Starting phenix.real_space_refine
on Wed May 14 05:40:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpj_36481/05_2025/8jpj_36481.cif"
  }
  resolution = 3.5
  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=   0.005 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     Cl      4      4.86       5
     C    7436      2.51       5
     N    1914      2.21       5
     O    2024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11448
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 733, 5722
          Classifications: {'peptide': 733}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 31, 'TRANS': 701}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 11.86, per 1000 atoms: 1.04
  Number of scatterers: 11448
  At special positions: 0
  Unit cell: (106.35, 82.9026, 116.399, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      70     16.00
     O    2024      8.00
     N    1914      7.00
     C    7436      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 319 " - pdb=" SG  CYS A 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 399 " - pdb=" SG  CYS A 430 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 319 " - pdb=" SG  CYS B 326 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 399 " - pdb=" SG  CYS B 430 " 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: 3.10
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      65.6% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 68
    Processing helix  chain 'A' and resid 69 through 124
      removed outlier: 3.646A  pdb=" N   PHE A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   SER A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A 123 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 151
      removed outlier: 3.932A  pdb=" N   LEU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 155
    Processing helix  chain 'A' and resid 158 through 168
      removed outlier: 4.077A  pdb=" N   CYS A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR A 165 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 3.882A  pdb=" N   LEU A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 218
      removed outlier: 4.239A  pdb=" N   HIS A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
      removed outlier: 3.591A  pdb=" N   GLN A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 255
    Processing helix  chain 'A' and resid 256 through 266
    Processing helix  chain 'A' and resid 276 through 299
      removed outlier: 3.850A  pdb=" N   PHE A 282 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN A 292 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE A 293 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 297 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 333 through 365
    Processing helix  chain 'A' and resid 375 through 395
      removed outlier: 3.570A  pdb=" N   LEU A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 444
      removed outlier: 3.553A  pdb=" N   ASN A 444 " --> pdb=" O   THR A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 456
    Processing helix  chain 'A' and resid 461 through 480
    Processing helix  chain 'A' and resid 488 through 511
      removed outlier: 3.945A  pdb=" N   CYS A 495 " --> pdb=" O   PRO A 491 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TYR A 510 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 534
      removed outlier: 4.135A  pdb=" N   ALA A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 549
    Processing helix  chain 'A' and resid 550 through 552
      No H-bonds generated for 'chain 'A' and resid 550 through 552'
    Processing helix  chain 'A' and resid 553 through 569
      removed outlier: 3.654A  pdb=" N   ILE A 557 " --> pdb=" O   TYR A 553 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 560 " --> pdb=" O   PRO A 556 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL A 563 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 582
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.679A  pdb=" N   LEU A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 650 through 664
      removed outlier: 3.788A  pdb=" N   ILE A 664 " --> pdb=" O   LYS A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 677
    Processing helix  chain 'A' and resid 732 through 736
    Processing helix  chain 'A' and resid 747 through 756
    Processing helix  chain 'A' and resid 773 through 780
      removed outlier: 4.288A  pdb=" N   ASP A 780 " --> pdb=" O   GLU A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 830
    Processing helix  chain 'A' and resid 849 through 853
    Processing helix  chain 'A' and resid 854 through 869
    Processing helix  chain 'B' and resid 58 through 68
    Processing helix  chain 'B' and resid 69 through 124
      removed outlier: 3.647A  pdb=" N   PHE B 101 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   SER B 116 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS B 123 " --> pdb=" O   GLU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 151
      removed outlier: 3.933A  pdb=" N   LEU B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 155
    Processing helix  chain 'B' and resid 158 through 168
      removed outlier: 4.077A  pdb=" N   CYS B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR B 165 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 193
