Starting phenix.real_space_refine
on Tue Jul 29 14:34:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpj_36481/07_2025/8jpj_36481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpj_36481/07_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_36481/07_2025/8jpj_36481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpj_36481/07_2025/8jpj_36481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpj_36481/07_2025/8jpj_36481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpj_36481/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 11.98, per 1000 atoms: 1.05
  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: 3.13
  Conformation dependent library (CDL) restraints added in 1.6 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: 1.31
  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: 3.26

  Time building geometry restraints manager: 3.39 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:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.340
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.530
-------------------------------------------------------------------------------
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  : 1.222 
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: 0.2870
  time to fit residues: 127.3948
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  : 1.121 
-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.149985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.140022 restraints weight = 12296.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.120897 restraints weight = 24840.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.121522 restraints weight = 21541.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3703

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   8.376  15890  Z= 0.324
  Chirality :  0.043   0.165   1834
  Planarity :  0.005   0.043   1994
  Dihedral  :  4.333  18.774   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       3.92007 ( 1980)
  SS BOND              : bond        0.00092 (    6)
  SS BOND              : angle       1.34620 (   12)
  covalent geometry    : bond        0.00393 (11708)
  covalent geometry    : angle       0.62799 (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  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6887 (pt0)
REVERT: A   82 MET cc_start: 0.7567 (mtt) cc_final: 0.7277 (mtt)
REVERT: A  161 GLU cc_start: 0.6913 (mp0) cc_final: 0.6640 (mp0)
REVERT: A  239 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7850 (ttt180)
REVERT: A  313 ASN cc_start: 0.7793 (p0) cc_final: 0.7501 (p0)
REVERT: A  360 LYS cc_start: 0.8262 (mttt) cc_final: 0.7978 (mtmt)
REVERT: A  573 LYS cc_start: 0.8508 (mttt) cc_final: 0.7998 (mmtm)
REVERT: A  587 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7997 (mp)
REVERT: A  589 GLU cc_start: 0.6918 (pt0) cc_final: 0.6450 (pm20)
REVERT: B   63 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6930 (pt0)
REVERT: B   82 MET cc_start: 0.7565 (mtt) cc_final: 0.7278 (mtt)
REVERT: B  161 GLU cc_start: 0.6907 (mp0) cc_final: 0.6647 (mp0)
REVERT: B  239 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7838 (ttt180)
REVERT: B  313 ASN cc_start: 0.7790 (p0) cc_final: 0.7531 (p0)
REVERT: B  360 LYS cc_start: 0.8256 (mttt) cc_final: 0.7984 (mtmt)
REVERT: B  573 LYS cc_start: 0.8519 (mttt) cc_final: 0.8009 (mmtm)
REVERT: B  587 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7986 (mp)
REVERT: B  589 GLU cc_start: 0.6927 (pt0) cc_final: 0.6447 (pm20)
  outliers start: 24
  outliers final: 8
  residues processed: 197
  average time/residue: 0.2853
  time to fit residues: 75.7907
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  : 1.210 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 91 optimal weight:    4.9990
   chunk 128 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0870
   chunk 24 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.1164

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.140070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.126962 restraints weight = 12412.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.112163 restraints weight = 22847.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.111039 restraints weight = 19240.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11714  Z= 0.149
  Angle     :  0.576  13.613  15890  Z= 0.291
  Chirality :  0.041   0.150   1834
  Planarity :  0.004   0.041   1994
  Dihedral  :  4.168  19.640   1574
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.02 %
    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:  1.54 (0.22), residues: 1446
  helix:  2.13 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -0.96 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 278 
 HIS   0.006   0.001   HIS A 865 
 PHE   0.019   0.002   PHE B 289 
 TYR   0.014   0.002   TYR B 613 
 ARG   0.004   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04510 (  670)
  hydrogen bonds       : angle       3.80601 ( 1980)
  SS BOND              : bond        0.00154 (    6)
  SS BOND              : angle       1.00799 (   12)
  covalent geometry    : bond        0.00352 (11708)
  covalent geometry    : angle       0.57548 (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
  166 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 1.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7620 (mtt) cc_final: 0.7320 (mtt)
