlier: 3.564A  pdb=" N   ARG A 236 " --> pdb=" O   TRP A 232 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.935A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.535A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 336
      removed outlier: 3.825A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
    Processing helix  chain 'A' and resid 367 through 382
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.568A  pdb=" N   PHE A 394 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.105A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.515A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 475 through 502
      removed outlier: 4.493A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ARG A 502 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.647A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 580
      removed outlier: 3.816A  pdb=" N   TYR A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR A 574 " --> pdb=" O   ARG A 570 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 577 " --> pdb=" O   TRP A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 620
      removed outlier: 3.658A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A 595 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 3.748A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ASN A 618 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A 619 " --> pdb=" O   GLU A 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.775A  pdb=" N   HIS B   6 " --> pdb=" O   LYS B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 19
      removed outlier: 5.221A  pdb=" N   LYS B  17 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 35
      removed outlier: 3.514A  pdb=" N   PHE B  25 " --> pdb=" O   GLN B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 51
      removed outlier: 3.732A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 103
      removed outlier: 3.525A  pdb=" N   LYS B  57 " --> pdb=" O   LYS B  53 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER B  93 " --> pdb=" O   ASN B  89 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER B  94 " --> pdb=" O   GLU B  90 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU B 100 " --> pdb=" O   ASP B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 168
      removed outlier: 3.513A  pdb=" N   ARG B 126 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   ASN B 127 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS B 129 " --> pdb=" O   HIS B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 179
      removed outlier: 3.632A  pdb=" N   ASP B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 189 through 206
      removed outlier: 3.728A  pdb=" N   GLN B 193 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 219
      removed outlier: 3.572A  pdb=" N   ALA B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 259
      removed outlier: 3.565A  pdb=" N   ARG B 236 " --> pdb=" O   TRP B 232 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.935A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE B 287 " --> pdb=" O   PHE B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
      removed outlier: 3.535A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 336
      removed outlier: 3.825A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 367 through 382
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.568A  pdb=" N   PHE B 394 " --> pdb=" O   GLY B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.104A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 475 through 502
      removed outlier: 4.494A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE B 488 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG B 502 " --> pdb=" O   THR B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.647A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 580
      removed outlier: 3.816A  pdb=" N   TYR B 560 " --> pdb=" O   LYS B 556 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE B 575 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE B 577 " --> pdb=" O   TRP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 620
      removed outlier: 3.658A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.748A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ASN B 618 " --> pdb=" O   ASN B 614 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN B 619 " --> pdb=" O   GLU B 615 " (cutoff:3.500A)

    692 hydrogen bonds defined for protein.
    2043 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 3.21 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1572
        1.31 -     1.43: 3167
        1.43 -     1.56: 6253
        1.56 -     1.69: 47
        1.69 -     1.82: 56
  Bond restraints: 11095
  Sorted by residual:
  bond pdb=" C31 POV A 713 "
       pdb=" O32 POV A 713 "
    ideal  model  delta    sigma   weight residual
    1.206  1.402 -0.196 2.00e-02 2.50e+03 9.56e+01
  bond pdb=" C31 POV A 711 "
       pdb=" O32 POV A 711 "
