Starting phenix.real_space_refine
on Fri Jan 17 12:47:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x5f_38068/01_2025/8x5f_38068_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x5f_38068/01_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_38068/01_2025/8x5f_38068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x5f_38068/01_2025/8x5f_38068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x5f_38068/01_2025/8x5f_38068_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x5f_38068/01_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-5571/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: 7.12, per 1000 atoms: 0.66
  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: 3.16
  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: 0.82
  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: 3.05

  Time building geometry restraints manager: 3.33 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:             2.270
  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:          0.500
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.250
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.960
-------------------------------------------------------------------------------
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  11095  Z= 0.680
  Angle     :  1.270  19.201  14927  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 

*********************** 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  : 1.167 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 181
  average time/residue: 1.4003
  time to fit residues: 271.9479
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  : 1.103 
-------------------------------------------------------------------------------
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 = 0.170095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.115377 restraints weight = 12446.699|
|-----------------------------------------------------------------------------|
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: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    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  11095  Z= 0.259
  Angle     :  0.573   7.138  14927  Z= 0.307
  Chirality :  0.040   0.141   1572
  Planarity :  0.005   0.045   1794
  Dihedral  : 15.404 139.120   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 

*********************** 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  : 1.166 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7961 (mtpp)
REVERT: A  529 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7809 (m-30)
REVERT: A  540 ASN cc_start: 0.8397 (p0) cc_final: 0.8152 (p0)
REVERT: B   64 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7884 (mtpp)
REVERT: B  468 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7240 (tmt170)
REVERT: B  540 ASN cc_start: 0.8431 (p0) cc_final: 0.8190 (p0)
  outliers start: 33
  outliers final: 13
  residues processed: 121
  average time/residue: 1.3961
  time to fit residues: 181.4510
Evaluate side-chains
  103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
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  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   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:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 102 optimal weight:    7.9990
   chunk 36 optimal weight:    0.3980
   chunk 120 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.166190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.111036 restraints weight = 12623.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.38
r_work: 0.3199 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  11095  Z= 0.306
  Angle     :  0.569   5.991  14927  Z= 0.305
  Chirality :  0.041   0.145   1572
  Planarity :  0.005   0.041   1794
  Dihedral  : 14.700 128.232   2044
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.28 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.19 %
    Favored  : 83.54 %
  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:  2.23 (0.25), residues: 1220
  helix:  2.38 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.48 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 607 
 HIS   0.008   0.001   HIS B 441 
 PHE   0.018   0.002   PHE B 571 
 TYR   0.020   0.002   TYR A 524 
 ARG   0.005   0.001   ARG B 176 

*********************** 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
  127 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 93
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A   64 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7902 (mtpp)
REVERT: A  159 ILE cc_start: 0.7781 (tp) cc_final: 0.7550 (tp)
REVERT: A  167 LEU cc_start: 0.6350 (mp) cc_final: 0.6019 (tt)
REVERT: A  309 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7776 (p)
REVERT: A  529 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (t0)
REVERT: A  540 ASN cc_start: 0.8350 (p0) cc_final: 0.8116 (p0)
REVERT: B   64 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7882 (mtpp)
REVERT: B  167 LEU cc_start: 0.6373 (mp) cc_final: 0.6047 (tt)
REVERT: B  211 ARG cc_start: 0.6653 (ttt90) cc_final: 0.6438 (ttt180)
REVERT: B  529 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (t0)
REVERT: B  540 ASN cc_start: 0.8429 (p0) cc_final: 0.8156 (p0)
  outliers start: 34
  outliers final: 15
  residues processed: 110
  average time/residue: 1.3181
  time to fit residues: 156.9109
Evaluate side-chains
  107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    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   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  538 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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0050
   chunk 84 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 163 HIS
A 499 HIS
B 163 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.167275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112938 restraints weight = 12547.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.34
r_work: 0.3210 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11095  Z= 0.270
  Angle     :  0.517   6.134  14927  Z= 0.280
  Chirality :  0.039   0.131   1572
  Planarity :  0.004   0.038   1794
  Dihedral  : 14.199 115.045   2044
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.38 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.53 %
    Favored  : 82.19 %
  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:  2.45 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.49 (0.36), residues: 302

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   0.016   0.002   PHE A 517 
 TYR   0.016   0.002   TYR B 496 
 ARG   0.008   0.001   ARG A 176 