REVERT: A  119 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5968 (mp0)
REVERT: A  161 GLU cc_start: 0.7416 (mp0) cc_final: 0.6840 (mp0)
REVERT: A  313 ASN cc_start: 0.7858 (p0) cc_final: 0.7617 (p0)
REVERT: A  360 LYS cc_start: 0.8277 (mttt) cc_final: 0.7897 (mtmm)
REVERT: A  573 LYS cc_start: 0.8662 (mttt) cc_final: 0.8378 (mtmm)
REVERT: A  587 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8209 (mp)
REVERT: A  589 GLU cc_start: 0.6878 (pt0) cc_final: 0.6431 (pm20)
REVERT: B   82 MET cc_start: 0.7634 (mtt) cc_final: 0.7342 (mtt)
REVERT: B  119 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5962 (mp0)
REVERT: B  161 GLU cc_start: 0.7425 (mp0) cc_final: 0.6862 (mp0)
REVERT: B  313 ASN cc_start: 0.7878 (p0) cc_final: 0.7644 (p0)
REVERT: B  360 LYS cc_start: 0.8283 (mttt) cc_final: 0.7906 (mtmm)
REVERT: B  573 LYS cc_start: 0.8650 (mttt) cc_final: 0.8355 (mtmm)
REVERT: B  587 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8203 (mp)
REVERT: B  589 GLU cc_start: 0.6906 (pt0) cc_final: 0.6454 (pm20)
  outliers start: 28
  outliers final: 14
  residues processed: 155
  average time/residue: 0.2926
  time to fit residues: 62.0855
Evaluate side-chains
  131 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
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  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  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:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 106 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0870
   chunk 71 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.5558

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.141330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.128668 restraints weight = 12381.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.112030 restraints weight = 21793.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.111817 restraints weight = 20288.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11714  Z= 0.106
  Angle     :  0.544  10.786  15890  Z= 0.273
  Chirality :  0.038   0.162   1834
  Planarity :  0.004   0.043   1994
  Dihedral  :  3.952  18.164   1574
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.42 %
    Favored  : 85.51 %
  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:  2.26 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.94 (0.25), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 278 
 HIS   0.007   0.001   HIS A 865 
 PHE   0.017   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        0.03586 (  670)
  hydrogen bonds       : angle       3.63825 ( 1980)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       3.00217 (   12)
  covalent geometry    : bond        0.00236 (11708)
  covalent geometry    : angle       0.53811 (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
  153 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7613 (mtt) cc_final: 0.7333 (mtt)
REVERT: A  119 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5804 (mp0)
REVERT: A  120 CYS cc_start: 0.6285 (OUTLIER) cc_final: 0.5968 (m)
REVERT: A  360 LYS cc_start: 0.8210 (mttt) cc_final: 0.7827 (mtmm)
REVERT: A  573 LYS cc_start: 0.8608 (mttt) cc_final: 0.8330 (mtmm)
REVERT: A  587 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: A  589 GLU cc_start: 0.6843 (pt0) cc_final: 0.6338 (pm20)
REVERT: B   82 MET cc_start: 0.7647 (mtt) cc_final: 0.7379 (mtt)
REVERT: B  119 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5792 (mp0)
REVERT: B  120 CYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5961 (m)
REVERT: B  360 LYS cc_start: 0.8214 (mttt) cc_final: 0.7839 (mtmm)
REVERT: B  573 LYS cc_start: 0.8607 (mttt) cc_final: 0.8322 (mtmm)
REVERT: B  587 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8137 (mp)
  outliers start: 26
  outliers final: 17
  residues processed: 147
  average time/residue: 0.2974
  time to fit residues: 60.8619
Evaluate side-chains
  136 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
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  484 VAL
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  484 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
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:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0030
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   overall best weight:    1.0394

-------------------------------------------------------------------------------
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 = 0.3377 r_free = 0.3377 target = 0.137691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.124103 restraints weight = 12377.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.108605 restraints weight = 24915.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.108019 restraints weight = 21378.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.5642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11714  Z= 0.133
  Angle     :  0.546  10.971  15890  Z= 0.276
  Chirality :  0.039   0.139   1834
  Planarity :  0.004   0.043   1994
  Dihedral  :  3.971  17.741   1574
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.34 %
    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:  1.62 (0.22), residues: 1446
  helix:  2.21 (0.17), residues: 916
  sheet: -3.23 (0.87), residues: 24
  loop : -0.87 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 278 
 HIS   0.006   0.001   HIS B 865 
 PHE   0.016   0.001   PHE A 473 
 TYR   0.012   0.001   TYR B 613 