      removed outlier: 3.882A  pdb=" N   LEU B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 218
      removed outlier: 4.239A  pdb=" N   HIS B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
      Proline residue:  B 215  - end of helix
      removed outlier: 3.591A  pdb=" N   GLN B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 255
    Processing helix  chain 'B' and resid 256 through 266
    Processing helix  chain 'B' and resid 276 through 299
      removed outlier: 3.851A  pdb=" N   PHE B 282 " --> pdb=" O   TRP B 278 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN B 292 " --> pdb=" O   THR B 288 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   PHE B 293 " --> pdb=" O   PHE B 289 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 297 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 332
      No H-bonds generated for 'chain 'B' and resid 330 through 332'
    Processing helix  chain 'B' and resid 333 through 365
    Processing helix  chain 'B' and resid 375 through 395
      removed outlier: 3.571A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 444
      removed outlier: 3.552A  pdb=" N   ASN B 444 " --> pdb=" O   THR B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 456
    Processing helix  chain 'B' and resid 461 through 480
    Processing helix  chain 'B' and resid 488 through 511
      removed outlier: 3.946A  pdb=" N   CYS B 495 " --> pdb=" O   PRO B 491 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY B 496 " --> pdb=" O   SER B 492 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER B 509 " --> pdb=" O   ASN B 505 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR B 510 " --> pdb=" O   VAL B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 534
      removed outlier: 4.134A  pdb=" N   ALA B 522 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 549
    Processing helix  chain 'B' and resid 550 through 552
      No H-bonds generated for 'chain 'B' and resid 550 through 552'
    Processing helix  chain 'B' and resid 553 through 569
      removed outlier: 3.655A  pdb=" N   ILE B 557 " --> pdb=" O   TYR B 553 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR B 560 " --> pdb=" O   PRO B 556 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 563 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TRP B 566 " --> pdb=" O   MET B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 582
    Processing helix  chain 'B' and resid 593 through 599
      removed outlier: 3.679A  pdb=" N   LEU B 599 " --> pdb=" O   GLU B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 628
    Processing helix  chain 'B' and resid 650 through 664
      removed outlier: 3.789A  pdb=" N   ILE B 664 " --> pdb=" O   LYS B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 677
    Processing helix  chain 'B' and resid 732 through 736
    Processing helix  chain 'B' and resid 747 through 756
    Processing helix  chain 'B' and resid 773 through 780
      removed outlier: 4.288A  pdb=" N   ASP B 780 " --> pdb=" O   GLU B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 819 through 830
    Processing helix  chain 'B' and resid 849 through 853
    Processing helix  chain 'B' and resid 854 through 869
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617
    Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638
      removed outlier: 6.482A  pdb=" N   THR A 637 " --> pdb=" O   PHE A 741 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   PHE A 741 " --> pdb=" O   THR A 637 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838
    Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401
    Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617
    Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638
      removed outlier: 6.482A  pdb=" N   THR B 637 " --> pdb=" O   PHE B 741 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   PHE B 741 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838

    670 hydrogen bonds defined for protein.
    1980 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: 3.66

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3613
        1.34 -     1.46: 2834
        1.46 -     1.58: 5151
        1.58 -     1.70: 0
        1.70 -     1.82: 110
  Bond restraints: 11708
  Sorted by residual:
  bond pdb=" CA  VAL A 758 "
       pdb=" CB  VAL A 758 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.35e+00
  bond pdb=" CA  VAL B 758 "
       pdb=" CB  VAL B 758 "
    ideal  model  delta    sigma   weight residual
    1.540  1.525  0.015 1.36e-02 5.41e+03 1.28e+00
  bond pdb=" N   PRO B 368 "
       pdb=" CA  PRO B 368 "
    ideal  model  delta    sigma   weight residual
    1.469  1.483 -0.014 1.28e-02 6.10e+03 1.21e+00
  bond pdb=" CA  ILE A 159 "
       pdb=" C   ILE A 159 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.009 8.80e-03 1.29e+04 9.51e-01
  bond pdb=" CA  ILE B 159 "
       pdb=" C   ILE B 159 "
    ideal  model  delta    sigma   weight residual
    1.520  1.528 -0.008 8.80e-03 1.29e+04 8.53e-01
  ... (remaining 11703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 15457
        1.52 -     3.04: 337
        3.04 -     4.57: 61
        4.57 -     6.09: 21
        6.09 -     7.61: 2
  Bond angle restraints: 15878
  Sorted by residual:
  angle pdb=" N   VAL B 375 "