    ideal  model  delta    sigma   weight residual
    1.206  1.401 -0.195 2.00e-02 2.50e+03 9.54e+01
  bond pdb=" C31 POV A 717 "
       pdb=" O32 POV A 717 "
    ideal  model  delta    sigma   weight residual
    1.206  1.400 -0.194 2.00e-02 2.50e+03 9.44e+01
  bond pdb=" C31 POV B1110 "
       pdb=" O32 POV B1110 "
    ideal  model  delta    sigma   weight residual
    1.206  1.399 -0.193 2.00e-02 2.50e+03 9.35e+01
  bond pdb=" C31 POV B1112 "
       pdb=" O32 POV B1112 "
    ideal  model  delta    sigma   weight residual
    1.206  1.398 -0.192 2.00e-02 2.50e+03 9.24e+01
  ... (remaining 11090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 14523
        3.84 -     7.68: 346
        7.68 -    11.52: 52
       11.52 -    15.36: 2
       15.36 -    19.20: 4
  Bond angle restraints: 14927
  Sorted by residual:
  angle pdb=" C28 POV A 718 "
        pdb=" C29 POV A 718 "
        pdb="C210 POV A 718 "
      ideal   model   delta    sigma   weight residual
     127.79  108.59   19.20 3.00e+00 1.11e-01 4.10e+01
  angle pdb=" C29 POV A 718 "
        pdb="C210 POV A 718 "
        pdb="C211 POV A 718 "
      ideal   model   delta    sigma   weight residual
     127.67  108.56   19.11 3.00e+00 1.11e-01 4.06e+01
  angle pdb=" C28 POV B1107 "
        pdb=" C29 POV B1107 "
        pdb="C210 POV B1107 "
      ideal   model   delta    sigma   weight residual
     127.79  108.81   18.98 3.00e+00 1.11e-01 4.00e+01
  angle pdb=" N   SER A  93 "
        pdb=" CA  SER A  93 "
        pdb=" C   SER A  93 "
      ideal   model   delta    sigma   weight residual
     111.28  118.12   -6.84 1.09e+00 8.42e-01 3.94e+01
  angle pdb=" N   SER B  93 "
        pdb=" CA  SER B  93 "
        pdb=" C   SER B  93 "
      ideal   model   delta    sigma   weight residual
     111.28  118.11   -6.83 1.09e+00 8.42e-01 3.93e+01
  ... (remaining 14922 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.27: 6376
       31.27 -    62.53: 284
       62.53 -    93.80: 30
       93.80 -   125.07: 5
      125.07 -   156.34: 4
  Dihedral angle restraints: 6699
    sinusoidal: 3053
      harmonic: 3646
  Sorted by residual:
  dihedral pdb=" CB  CYS B 415 "
           pdb=" SG  CYS B 415 "
           pdb=" SG  CYS B 440 "
           pdb=" CB  CYS B 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.35  -70.35     1      1.00e+01 1.00e-02 6.37e+01
  dihedral pdb=" C   VAL B 626 "
           pdb=" N   VAL B 626 "
           pdb=" CA  VAL B 626 "
           pdb=" CB  VAL B 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.65   13.65     0      2.50e+00 1.60e-01 2.98e+01
  dihedral pdb=" N   VAL B 626 "
           pdb=" C   VAL B 626 "
           pdb=" CA  VAL B 626 "
           pdb=" CB  VAL B 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.07  -11.67     0      2.50e+00 1.60e-01 2.18e+01
  ... (remaining 6696 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1383
       0.076 -    0.151: 152
       0.151 -    0.227: 22
       0.227 -    0.302: 12
       0.302 -    0.378: 3
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  THR B 582 "
            pdb=" N   THR B 582 "
            pdb=" C   THR B 582 "
            pdb=" CB  THR B 582 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.15    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  VAL B 626 "
            pdb=" N   VAL B 626 "
            pdb=" C   VAL B 626 "
            pdb=" CB  VAL B 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.07    0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CA  HIS B 441 "
            pdb=" N   HIS B 441 "
            pdb=" C   HIS B 441 "
            pdb=" CB  HIS B 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 1569 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV B1107 "   -0.152 2.00e-02 2.50e+03   2.51e-01 6.30e+02
        pdb=" C29 POV B1107 "    0.321 2.00e-02 2.50e+03
        pdb="C210 POV B1107 "   -0.321 2.00e-02 2.50e+03
        pdb="C211 POV B1107 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A 718 "    0.141 2.00e-02 2.50e+03   2.20e-01 4.82e+02
        pdb=" C29 POV A 718 "   -0.277 2.00e-02 2.50e+03
        pdb="C210 POV A 718 "    0.277 2.00e-02 2.50e+03
        pdb="C211 POV A 718 "   -0.141 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  35 "   -0.019 2.00e-02 2.50e+03   3.72e-02 1.39e+01
        pdb=" C   GLN B  35 "    0.064 2.00e-02 2.50e+03
        pdb=" O   GLN B  35 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ALA B  36 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 222
        2.70 -     3.25: 10150
        3.25 -     3.80: 16045
        3.80 -     4.35: 20221
        4.35 -     4.90: 35841
  Nonbonded interactions: 82479
  Sorted by model distance:
  nonbonded pdb=" N   GLN A 227 "
            pdb=" OE1 GLN A 227 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" OG  SER B 497 "
            pdb=" O   THR B 582 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ARG B 217 "