 ARG   0.004   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  670)
  hydrogen bonds       : angle       3.68423 ( 1980)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       1.51946 (   12)
  covalent geometry    : bond        0.00320 (11708)
  covalent geometry    : angle       0.54478 (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
  162 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7648 (mtt) cc_final: 0.7392 (mtt)
REVERT: A  119 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5863 (mp0)
REVERT: A  360 LYS cc_start: 0.8248 (mttt) cc_final: 0.8031 (mtmt)
REVERT: A  508 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7634 (mttp)
REVERT: A  573 LYS cc_start: 0.8656 (mttt) cc_final: 0.8127 (mmtm)
REVERT: A  587 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8167 (mp)
REVERT: A  589 GLU cc_start: 0.6877 (pt0) cc_final: 0.6439 (pm20)
REVERT: B   82 MET cc_start: 0.7664 (mtt) cc_final: 0.7408 (mtt)
REVERT: B  119 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5871 (mp0)
REVERT: B  360 LYS cc_start: 0.8260 (mttt) cc_final: 0.8056 (mtmt)
REVERT: B  508 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7748 (mttm)
REVERT: B  573 LYS cc_start: 0.8662 (mttt) cc_final: 0.8117 (mmtm)
REVERT: B  587 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8163 (mp)
REVERT: B  589 GLU cc_start: 0.6902 (pt0) cc_final: 0.6466 (pm20)
  outliers start: 34
  outliers final: 24
  residues processed: 150
  average time/residue: 0.3427
  time to fit residues: 72.7748
Evaluate side-chains
  147 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
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  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  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  119 GLU
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  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:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 144 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 136 optimal weight:    0.0770
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.5742

-------------------------------------------------------------------------------
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 = 0.3334 r_free = 0.3334 target = 0.134270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.121040 restraints weight = 12622.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.105594 restraints weight = 22841.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.105177 restraints weight = 21603.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.6149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11714  Z= 0.177
  Angle     :  0.608   9.991  15890  Z= 0.307
  Chirality :  0.042   0.205   1834
  Planarity :  0.005   0.043   1994
  Dihedral  :  4.320  19.917   1574
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.82 %
    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:  1.36 (0.22), residues: 1446
  helix:  2.08 (0.17), residues: 910
  sheet: -3.19 (0.88), residues: 24
  loop : -1.12 (0.26), residues: 512

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04418 (  670)
  hydrogen bonds       : angle       3.97204 ( 1980)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       4.01525 (   12)
  covalent geometry    : bond        0.00438 (11708)
  covalent geometry    : angle       0.59825 (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
  161 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7664 (mtt) cc_final: 0.7416 (mtt)
REVERT: A  360 LYS cc_start: 0.8282 (mttt) cc_final: 0.7941 (mtmm)
REVERT: A  508 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7950 (mttm)
REVERT: A  573 LYS cc_start: 0.8704 (mttt) cc_final: 0.8283 (mmtm)
REVERT: A  587 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8138 (mp)
REVERT: A  589 GLU cc_start: 0.6871 (pt0) cc_final: 0.6459 (pm20)
REVERT: B   82 MET cc_start: 0.7670 (mtt) cc_final: 0.7429 (mtt)
REVERT: B  360 LYS cc_start: 0.8290 (mttt) cc_final: 0.7950 (mtmm)
REVERT: B  508 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7943 (mttm)
REVERT: B  573 LYS cc_start: 0.8702 (mttt) cc_final: 0.8267 (mmtm)
REVERT: B  587 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8133 (mp)
REVERT: B  589 GLU cc_start: 0.6888 (pt0) cc_final: 0.6480 (pm20)
  outliers start: 35
  outliers final: 27
  residues processed: 147
  average time/residue: 0.2785
  time to fit residues: 57.4732
Evaluate side-chains
  146 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
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  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  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:    7.9990
   chunk 131 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.136258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.123043 restraints weight = 12561.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.120888 restraints weight = 25436.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.107086 restraints weight = 29729.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.6266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11714  Z= 0.115
  Angle     :  0.528   9.096  15890  Z= 0.268
  Chirality :  0.038   0.149   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  4.037  19.586   1574
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.61 %
    Favored  : 84.47 %
  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:  1.55 (0.22), residues: 1446