        pdb=" CA  VAL B 375 "
        pdb=" C   VAL B 375 "
      ideal   model   delta    sigma   weight residual
     112.96  107.81    5.15 1.00e+00 1.00e+00 2.65e+01
  angle pdb=" N   VAL A 375 "
        pdb=" CA  VAL A 375 "
        pdb=" C   VAL A 375 "
      ideal   model   delta    sigma   weight residual
     112.96  107.83    5.13 1.00e+00 1.00e+00 2.64e+01
  angle pdb=" N   VAL B 175 "
        pdb=" CA  VAL B 175 "
        pdb=" C   VAL B 175 "
      ideal   model   delta    sigma   weight residual
     113.71  109.48    4.23 9.50e-01 1.11e+00 1.99e+01
  angle pdb=" N   VAL A 175 "
        pdb=" CA  VAL A 175 "
        pdb=" C   VAL A 175 "
      ideal   model   delta    sigma   weight residual
     113.71  109.55    4.16 9.50e-01 1.11e+00 1.92e+01
  angle pdb=" C   GLY A 158 "
        pdb=" N   ILE A 159 "
        pdb=" CA  ILE A 159 "
      ideal   model   delta    sigma   weight residual
     120.24  122.83   -2.59 6.30e-01 2.52e+00 1.69e+01
  ... (remaining 15873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 6253
       17.54 -    35.08: 521
       35.08 -    52.62: 96
       52.62 -    70.16: 12
       70.16 -    87.70: 14
  Dihedral angle restraints: 6896
    sinusoidal: 2698
      harmonic: 4198
  Sorted by residual:
  dihedral pdb=" CB  CYS B 399 "
           pdb=" SG  CYS B 399 "
           pdb=" SG  CYS B 430 "
           pdb=" CB  CYS B 430 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.30  -87.70     1      1.00e+01 1.00e-02 9.22e+01
  dihedral pdb=" CB  CYS A 399 "
           pdb=" SG  CYS A 399 "
           pdb=" SG  CYS A 430 "
           pdb=" CB  CYS A 430 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.31  -87.69     1      1.00e+01 1.00e-02 9.21e+01
  dihedral pdb=" CB  CYS A 120 "
           pdb=" SG  CYS A 120 "
           pdb=" SG  CYS A 125 "
           pdb=" CB  CYS A 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.98   73.98     1      1.00e+01 1.00e-02 6.95e+01
  ... (remaining 6893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1144
       0.029 -    0.058: 452
       0.058 -    0.088: 139
       0.088 -    0.117: 83
       0.117 -    0.146: 16
  Chirality restraints: 1834
  Sorted by residual:
  chirality pdb=" CB  THR A 427 "
            pdb=" CA  THR A 427 "
            pdb=" OG1 THR A 427 "
            pdb=" CG2 THR A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CB  THR B 427 "
            pdb=" CA  THR B 427 "
            pdb=" OG1 THR B 427 "
            pdb=" CG2 THR B 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE A 847 "
            pdb=" N   ILE A 847 "
            pdb=" C   ILE A 847 "
            pdb=" CB  ILE A 847 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 1831 not shown)

  Planarity restraints: 1994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 369 "   -0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO B 370 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 370 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 370 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 369 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO A 370 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 370 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 370 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 769 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A 770 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 770 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 770 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1991 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2875
        2.80 -     3.33: 11376
        3.33 -     3.85: 17984
        3.85 -     4.38: 19763
        4.38 -     4.90: 35939
  Nonbonded interactions: 87937
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 137 "
            pdb=" OG1 THR B 386 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" ND2 ASN A 137 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   ILE B 624 "
            pdb=" OG1 THR B 628 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ILE A 624 "
            pdb=" OG1 THR A 628 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG1 THR B 520 "
            pdb=" OH  TYR B 553 "
     model   vdw
     2.317 3.040
  ... (remaining 87932 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             9.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.830
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     34.270
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.070
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11714  Z= 0.147
  Angle     :  0.576   7.608  15890  Z= 0.325
  Chirality :  0.039   0.146   1834
  Planarity :  0.004   0.037   1994
  Dihedral  : 13.482  83.984   4182
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.23), residues: 1446
  helix:  2.20 (0.18), residues: 892
  sheet: -1.52 (1.08), residues: 24
  loop : -1.08 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 303 
 HIS   0.002   0.000   HIS A 515 
 PHE   0.012   0.001   PHE B 101 
 TYR   0.012   0.001   TYR A 866 
 ARG   0.003   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13979 (  670)
  hydrogen bonds       : angle       5.01418 ( 1980)
  SS BOND              : bond        0.00270 (    6)
  SS BOND              : angle       1.09956 (   12)