            pdb=" NH1 ARG B 308 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ARG A 217 "
            pdb=" NH1 ARG A 308 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" OG  SER A 497 "
            pdb=" O   THR A 582 "
     model   vdw
     2.305 3.040
  ... (remaining 82474 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 441 or (resid 442 through 443 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 444 through 635 or resid 702 thr \ 
ough 704 or resid 707 or (resid 708 and (name C31 or name C32 or name C33 or nam \ 
e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O31 or \ 
 name O32 or name C310 or name C311)) or resid 710 or resid 712 through 716 or ( \ 
resid 719 and (name C31 or name C32 or name C33 or name C34 or name C35 or name  \ 
C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 or  \ 
name C311 or name C312 or name C313 or name C314)) or resid 720 or (resid 721 an \ 
d (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 
5 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or name \ 
 C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or  \ 
name O31 or name O32 or name P ))))
  selection = (chain 'B' and (resid 1 through 635 or resid 1102 through 1104 or resid 1107 or  \ 
(resid 1108 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ 
e C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 o \ 
r name C311)) or resid 1110 or resid 1112 or (resid 1113 and (name C31 or name C \ 
32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ 
me C39 or name O31 or name O32 or name C310 or name C311 or name C312)) or resid \ 
 1114 through 1116 or resid 1119 or (resid 1120 and (name N or name C1 or name C \ 
11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or nam \ 
e C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ 
 name C3 or name C31 or name C32 or name C33 or name O11 or name O12 or name O13 \ 
 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (re \ 
sid 1121 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 \ 
 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name  \ 
C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ 
ame O22 or name O31 or name O32 or name P ))))
}

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=0.45 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:             1.840
  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:          0.390
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     25.940
  Find NCS groups from input model:        0.460
  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:11.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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      :  0.011   0.196  11097  Z= 0.548
  Angle     :  1.270  19.201  14931  Z= 0.591
  Chirality :  0.057   0.378   1572
  Planarity :  0.009   0.251   1794
  Dihedral  : 17.296 156.336   4329
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.77 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  2.12 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.24), residues: 1220
  helix:  2.14 (0.17), residues: 902
  sheet:  None (None), residues: 0
  loop : -1.49 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 607 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.019   0.002   PHE B 571 
 TYR   0.035   0.002   TYR B 524 
 ARG   0.004   0.000   ARG B 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16941 (  692)
  hydrogen bonds       : angle       5.03569 ( 2043)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       1.86591 (    4)
  covalent geometry    : bond        0.01054 (11095)
  covalent geometry    : angle       1.26970 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 175
  time to evaluate  : 1.157 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 181
  average time/residue: 1.5029
  time to fit residues: 292.5122
Evaluate side-chains
  97 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
A 499 HIS
B 127 ASN
B 452 GLN
B 499 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.170103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.115396 restraints weight = 12447.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.37
r_work: 0.3250 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11097  Z= 0.177
  Angle     :  0.574   7.133  14931  Z= 0.307
  Chirality :  0.040   0.141   1572
  Planarity :  0.005   0.045   1794
  Dihedral  : 15.405 139.148   2045
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.03 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 11.16 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.24), residues: 1220
  helix:  2.41 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -1.45 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 607 
 HIS   0.010   0.002   HIS B 441 
 PHE   0.015   0.002   PHE B 517 
 TYR   0.027   0.002   TYR B 524 
 ARG   0.006   0.001   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07228 (  692)
  hydrogen bonds       : angle       3.78915 ( 2043)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       0.91407 (    4)