  helix:  2.25 (0.17), residues: 918
  sheet: -3.35 (0.89), residues: 24
  loop : -1.12 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 590 
 HIS   0.008   0.001   HIS A 865 
 PHE   0.018   0.001   PHE B 429 
 TYR   0.010   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  670)
  hydrogen bonds       : angle       3.68554 ( 1980)
  SS BOND              : bond        0.00610 (    6)
  SS BOND              : angle       3.55178 (   12)
  covalent geometry    : bond        0.00267 (11708)
  covalent geometry    : angle       0.51938 (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
  146 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7655 (mtt) cc_final: 0.7409 (mtt)
REVERT: A  360 LYS cc_start: 0.8291 (mttt) cc_final: 0.8050 (mtmt)
REVERT: A  573 LYS cc_start: 0.8617 (mttt) cc_final: 0.8141 (mmtm)
REVERT: A  587 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: A  589 GLU cc_start: 0.6844 (pt0) cc_final: 0.6416 (pm20)
REVERT: A  670 GLU cc_start: 0.8142 (tp30) cc_final: 0.7733 (tp30)
REVERT: B   82 MET cc_start: 0.7652 (mtt) cc_final: 0.7414 (mtt)
REVERT: B  360 LYS cc_start: 0.8279 (mttt) cc_final: 0.8044 (mtmt)
REVERT: B  573 LYS cc_start: 0.8621 (mttt) cc_final: 0.8110 (mmtm)
REVERT: B  587 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8223 (mp)
REVERT: B  589 GLU cc_start: 0.6867 (pt0) cc_final: 0.6449 (pm20)
REVERT: B  670 GLU cc_start: 0.8144 (tp30) cc_final: 0.7747 (tp30)
  outliers start: 24
  outliers final: 15
  residues processed: 138
  average time/residue: 0.3082
  time to fit residues: 59.2724
Evaluate side-chains
  132 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  484 VAL
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  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue  112 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  665 LEU
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:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 125 optimal weight:    3.9990
   chunk 140 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.134679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.110339 restraints weight = 12529.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.107928 restraints weight = 18501.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.107987 restraints weight = 18605.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.6432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11714  Z= 0.143
  Angle     :  0.573   9.485  15890  Z= 0.285
  Chirality :  0.040   0.139   1834
  Planarity :  0.004   0.044   1994
  Dihedral  :  4.083  18.495   1574
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.54 %
    Favored  : 84.47 %
  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:  1.50 (0.22), residues: 1446
  helix:  2.25 (0.17), residues: 912
  sheet: -3.31 (0.89), residues: 24
  loop : -1.19 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 278 
 HIS   0.009   0.001   HIS A 865 
 PHE   0.017   0.001   PHE A 110 
 TYR   0.011   0.001   TYR A 613 
 ARG   0.003   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  670)
  hydrogen bonds       : angle       3.74149 ( 1980)
  SS BOND              : bond        0.00246 (    6)
  SS BOND              : angle       3.31622 (   12)
  covalent geometry    : bond        0.00348 (11708)
  covalent geometry    : angle       0.56637 (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
  143 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7619 (mtt) cc_final: 0.7371 (mtt)
REVERT: A  123 LYS cc_start: 0.7486 (mtpp) cc_final: 0.6625 (mmtt)
REVERT: A  360 LYS cc_start: 0.8284 (mttt) cc_final: 0.8068 (mtmt)
REVERT: A  573 LYS cc_start: 0.8662 (mttt) cc_final: 0.8273 (mmtm)
REVERT: A  587 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8127 (mp)
REVERT: A  589 GLU cc_start: 0.6827 (pt0) cc_final: 0.6432 (pm20)
REVERT: A  670 GLU cc_start: 0.8228 (tp30) cc_final: 0.7856 (tp30)
REVERT: B   82 MET cc_start: 0.7633 (mtt) cc_final: 0.7399 (mtt)
REVERT: B  360 LYS cc_start: 0.8286 (mttt) cc_final: 0.8080 (mtmt)
REVERT: B  396 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8673 (tp)
REVERT: B  573 LYS cc_start: 0.8662 (mttt) cc_final: 0.8266 (mmtm)
REVERT: B  587 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: B  589 GLU cc_start: 0.6873 (pt0) cc_final: 0.6465 (pm20)
REVERT: B  670 GLU cc_start: 0.8234 (tp30) cc_final: 0.7867 (tp30)
  outliers start: 25
  outliers final: 21
  residues processed: 132
  average time/residue: 0.2948
  time to fit residues: 54.7666
Evaluate side-chains
  140 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
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  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  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  396 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 128 optimal weight:    8.9990
   chunk 137 optimal weight:    0.3980
   chunk 98 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.136341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.123764 restraints weight = 12627.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.108137 restraints weight = 25631.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.107056 restraints weight = 21039.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.6493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11714  Z= 0.112
  Angle     :  0.526   9.034  15890  Z= 0.262