  covalent geometry    : bond        0.00319 (11708)
  covalent geometry    : angle       0.57516 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6371 (pt0)
REVERT: A   71 LYS cc_start: 0.5897 (mmtt) cc_final: 0.5676 (mttp)
REVERT: A   75 ARG cc_start: 0.6007 (ttt90) cc_final: 0.5357 (tpt170)
REVERT: A   82 MET cc_start: 0.6724 (mtt) cc_final: 0.6399 (mtt)
REVERT: A  200 GLU cc_start: 0.6712 (mp0) cc_final: 0.5364 (mp0)
REVERT: A  589 GLU cc_start: 0.6415 (pt0) cc_final: 0.5722 (pm20)
REVERT: A  611 TYR cc_start: 0.6042 (p90) cc_final: 0.5560 (p90)
REVERT: A  822 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6335 (mt0)
REVERT: A  843 GLU cc_start: 0.5157 (tt0) cc_final: 0.4747 (tm-30)
REVERT: A  844 ILE cc_start: 0.6251 (tt) cc_final: 0.5831 (tt)
REVERT: A  855 TYR cc_start: 0.7427 (t80) cc_final: 0.6911 (t80)
REVERT: B   63 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6370 (pt0)
REVERT: B   71 LYS cc_start: 0.5899 (mmtt) cc_final: 0.5676 (mttp)
REVERT: B   75 ARG cc_start: 0.6013 (ttt90) cc_final: 0.5360 (tpt170)
REVERT: B   82 MET cc_start: 0.6721 (mtt) cc_final: 0.6394 (mtt)
REVERT: B  200 GLU cc_start: 0.6696 (mp0) cc_final: 0.5348 (mp0)
REVERT: B  589 GLU cc_start: 0.6405 (pt0) cc_final: 0.5716 (pm20)
REVERT: B  611 TYR cc_start: 0.6094 (p90) cc_final: 0.5605 (p90)
REVERT: B  822 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6337 (mt0)
REVERT: B  843 GLU cc_start: 0.5203 (tt0) cc_final: 0.4748 (tm-30)
REVERT: B  844 ILE cc_start: 0.6289 (tt) cc_final: 0.5874 (tt)
REVERT: B  855 TYR cc_start: 0.7431 (t80) cc_final: 0.6885 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 332
  average time/residue: 0.3008
  time to fit residues: 133.0059
Evaluate side-chains
  168 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 132 optimal weight:   10.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 167 ASN
A 355 ASN
A 819 HIS
A 859 GLN
B 167 ASN
B 355 ASN
B 819 HIS
B 852 ASN
B 859 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.150487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.138647 restraints weight = 12369.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.122742 restraints weight = 24026.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.122072 restraints weight = 22693.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11714  Z= 0.165
  Angle     :  0.629   8.379  15890  Z= 0.324
  Chirality :  0.043   0.165   1834
  Planarity :  0.005   0.043   1994
  Dihedral  :  4.333  18.771   1574
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.18 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.22), residues: 1446
  helix:  1.98 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -0.90 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 272 
 HIS   0.007   0.001   HIS A 865 
 PHE   0.030   0.002   PHE A 473 
 TYR   0.016   0.002   TYR B 806 
 ARG   0.010   0.001   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04315 (  670)
  hydrogen bonds       : angle       3.92038 ( 1980)
  SS BOND              : bond        0.00091 (    6)
  SS BOND              : angle       1.34655 (   12)
  covalent geometry    : bond        0.00393 (11708)
  covalent geometry    : angle       0.62819 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6939 (pt0)
REVERT: A   82 MET cc_start: 0.7558 (mtt) cc_final: 0.7267 (mtt)
REVERT: A  161 GLU cc_start: 0.6916 (mp0) cc_final: 0.6651 (mp0)
REVERT: A  239 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7861 (ttt180)
REVERT: A  313 ASN cc_start: 0.7818 (p0) cc_final: 0.7523 (p0)
REVERT: A  360 LYS cc_start: 0.8272 (mttt) cc_final: 0.7993 (mtmt)
REVERT: A  573 LYS cc_start: 0.8485 (mttt) cc_final: 0.7929 (mmtm)
REVERT: A  587 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8018 (mp)
REVERT: A  589 GLU cc_start: 0.6935 (pt0) cc_final: 0.6467 (pm20)
REVERT: B   63 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6977 (pt0)
REVERT: B   82 MET cc_start: 0.7595 (mtt) cc_final: 0.7309 (mtt)
REVERT: B  161 GLU cc_start: 0.6904 (mp0) cc_final: 0.6642 (mp0)
REVERT: B  239 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7846 (ttt180)
REVERT: B  313 ASN cc_start: 0.7810 (p0) cc_final: 0.7551 (p0)
REVERT: B  360 LYS cc_start: 0.8272 (mttt) cc_final: 0.7999 (mtmt)
REVERT: B  573 LYS cc_start: 0.8532 (mttt) cc_final: 0.7976 (mmtm)
REVERT: B  587 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8001 (mp)
REVERT: B  589 GLU cc_start: 0.6941 (pt0) cc_final: 0.6468 (pm20)
  outliers start: 24
  outliers final: 8
  residues processed: 197
  average time/residue: 0.2849
  time to fit residues: 75.6925
Evaluate side-chains
  159 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0060
   chunk 91 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
B 456 GLN
B 852 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.138216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.125244 restraints weight = 12437.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.110040 restraints weight = 22366.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.107926 restraints weight = 23797.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11714  Z= 0.171
  Angle     :  0.604  13.378  15890  Z= 0.306
  Chirality :  0.043   0.272   1834
  Planarity :  0.005   0.044   1994
  Dihedral  :  4.290  20.168   1574