  covalent geometry    : bond        0.00398 (11095)
  covalent geometry    : angle       0.57354 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 3.275 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7960 (mtpp)
REVERT: A  529 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7811 (m-30)
REVERT: A  540 ASN cc_start: 0.8397 (p0) cc_final: 0.8151 (p0)
REVERT: B   64 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7884 (mtpp)
REVERT: B  468 ARG cc_start: 0.7487 (tmt170) cc_final: 0.7239 (tmt170)
REVERT: B  540 ASN cc_start: 0.8433 (p0) cc_final: 0.8191 (p0)
  outliers start: 33
  outliers final: 12
  residues processed: 121
  average time/residue: 1.6241
  time to fit residues: 210.8037
Evaluate side-chains
  102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  468 ARG
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0770
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.6144

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 499 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.167478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112683 restraints weight = 12589.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.36
r_work: 0.3208 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11097  Z= 0.173
  Angle     :  0.533   5.786  14931  Z= 0.287
  Chirality :  0.039   0.142   1572
  Planarity :  0.005   0.041   1794
  Dihedral  : 14.278 122.391   2044
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.03 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 12.90 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.25), residues: 1220
  helix:  2.49 (0.17), residues: 920
  sheet:  None (None), residues: 0
  loop : -1.43 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 607 
 HIS   0.008   0.001   HIS B 441 
 PHE   0.017   0.002   PHE A 571 
 TYR   0.020   0.002   TYR A 524 
 ARG   0.006   0.001   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07119 (  692)
  hydrogen bonds       : angle       3.61421 ( 2043)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       0.96653 (    4)
  covalent geometry    : bond        0.00396 (11095)
  covalent geometry    : angle       0.53318 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 100
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7846 (mtpp)
REVERT: A  159 ILE cc_start: 0.7703 (tp) cc_final: 0.7487 (tp)
REVERT: A  167 LEU cc_start: 0.6170 (mp) cc_final: 0.5854 (tt)
REVERT: A  211 ARG cc_start: 0.6577 (ttt90) cc_final: 0.6361 (ttt180)
REVERT: A  309 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7684 (p)
REVERT: A  529 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (t0)
REVERT: A  579 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6662 (mp)
REVERT: B   64 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7834 (mtpp)
REVERT: B  159 ILE cc_start: 0.7711 (tp) cc_final: 0.7476 (tp)
REVERT: B  167 LEU cc_start: 0.6131 (mp) cc_final: 0.5848 (tt)
REVERT: B  211 ARG cc_start: 0.6582 (ttt90) cc_final: 0.6377 (ttt180)
REVERT: B  529 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7863 (t0)
REVERT: B  540 ASN cc_start: 0.8406 (p0) cc_final: 0.8109 (p0)
  outliers start: 31
  outliers final: 13
  residues processed: 114
  average time/residue: 1.2131
  time to fit residues: 149.6976
Evaluate side-chains
  108 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
B  21 GLN
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.165112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.109995 restraints weight = 12607.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.39
r_work: 0.3172 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  11097  Z= 0.239
  Angle     :  0.597   6.612  14931  Z= 0.320
  Chirality :  0.042   0.145   1572
  Planarity :  0.005   0.039   1794
  Dihedral  : 14.760 122.387   2042
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.20 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 13.86 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.25), residues: 1220
  helix:  2.27 (0.17), residues: 914
  sheet:  None (None), residues: 0
  loop : -1.59 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 607 
 HIS   0.008   0.002   HIS B 441 
 PHE   0.020   0.002   PHE B 517 
 TYR   0.019   0.002   TYR A 524 
 ARG   0.007   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08265 (  692)
  hydrogen bonds       : angle       3.80093 ( 2043)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.82735 (    4)
  covalent geometry    : bond        0.00578 (11095)
  covalent geometry    : angle       0.59713 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 97
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A  167 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6211 (tt)
REVERT: A  309 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7917 (p)
REVERT: A  529 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8055 (t0)