*********************** 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
  131 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 1.291 
Fit side-chains
REVERT: A  159 ILE cc_start: 0.7738 (tp) cc_final: 0.7526 (tp)
REVERT: A  167 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5995 (tt)
REVERT: A  309 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7919 (p)
REVERT: A  529 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (t0)
REVERT: A  540 ASN cc_start: 0.8448 (p0) cc_final: 0.8247 (p0)
REVERT: A  579 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6789 (mp)
REVERT: B   17 LYS cc_start: 0.8052 (mttt) cc_final: 0.7435 (tptp)
REVERT: B  167 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6077 (tt)
REVERT: B  199 GLU cc_start: 0.6329 (pt0) cc_final: 0.6086 (pt0)
REVERT: B  345 TYR cc_start: 0.8459 (p90) cc_final: 0.8257 (p90)
REVERT: B  529 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8006 (t0)
REVERT: B  540 ASN cc_start: 0.8389 (p0) cc_final: 0.8135 (p0)
REVERT: B  579 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (mp)
  outliers start: 34
  outliers final: 15
  residues processed: 115
  average time/residue: 1.2946
  time to fit residues: 161.3624
Evaluate side-chains
  108 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
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  167 LEU
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  538 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  167 LEU
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  259 LEU
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:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 113 optimal weight:    0.0470
   chunk 120 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 110 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7880

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.170266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.117611 restraints weight = 12609.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.20
r_work: 0.3252 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11095  Z= 0.170
  Angle     :  0.458   6.232  14927  Z= 0.249
  Chirality :  0.036   0.122   1572
  Planarity :  0.004   0.038   1794
  Dihedral  : 13.300 109.858   2044
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.30 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.69 %
    Favored  : 81.81 %
  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:  2.78 (0.25), residues: 1220
  helix:  2.78 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.31 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 607 
 HIS   0.008   0.001   HIS B 441 
 PHE   0.012   0.001   PHE A 460 
 TYR   0.022   0.001   TYR B 496 
 ARG   0.006   0.000   ARG A 176 

*********************** 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
  119 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.7738 (m-40) cc_final: 0.7350 (m-40)
REVERT: A  529 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (m-30)
REVERT: B   17 LYS cc_start: 0.7939 (mttt) cc_final: 0.7280 (tptp)
REVERT: B  147 ASN cc_start: 0.7674 (m-40) cc_final: 0.7291 (m-40)
REVERT: B  529 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7664 (m-30)
REVERT: B  540 ASN cc_start: 0.8189 (p0) cc_final: 0.7896 (p0)
  outliers start: 26
  outliers final: 14
  residues processed: 107
  average time/residue: 1.2347
  time to fit residues: 143.5450
Evaluate side-chains
  102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
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  498 THR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  529 ASP
Chi-restraints excluded: chain A residue  538 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  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  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:    0.4980
   chunk 5 optimal weight:    5.9990
   chunk 72 optimal weight:    0.3980
   chunk 35 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.171073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.118570 restraints weight = 12723.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.22
r_work: 0.3277 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11095  Z= 0.158
  Angle     :  0.456   7.754  14927  Z= 0.247
  Chirality :  0.035   0.128   1572
  Planarity :  0.004   0.039   1794
  Dihedral  : 12.862 110.979   2040
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.13 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.82 %
    Favored  : 82.58 %
  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:  2.97 (0.25), residues: 1220
  helix:  2.94 (0.17), residues: 916
  sheet:  None (None), residues: 0
  loop : -1.27 (0.36), residues: 304

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   0.011   0.001   PHE A 460 
 TYR   0.023   0.001   TYR A 496 
 ARG   0.008   0.000   ARG B 176 

*********************** 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
  124 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 1.488 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.7869 (m-40) cc_final: 0.7466 (m-40)
REVERT: A  529 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7453 (m-30)
REVERT: B   17 LYS cc_start: 0.7952 (mttt) cc_final: 0.7309 (tptp)
REVERT: B  147 ASN cc_start: 0.7727 (m-40) cc_final: 0.7343 (m-40)
REVERT: B  529 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7475 (m-30)
REVERT: B  540 ASN cc_start: 0.8209 (p0) cc_final: 0.7941 (p0)
  outliers start: 27
  outliers final: 11
  residues processed: 113
  average time/residue: 1.2520
  time to fit residues: 153.4886
Evaluate side-chains
  101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
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  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  156 PHE
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  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:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.3982 r_free = 0.3982 target = 0.171648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.128147 restraints weight = 12893.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.99
r_work: 0.3240 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11095  Z= 0.213
  Angle     :  0.511   9.915  14927  Z= 0.269
  Chirality :  0.037   0.154   1572
  Planarity :  0.004   0.037   1794
  Dihedral  : 12.967 112.456   2040
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.79 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.30 %
    Favored  : 81.62 %
  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:  2.80 (0.25), residues: 1220
  helix:  2.78 (0.17), residues: 920
  sheet:  None (None), residues: 0
  loop : -1.30 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.014   0.001   PHE B 517 
 TYR   0.026   0.002   TYR B 496 
 ARG   0.008   0.000   ARG A 176 