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.86 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.22), residues: 1446
  helix:  2.04 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.96 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 278 
 HIS   0.006   0.001   HIS B 865 
 PHE   0.018   0.002   PHE A 110 
 TYR   0.014   0.002   TYR B 613 
 ARG   0.004   0.001   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  670)
  hydrogen bonds       : angle       3.89590 ( 1980)
  SS BOND              : bond        0.00710 (    6)
  SS BOND              : angle       0.85705 (   12)
  covalent geometry    : bond        0.00414 (11708)
  covalent geometry    : angle       0.60425 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7042 (pt0)
REVERT: A   82 MET cc_start: 0.7600 (mtt) cc_final: 0.7306 (mtt)
REVERT: A  119 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6113 (mp0)
REVERT: A  313 ASN cc_start: 0.7891 (p0) cc_final: 0.7629 (p0)
REVERT: A  360 LYS cc_start: 0.8285 (mttt) cc_final: 0.7920 (mtmm)
REVERT: A  573 LYS cc_start: 0.8675 (mttt) cc_final: 0.8390 (mtmm)
REVERT: A  587 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8173 (mp)
REVERT: A  589 GLU cc_start: 0.6904 (pt0) cc_final: 0.6424 (pm20)
REVERT: A  653 ILE cc_start: 0.8462 (mm) cc_final: 0.8107 (mt)
REVERT: B   82 MET cc_start: 0.7632 (mtt) cc_final: 0.7348 (mtt)
REVERT: B  119 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6124 (mp0)
REVERT: B  313 ASN cc_start: 0.7896 (p0) cc_final: 0.7646 (p0)
REVERT: B  360 LYS cc_start: 0.8289 (mttt) cc_final: 0.7922 (mtmm)
REVERT: B  573 LYS cc_start: 0.8664 (mttt) cc_final: 0.8392 (mtmm)
REVERT: B  587 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8164 (mp)
REVERT: B  589 GLU cc_start: 0.6913 (pt0) cc_final: 0.6427 (pm20)
  outliers start: 30
  outliers final: 16
  residues processed: 149
  average time/residue: 0.2914
  time to fit residues: 58.9079
Evaluate side-chains
  135 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  847 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0270
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 125 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
A 456 GLN
A 579 HIS
B 355 ASN
B 456 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.138886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.127430 restraints weight = 12384.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.108028 restraints weight = 22023.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.108196 restraints weight = 20385.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.5433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11714  Z= 0.123
  Angle     :  0.541  10.151  15890  Z= 0.272
  Chirality :  0.039   0.147   1834
  Planarity :  0.004   0.043   1994
  Dihedral  :  4.046  19.388   1574
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.66 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.22), residues: 1446
  helix:  2.14 (0.17), residues: 910
  sheet: -3.20 (0.88), residues: 24
  loop : -0.86 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 278 
 HIS   0.007   0.001   HIS A 865 
 PHE   0.018   0.001   PHE A 473 
 TYR   0.011   0.001   TYR B 613 
 ARG   0.003   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  670)
  hydrogen bonds       : angle       3.72065 ( 1980)
  SS BOND              : bond        0.00583 (    6)
  SS BOND              : angle       0.72654 (   12)
  covalent geometry    : bond        0.00290 (11708)
  covalent geometry    : angle       0.54066 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6878 (pt0)
REVERT: A   82 MET cc_start: 0.7641 (mtt) cc_final: 0.7367 (mtt)
REVERT: A  119 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5843 (mp0)
REVERT: A  120 CYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5972 (m)
REVERT: A  360 LYS cc_start: 0.8243 (mttt) cc_final: 0.7895 (mtmm)
REVERT: A  508 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7584 (mttm)
REVERT: A  573 LYS cc_start: 0.8631 (mttt) cc_final: 0.8090 (mmtm)
REVERT: A  587 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8201 (mp)
REVERT: A  589 GLU cc_start: 0.6837 (pt0) cc_final: 0.6399 (pm20)
REVERT: B   82 MET cc_start: 0.7663 (mtt) cc_final: 0.7396 (mtt)
REVERT: B  119 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5813 (mp0)
REVERT: B  120 CYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5991 (m)
REVERT: B  360 LYS cc_start: 0.8248 (mttt) cc_final: 0.7899 (mtmm)
REVERT: B  508 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7517 (mttp)
REVERT: B  573 LYS cc_start: 0.8625 (mttt) cc_final: 0.8093 (mmtm)
REVERT: B  587 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8195 (mp)
REVERT: B  589 GLU cc_start: 0.6853 (pt0) cc_final: 0.6420 (pm20)
  outliers start: 30
  outliers final: 22
  residues processed: 142
  average time/residue: 0.2671
  time to fit residues: 53.1315
Evaluate side-chains
  142 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  120 CYS
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0170
   chunk 108 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0870
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.139327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.126500 restraints weight = 12354.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.111031 restraints weight = 23157.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.109679 restraints weight = 21154.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.5628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11714  Z= 0.108