REVERT: A  540 ASN cc_start: 0.8455 (p0) cc_final: 0.8255 (p0)
REVERT: B  167 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6325 (tt)
REVERT: B  211 ARG cc_start: 0.6671 (ttt90) cc_final: 0.6448 (ttt180)
REVERT: B  529 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8064 (t0)
REVERT: B  540 ASN cc_start: 0.8468 (p0) cc_final: 0.8194 (p0)
  outliers start: 42
  outliers final: 22
  residues processed: 119
  average time/residue: 1.2809
  time to fit residues: 164.9018
Evaluate side-chains
  115 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 120 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 110 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 163 HIS
A 192 ASN
B 163 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.167980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123731 restraints weight = 12677.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.79
r_work: 0.3243 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11097  Z= 0.173
  Angle     :  0.518   7.456  14931  Z= 0.280
  Chirality :  0.038   0.129   1572
  Planarity :  0.004   0.038   1794
  Dihedral  : 14.137 113.869   2042
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.70 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.11 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.25), residues: 1220
  helix:  2.46 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -1.50 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 607 
 HIS   0.008   0.001   HIS B 441 
 PHE   0.015   0.001   PHE B 517 
 TYR   0.023   0.002   TYR B 496 
 ARG   0.007   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07092 (  692)
  hydrogen bonds       : angle       3.62274 ( 2043)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.71921 (    4)
  covalent geometry    : bond        0.00400 (11095)
  covalent geometry    : angle       0.51805 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 1.292 
Fit side-chains
REVERT: A  159 ILE cc_start: 0.7956 (tp) cc_final: 0.7732 (tp)
REVERT: A  167 LEU cc_start: 0.6480 (mp) cc_final: 0.6220 (tt)
REVERT: A  211 ARG cc_start: 0.7033 (mtp85) cc_final: 0.6575 (ttt180)
REVERT: A  309 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8156 (p)
REVERT: A  529 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8193 (t0)
REVERT: A  540 ASN cc_start: 0.8511 (p0) cc_final: 0.8290 (p0)
REVERT: B  159 ILE cc_start: 0.7965 (tp) cc_final: 0.7740 (tp)
REVERT: B  167 LEU cc_start: 0.6560 (mp) cc_final: 0.6235 (tt)
REVERT: B  199 GLU cc_start: 0.6618 (pt0) cc_final: 0.6352 (pt0)
REVERT: B  529 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (t0)
REVERT: B  540 ASN cc_start: 0.8527 (p0) cc_final: 0.8244 (p0)
REVERT: B  579 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7050 (mp)
  outliers start: 36
  outliers final: 20
  residues processed: 115
  average time/residue: 1.6916
  time to fit residues: 211.0682
Evaluate side-chains
  106 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 45 optimal weight:    0.0050
   chunk 5 optimal weight:    0.0370
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0010
   chunk 74 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8082

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN
B 192 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.173631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.130532 restraints weight = 12622.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.89
r_work: 0.3277 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11097  Z= 0.123
  Angle     :  0.457   6.364  14931  Z= 0.248
  Chirality :  0.036   0.121   1572
  Planarity :  0.004   0.037   1794
  Dihedral  : 13.228 109.991   2040
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.13 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.27 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.25), residues: 1220
  helix:  2.81 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.30 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 460 
 TYR   0.020   0.001   TYR B 496 
 ARG   0.007   0.000   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05566 (  692)
  hydrogen bonds       : angle       3.40225 ( 2043)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       0.65113 (    4)
  covalent geometry    : bond        0.00257 (11095)
  covalent geometry    : angle       0.45648 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 1.387 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8432 (m-40) cc_final: 0.8013 (m-40)
REVERT: A  159 ILE cc_start: 0.7728 (tp) cc_final: 0.7516 (tp)
REVERT: A  167 LEU cc_start: 0.6012 (mp) cc_final: 0.5801 (tt)
REVERT: A  196 SER cc_start: 0.6798 (OUTLIER) cc_final: 0.6540 (m)
REVERT: A  529 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (m-30)
REVERT: B   17 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7550 (tptp)
REVERT: B  147 ASN cc_start: 0.8390 (m-40) cc_final: 0.7982 (m-40)
REVERT: B  159 ILE cc_start: 0.7790 (tp) cc_final: 0.7574 (tp)