*********************** 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
  122 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 1.309 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8458 (m-40) cc_final: 0.8028 (m-40)
REVERT: A  529 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7821 (m-30)
REVERT: B   17 LYS cc_start: 0.8210 (mttt) cc_final: 0.7642 (tptp)
REVERT: B  147 ASN cc_start: 0.8394 (m-40) cc_final: 0.7974 (m-40)
REVERT: B  529 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7811 (m-30)
REVERT: B  540 ASN cc_start: 0.8358 (p0) cc_final: 0.8141 (p0)
  outliers start: 32
  outliers final: 21
  residues processed: 111
  average time/residue: 1.1876
  time to fit residues: 143.6386
Evaluate side-chains
  111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
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  167 LEU
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  515 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   28 MET
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  156 PHE
Chi-restraints excluded: chain B residue  167 LEU
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  515 ILE
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=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:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 113 optimal weight:    4.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.167604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123748 restraints weight = 12719.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.74
r_work: 0.3228 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    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 = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11095  Z= 0.322
  Angle     :  0.590  10.946  14927  Z= 0.308
  Chirality :  0.041   0.139   1572
  Planarity :  0.004   0.038   1794
  Dihedral  : 13.651 114.573   2040
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.52 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.69 %
    Favored  : 81.52 %
  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:  2.37 (0.24), residues: 1220
  helix:  2.47 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.40 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.018   0.002   PHE B 517 
 TYR   0.029   0.002   TYR B 496 
 ARG   0.008   0.001   ARG A 176 

*********************** 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
  118 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A  309 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (p)
REVERT: A  529 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (t0)
REVERT: B   17 LYS cc_start: 0.8248 (mttt) cc_final: 0.7655 (tptp)
REVERT: B  529 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8131 (t0)
REVERT: B  540 ASN cc_start: 0.8453 (p0) cc_final: 0.8188 (p0)
  outliers start: 29
  outliers final: 20
  residues processed: 111
  average time/residue: 1.2358
  time to fit residues: 152.4883
Evaluate side-chains
  105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
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  197 GLU
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  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   28 MET
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  156 PHE
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.169794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124737 restraints weight = 12888.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.83
r_work: 0.3239 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    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 = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11095  Z= 0.244
  Angle     :  0.549  12.019  14927  Z= 0.288
  Chirality :  0.039   0.151   1572
  Planarity :  0.004   0.039   1794
  Dihedral  : 13.251 112.114   2040
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.62 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.36 %
    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:  2.48 (0.24), residues: 1220
  helix:  2.55 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.39 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.014   0.001   PHE A 517 
 TYR   0.030   0.002   TYR A 496 
 ARG   0.008   0.000   ARG A 176 

*********************** 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
  111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A  309 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (p)
REVERT: A  498 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7859 (t)
REVERT: B   17 LYS cc_start: 0.8297 (mttt) cc_final: 0.7718 (tptp)
REVERT: B  540 ASN cc_start: 0.8458 (p0) cc_final: 0.8196 (p0)
  outliers start: 26
  outliers final: 19
  residues processed: 104
  average time/residue: 1.1501
  time to fit residues: 130.8830
Evaluate side-chains
  107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
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  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  461 ILE
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  156 PHE
Chi-restraints excluded: chain B residue  167 LEU
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  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:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 119 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.170472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125710 restraints weight = 12724.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.79
r_work: 0.3276 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11095  Z= 0.204
  Angle     :  0.526  12.044  14927  Z= 0.276
  Chirality :  0.037   0.168   1572
  Planarity :  0.004   0.039   1794
  Dihedral  : 12.839 111.102   2040
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.95 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.75 %
    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:  2.70 (0.25), residues: 1220
  helix:  2.70 (0.17), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.27 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 607 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.013   0.001   PHE A 460 
 TYR   0.028   0.001   TYR B 496 
 ARG   0.009   0.000   ARG A 176 

********************** 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
  107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.131 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.8563 (m-40) cc_final: 0.8147 (m-40)
REVERT: A  309 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (p)
REVERT: B   17 LYS cc_start: 0.8318 (mttt) cc_final: 0.7764 (tptp)
REVERT: B  147 ASN cc_start: 0.8501 (m-40) cc_final: 0.8095 (m-40)
REVERT: B  540 ASN cc_start: 0.8442 (p0) cc_final: 0.8212 (p0)
  outliers start: 19
  outliers final: 16
  residues processed: 103
  average time/residue: 1.2239
  time to fit residues: 136.9635
Evaluate side-chains
  102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
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  167 LEU
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  498 THR
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  156 PHE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  441 HIS
Chi-restraints excluded: chain B residue  461 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 77 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3944 r_free = 0.3944 target = 0.168235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.123858 restraints weight = 12700.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.76
r_work: 0.3235 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    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 = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11095  Z= 0.302
  Angle     :  0.588  12.159  14927  Z= 0.307
  Chirality :  0.040   0.167   1572
  Planarity :  0.004   0.041   1794
  Dihedral  : 13.315 113.421   2040
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.44 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.55 %
    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:  2.36 (0.24), residues: 1220
  helix:  2.46 (0.17), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.34 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 607 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.016   0.002   PHE A 517 
 TYR   0.027   0.002   TYR B 496 
 ARG   0.008   0.001   ARG A 176 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 7376.41 seconds
wall clock time: 131 minutes 2.84 seconds (7862.84 seconds total)