  Angle     :  0.544  10.546  15890  Z= 0.271
  Chirality :  0.038   0.161   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.923  17.826   1574
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.10 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.22), residues: 1446
  helix:  2.28 (0.17), residues: 914
  sheet: -3.34 (0.88), residues: 24
  loop : -0.86 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 278 
 HIS   0.006   0.001   HIS B 865 
 PHE   0.016   0.001   PHE A 473 
 TYR   0.010   0.001   TYR B 613 
 ARG   0.004   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  670)
  hydrogen bonds       : angle       3.61793 ( 1980)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       3.21062 (   12)
  covalent geometry    : bond        0.00247 (11708)
  covalent geometry    : angle       0.53705 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7639 (mtt) cc_final: 0.7385 (mtt)
REVERT: A  119 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5920 (mp0)
REVERT: A  360 LYS cc_start: 0.8220 (mttt) cc_final: 0.7990 (mtmt)
REVERT: A  508 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7557 (mttp)
REVERT: A  573 LYS cc_start: 0.8630 (mttt) cc_final: 0.8097 (mmtm)
REVERT: A  587 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8194 (mp)
REVERT: A  589 GLU cc_start: 0.6864 (pt0) cc_final: 0.6439 (pm20)
REVERT: B   82 MET cc_start: 0.7656 (mtt) cc_final: 0.7402 (mtt)
REVERT: B  119 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5909 (mp0)
REVERT: B  360 LYS cc_start: 0.8243 (mttt) cc_final: 0.8014 (mtmt)
REVERT: B  508 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7552 (mttp)
REVERT: B  573 LYS cc_start: 0.8656 (mttt) cc_final: 0.8101 (mmtm)
REVERT: B  587 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8189 (mp)
REVERT: B  589 GLU cc_start: 0.6896 (pt0) cc_final: 0.6479 (pm20)
  outliers start: 35
  outliers final: 24
  residues processed: 144
  average time/residue: 0.2646
  time to fit residues: 53.2471
Evaluate side-chains
  143 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 129 optimal weight:    8.9990
   chunk 121 optimal weight:    0.6980
   chunk 136 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.134060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.120633 restraints weight = 12613.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.103863 restraints weight = 27541.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.103493 restraints weight = 23710.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.6049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11714  Z= 0.172
  Angle     :  0.607   9.845  15890  Z= 0.307
  Chirality :  0.042   0.204   1834
  Planarity :  0.005   0.044   1994
  Dihedral  :  4.201  19.164   1574
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.86 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.22), residues: 1446
  helix:  2.10 (0.17), residues: 910
  sheet: -3.24 (0.88), residues: 24
  loop : -1.08 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 278 
 HIS   0.008   0.001   HIS A 865 
 PHE   0.018   0.002   PHE A 110 
 TYR   0.013   0.002   TYR A 613 
 ARG   0.003   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04343 (  670)
  hydrogen bonds       : angle       3.89916 ( 1980)
  SS BOND              : bond        0.00572 (    6)
  SS BOND              : angle       4.22091 (   12)
  covalent geometry    : bond        0.00426 (11708)
  covalent geometry    : angle       0.59578 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7726 (mtt) cc_final: 0.7481 (mtt)
REVERT: A  119 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5178 (mp0)
REVERT: A  360 LYS cc_start: 0.8259 (mttt) cc_final: 0.7903 (mtmm)
REVERT: A  508 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7821 (mttm)
REVERT: A  573 LYS cc_start: 0.8688 (mttt) cc_final: 0.8250 (mmtm)
REVERT: A  587 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: A  589 GLU cc_start: 0.6896 (pt0) cc_final: 0.6473 (pm20)
REVERT: B   82 MET cc_start: 0.7708 (mtt) cc_final: 0.7464 (mtt)
REVERT: B  119 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5189 (mp0)
REVERT: B  360 LYS cc_start: 0.8263 (mttt) cc_final: 0.7902 (mtmm)
REVERT: B  508 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7813 (mttm)
REVERT: B  573 LYS cc_start: 0.8671 (mttt) cc_final: 0.8219 (mmtm)
REVERT: B  587 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: B  589 GLU cc_start: 0.6903 (pt0) cc_final: 0.6478 (pm20)
  outliers start: 38
  outliers final: 30
  residues processed: 147
  average time/residue: 0.2675
  time to fit residues: 54.7051
Evaluate side-chains
  149 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  624 ILE
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 131 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0870
   chunk 15 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.138048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.125603 restraints weight = 12500.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.110176 restraints weight = 21720.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.108279 restraints weight = 22702.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.6164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11714  Z= 0.108