REVERT: B  196 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6556 (m)
REVERT: B  529 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (m-30)
REVERT: B  540 ASN cc_start: 0.8425 (p0) cc_final: 0.8158 (p0)
REVERT: B  579 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7073 (mp)
  outliers start: 31
  outliers final: 14
  residues processed: 113
  average time/residue: 1.5677
  time to fit residues: 193.5768
Evaluate side-chains
  105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 53 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 21 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.172656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123296 restraints weight = 12881.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.95
r_work: 0.3322 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11097  Z= 0.118
  Angle     :  0.464   7.833  14931  Z= 0.250
  Chirality :  0.035   0.136   1572
  Planarity :  0.004   0.037   1794
  Dihedral  : 12.720 111.060   2040
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.21 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.75 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.25), residues: 1220
  helix:  2.97 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.28 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.012   0.001   PHE A 460 
 TYR   0.024   0.001   TYR B 496 
 ARG   0.009   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05261 (  692)
  hydrogen bonds       : angle       3.32282 ( 2043)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.57582 (    4)
  covalent geometry    : bond        0.00243 (11095)
  covalent geometry    : angle       0.46415 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 1.315 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8401 (m-40) cc_final: 0.7992 (m-40)
REVERT: A  529 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7762 (t0)
REVERT: B   17 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7628 (tptp)
REVERT: B  147 ASN cc_start: 0.8296 (m-40) cc_final: 0.7896 (m-40)
REVERT: B  540 ASN cc_start: 0.8385 (p0) cc_final: 0.8125 (p0)
REVERT: B  579 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6844 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 112
  average time/residue: 1.9534
  time to fit residues: 237.7588
Evaluate side-chains
  104 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  550 GLU
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.166652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.122830 restraints weight = 12775.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.79
r_work: 0.3212 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  11097  Z= 0.257
  Angle     :  0.618  10.344  14931  Z= 0.323
  Chirality :  0.042   0.158   1572
  Planarity :  0.005   0.038   1794
  Dihedral  : 13.775 116.157   2039
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.36 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.78 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.24), residues: 1220
  helix:  2.44 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.45 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.019   0.002   PHE B 517 
 TYR   0.020   0.002   TYR A 496 
 ARG   0.005   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07872 (  692)
  hydrogen bonds       : angle       3.68006 ( 2043)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       0.57690 (    4)
  covalent geometry    : bond        0.00631 (11095)
  covalent geometry    : angle       0.61851 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 1.568 
Fit side-chains
REVERT: A  579 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6872 (mp)
REVERT: B  196 SER cc_start: 0.6914 (OUTLIER) cc_final: 0.6704 (m)
REVERT: B  540 ASN cc_start: 0.8474 (p0) cc_final: 0.8200 (p0)
REVERT: B  579 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7015 (mp)
  outliers start: 32
  outliers final: 18
  residues processed: 107
  average time/residue: 1.9296
  time to fit residues: 224.4603
Evaluate side-chains
  101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   28 MET
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue   28 MET
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0070
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 192 ASN
B 146 GLN
B 192 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.170342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125622 restraints weight = 12901.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.78
r_work: 0.3277 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11097  Z= 0.135
  Angle     :  0.508  11.015  14931  Z= 0.269
  Chirality :  0.037   0.180   1572
  Planarity :  0.004   0.037   1794
  Dihedral  : 12.933 110.790   2039
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.97 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.42 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.25), residues: 1220