  Angle     :  0.522   8.408  15890  Z= 0.264
  Chirality :  0.038   0.137   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  4.007  20.110   1574
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.50 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.22), residues: 1446
  helix:  2.29 (0.17), residues: 916
  sheet: -3.39 (0.88), residues: 24
  loop : -1.05 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 590 
 HIS   0.008   0.001   HIS A 865 
 PHE   0.015   0.001   PHE A 473 
 TYR   0.009   0.001   TYR B 613 
 ARG   0.003   0.000   ARG B 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03560 (  670)
  hydrogen bonds       : angle       3.65042 ( 1980)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       3.97125 (   12)
  covalent geometry    : bond        0.00249 (11708)
  covalent geometry    : angle       0.51056 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7662 (mtt) cc_final: 0.7418 (mtt)
REVERT: A  360 LYS cc_start: 0.8256 (mttt) cc_final: 0.8033 (mtmt)
REVERT: A  573 LYS cc_start: 0.8610 (mttt) cc_final: 0.8076 (mmtm)
REVERT: A  589 GLU cc_start: 0.6886 (pt0) cc_final: 0.6445 (pm20)
REVERT: A  670 GLU cc_start: 0.8076 (tp30) cc_final: 0.7648 (tp30)
REVERT: B   82 MET cc_start: 0.7668 (mtt) cc_final: 0.7430 (mtt)
REVERT: B  360 LYS cc_start: 0.8268 (mttt) cc_final: 0.8053 (mtmt)
REVERT: B  573 LYS cc_start: 0.8615 (mttt) cc_final: 0.8106 (mmtm)
REVERT: B  589 GLU cc_start: 0.6912 (pt0) cc_final: 0.6482 (pm20)
REVERT: B  670 GLU cc_start: 0.8080 (tp30) cc_final: 0.7658 (tp30)
  outliers start: 34
  outliers final: 28
  residues processed: 137
  average time/residue: 0.2631
  time to fit residues: 50.1361
Evaluate side-chains
  137 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 125 optimal weight:    3.9990
   chunk 140 optimal weight:    0.7980
   chunk 121 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.136086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.122628 restraints weight = 12467.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.119755 restraints weight = 24088.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.106280 restraints weight = 28759.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.6319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11714  Z= 0.120
  Angle     :  0.539   8.807  15890  Z= 0.270
  Chirality :  0.038   0.135   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.944  17.367   1574
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.06 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.22), residues: 1446
  helix:  2.31 (0.17), residues: 916
  sheet: -3.35 (0.89), residues: 24
  loop : -1.11 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 278 
 HIS   0.008   0.001   HIS A 865 
 PHE   0.015   0.001   PHE A 473 
 TYR   0.010   0.001   TYR A 613 
 ARG   0.002   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  670)
  hydrogen bonds       : angle       3.65901 ( 1980)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       2.53643 (   12)
  covalent geometry    : bond        0.00284 (11708)
  covalent geometry    : angle       0.53444 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7656 (mtt) cc_final: 0.7419 (mtt)
REVERT: A  360 LYS cc_start: 0.8264 (mttt) cc_final: 0.8013 (mtmt)
REVERT: A  573 LYS cc_start: 0.8614 (mttt) cc_final: 0.8078 (mmtm)
REVERT: A  587 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: A  589 GLU cc_start: 0.6854 (pt0) cc_final: 0.6421 (pm20)
REVERT: A  670 GLU cc_start: 0.8156 (tp30) cc_final: 0.7760 (tp30)
REVERT: B   82 MET cc_start: 0.7662 (mtt) cc_final: 0.7432 (mtt)
REVERT: B  360 LYS cc_start: 0.8274 (mttt) cc_final: 0.8038 (mtmt)
REVERT: B  573 LYS cc_start: 0.8616 (mttt) cc_final: 0.8072 (mmtm)
REVERT: B  587 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8218 (mp)
REVERT: B  589 GLU cc_start: 0.6870 (pt0) cc_final: 0.6448 (pm20)
REVERT: B  670 GLU cc_start: 0.8143 (tp30) cc_final: 0.7753 (tp30)
  outliers start: 29
  outliers final: 25
  residues processed: 129
  average time/residue: 0.2710
  time to fit residues: 48.8862
Evaluate side-chains
  138 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 128 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 444 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.136233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.123763 restraints weight = 12602.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.107472 restraints weight = 23255.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.106388 restraints weight = 19732.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.6551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11714  Z= 0.123
  Angle     :  0.532   8.879  15890  Z= 0.266
  Chirality :  0.039   0.138   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.920  17.620   1574
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.66 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.22), residues: 1446
  helix:  2.33 (0.17), residues: 914
  sheet: -3.43 (0.89), residues: 24
  loop : -1.14 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 590 
 HIS   0.009   0.001   HIS A 865 
 PHE   0.017   0.001   PHE A 110 