  helix:  2.70 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.26 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 460 
 TYR   0.025   0.001   TYR B 496 
 ARG   0.007   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05962 (  692)
  hydrogen bonds       : angle       3.44727 ( 2043)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       0.59243 (    4)
  covalent geometry    : bond        0.00289 (11095)
  covalent geometry    : angle       0.50834 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.143 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8552 (m-40) cc_final: 0.8143 (m-40)
REVERT: A  309 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8105 (p)
REVERT: A  529 ASP cc_start: 0.8231 (m-30) cc_final: 0.7992 (t0)
REVERT: B   17 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7725 (tptp)
REVERT: B  147 ASN cc_start: 0.8505 (m-40) cc_final: 0.8105 (m-40)
REVERT: B  196 SER cc_start: 0.6986 (OUTLIER) cc_final: 0.6771 (m)
REVERT: B  529 ASP cc_start: 0.8194 (m-30) cc_final: 0.7954 (t0)
REVERT: B  540 ASN cc_start: 0.8454 (p0) cc_final: 0.8196 (p0)
REVERT: B  579 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6985 (mp)
  outliers start: 17
  outliers final: 11
  residues processed: 99
  average time/residue: 1.1208
  time to fit residues: 121.2307
Evaluate side-chains
  100 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 119 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.170382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.125536 restraints weight = 12730.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.80
r_work: 0.3272 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11097  Z= 0.140
  Angle     :  0.522  12.293  14931  Z= 0.274
  Chirality :  0.037   0.191   1572
  Planarity :  0.004   0.037   1794
  Dihedral  : 12.633 112.000   2039
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.11 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.94 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.25), residues: 1220
  helix:  2.79 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.29 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 607 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 460 
 TYR   0.025   0.001   TYR B 496 
 ARG   0.006   0.000   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05910 (  692)
  hydrogen bonds       : angle       3.41736 ( 2043)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       0.60812 (    4)
  covalent geometry    : bond        0.00311 (11095)
  covalent geometry    : angle       0.52247 (14927)

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

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

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2440 Ramachandran restraints generated.
    1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8570 (m-40) cc_final: 0.8167 (m-40)
REVERT: A  309 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8104 (p)
REVERT: B   17 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7753 (tptp)
REVERT: B  147 ASN cc_start: 0.8506 (m-40) cc_final: 0.8109 (m-40)
REVERT: B  196 SER cc_start: 0.6965 (OUTLIER) cc_final: 0.6765 (m)
REVERT: B  540 ASN cc_start: 0.8443 (p0) cc_final: 0.8198 (p0)
REVERT: B  579 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7048 (mp)
  outliers start: 21
  outliers final: 14
  residues processed: 107
  average time/residue: 1.1217
  time to fit residues: 130.6372
Evaluate side-chains
  107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  156 PHE
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  588 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 192 ASN
B 146 GLN
B 192 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.168309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123600 restraints weight = 12679.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.78
r_work: 0.3232 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11097  Z= 0.200
  Angle     :  0.589  12.503  14931  Z= 0.307
  Chirality :  0.040   0.160   1572
  Planarity :  0.004   0.038   1794
  Dihedral  : 13.190 113.570   2039
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.03 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.13 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.24), residues: 1220
  helix:  2.51 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.31 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 607 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.016   0.002   PHE B 517 
 TYR   0.030   0.002   TYR B 496 
 ARG   0.006   0.001   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07165 (  692)
  hydrogen bonds       : angle       3.61044 ( 2043)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.61756 (    4)
  covalent geometry    : bond        0.00478 (11095)
  covalent geometry    : angle       0.58876 (14927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9636.01 seconds
wall clock time: 178 minutes 29.38 seconds (10709.38 seconds total)