 TYR   0.010   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  670)
  hydrogen bonds       : angle       3.67478 ( 1980)
  SS BOND              : bond        0.00281 (    6)
  SS BOND              : angle       1.91615 (   12)
  covalent geometry    : bond        0.00293 (11708)
  covalent geometry    : angle       0.52937 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 1.216 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7666 (mtt) cc_final: 0.7439 (mtt)
REVERT: A  360 LYS cc_start: 0.8263 (mttt) cc_final: 0.8035 (mtmt)
REVERT: A  573 LYS cc_start: 0.8589 (mttt) cc_final: 0.8131 (mmtm)
REVERT: A  587 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8171 (mp)
REVERT: A  670 GLU cc_start: 0.8149 (tp30) cc_final: 0.7589 (tp30)
REVERT: A  764 GLN cc_start: 0.7870 (tp40) cc_final: 0.7641 (tt0)
REVERT: B   82 MET cc_start: 0.7663 (mtt) cc_final: 0.7449 (mtt)
REVERT: B  360 LYS cc_start: 0.8269 (mttt) cc_final: 0.8036 (mtmt)
REVERT: B  573 LYS cc_start: 0.8604 (mttt) cc_final: 0.8131 (mmtm)
REVERT: B  587 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8155 (mp)
REVERT: B  670 GLU cc_start: 0.8165 (tp30) cc_final: 0.7750 (tp30)
REVERT: B  764 GLN cc_start: 0.7865 (tp40) cc_final: 0.7659 (tt0)
  outliers start: 34
  outliers final: 28
  residues processed: 132
  average time/residue: 0.2648
  time to fit residues: 48.7112
Evaluate side-chains
  139 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 129 optimal weight:    0.9990
   chunk 135 optimal weight:    0.0040
   chunk 101 optimal weight:    2.9990
   chunk 139 optimal weight:    3.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.136228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.122486 restraints weight = 12483.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.119668 restraints weight = 26871.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.105908 restraints weight = 30633.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.6611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11714  Z= 0.114
  Angle     :  0.527   8.813  15890  Z= 0.264
  Chirality :  0.038   0.147   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.905  17.439   1574
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.61 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1446
  helix:  2.35 (0.17), residues: 918
  sheet: -3.42 (0.89), residues: 24
  loop : -1.12 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 590 
 HIS   0.009   0.001   HIS A 865 
 PHE   0.015   0.001   PHE B 110 
 TYR   0.009   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  670)
  hydrogen bonds       : angle       3.64548 ( 1980)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       1.79498 (   12)
  covalent geometry    : bond        0.00267 (11708)
  covalent geometry    : angle       0.52510 (15878)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.276 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7654 (mtt) cc_final: 0.7419 (mtt)
REVERT: A  360 LYS cc_start: 0.8291 (mttt) cc_final: 0.8042 (mtmt)
REVERT: A  573 LYS cc_start: 0.8590 (mttt) cc_final: 0.8062 (mmtm)
REVERT: A  587 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: A  670 GLU cc_start: 0.8168 (tp30) cc_final: 0.7627 (tp30)
REVERT: B   82 MET cc_start: 0.7673 (mtt) cc_final: 0.7460 (mtt)
REVERT: B  360 LYS cc_start: 0.8274 (mttt) cc_final: 0.8040 (mtmt)
REVERT: B  573 LYS cc_start: 0.8590 (mttt) cc_final: 0.8072 (mmtm)
REVERT: B  587 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8206 (mp)
REVERT: B  670 GLU cc_start: 0.8172 (tp30) cc_final: 0.7788 (tp30)
  outliers start: 29
  outliers final: 27
  residues processed: 125
  average time/residue: 0.2803
  time to fit residues: 48.7166
Evaluate side-chains
  137 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 108 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 121 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3351 r_free = 0.3351 target = 0.135774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.122717 restraints weight = 12474.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.107285 restraints weight = 25851.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.106497 restraints weight = 21077.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.6680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11714  Z= 0.119
  Angle     :  0.531   8.647  15890  Z= 0.266
  Chirality :  0.038   0.137   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.918  17.434   1574
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.30 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1446
  helix:  2.38 (0.17), residues: 914
  sheet: -3.42 (0.89), residues: 24
  loop : -1.15 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 278 
 HIS   0.009   0.001   HIS A 865 
 PHE   0.016   0.001   PHE B 110 
 TYR   0.010   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 771 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  670)
  hydrogen bonds       : angle       3.64388 ( 1980)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       1.74543 (   12)
  covalent geometry    : bond        0.00282 (11708)
  covalent geometry    : angle       0.52911 (15878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3599.45 seconds
wall clock time: 64 minutes 22.18 seconds (3862.18 seconds total)