  Chirality :  0.038   0.139   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.898  17.916   1574
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.61 %
    Favored  : 84.32 %
  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:  1.62 (0.22), residues: 1446
  helix:  2.33 (0.17), residues: 918
  sheet: -3.42 (0.89), residues: 24
  loop : -1.14 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 590 
 HIS   0.009   0.001   HIS A 865 
 PHE   0.014   0.001   PHE A 473 
 TYR   0.009   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  670)
  hydrogen bonds       : angle       3.63603 ( 1980)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       2.65382 (   12)
  covalent geometry    : bond        0.00261 (11708)
  covalent geometry    : angle       0.52099 (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
  145 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7677 (mtt) cc_final: 0.7447 (mtt)
REVERT: A  119 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6178 (mp0)
REVERT: A  360 LYS cc_start: 0.8225 (mttt) cc_final: 0.7980 (mtmt)
REVERT: A  573 LYS cc_start: 0.8589 (mttt) cc_final: 0.8112 (mmtm)
REVERT: A  587 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: A  589 GLU cc_start: 0.6806 (pt0) cc_final: 0.6376 (pm20)
REVERT: A  670 GLU cc_start: 0.8137 (tp30) cc_final: 0.7567 (tp30)
REVERT: B   82 MET cc_start: 0.7672 (mtt) cc_final: 0.7451 (mtt)
REVERT: B  119 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6129 (mp0)
REVERT: B  360 LYS cc_start: 0.8222 (mttt) cc_final: 0.7980 (mtmt)
REVERT: B  573 LYS cc_start: 0.8665 (mttt) cc_final: 0.8125 (mmtm)
REVERT: B  587 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8168 (mp)
REVERT: B  589 GLU cc_start: 0.6827 (pt0) cc_final: 0.6404 (pm20)
REVERT: B  670 GLU cc_start: 0.8146 (tp30) cc_final: 0.7577 (tp30)
  outliers start: 26
  outliers final: 19
  residues processed: 137
  average time/residue: 0.3484
  time to fit residues: 67.1055
Evaluate side-chains
  137 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
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  484 VAL
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  119 GLU
Chi-restraints excluded: chain B residue  394 MET
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  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:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 129 optimal weight:    0.6980
   chunk 135 optimal weight:    8.9990
   chunk 101 optimal weight:    0.7980
   chunk 139 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.134421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.121545 restraints weight = 12523.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.105642 restraints weight = 23183.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.104607 restraints weight = 21103.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.6603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11714  Z= 0.134
  Angle     :  0.558  11.033  15890  Z= 0.276
  Chirality :  0.039   0.135   1834
  Planarity :  0.004   0.044   1994
  Dihedral  :  3.991  17.756   1574
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.77 %
    Favored  : 84.24 %
  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:  1.58 (0.22), residues: 1446
  helix:  2.32 (0.17), residues: 914
  sheet: -3.37 (0.89), residues: 24
  loop : -1.18 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 278 
 HIS   0.008   0.001   HIS B 865 
 PHE   0.016   0.001   PHE B 110 
 TYR   0.011   0.001   TYR A 613 
 ARG   0.003   0.000   ARG B 861 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  670)
  hydrogen bonds       : angle       3.71079 ( 1980)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       2.49701 (   12)
  covalent geometry    : bond        0.00325 (11708)
  covalent geometry    : angle       0.55392 (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
  141 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7641 (mtt) cc_final: 0.7404 (mtt)
REVERT: A  119 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6045 (mp0)
REVERT: A  360 LYS cc_start: 0.8250 (mttt) cc_final: 0.8003 (mtmt)
REVERT: A  573 LYS cc_start: 0.8628 (mttt) cc_final: 0.8127 (mmtm)
REVERT: A  587 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: A  670 GLU cc_start: 0.8157 (tp30) cc_final: 0.7747 (tp30)
REVERT: B   82 MET cc_start: 0.7652 (mtt) cc_final: 0.7424 (mtt)
REVERT: B  119 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6044 (mp0)
REVERT: B  360 LYS cc_start: 0.8243 (mttt) cc_final: 0.8007 (mtmt)
REVERT: B  573 LYS cc_start: 0.8652 (mttt) cc_final: 0.8170 (mmtm)
REVERT: B  587 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: B  670 GLU cc_start: 0.8168 (tp30) cc_final: 0.7753 (tp30)
  outliers start: 25
  outliers final: 21
  residues processed: 134
  average time/residue: 0.3986
  time to fit residues: 75.2161
Evaluate side-chains
  140 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 2.643 
-------------------------------------------------------------------------------
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  484 VAL
Chi-restraints excluded: chain A residue  486 SER
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  119 GLU
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  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:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 128 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0270
   chunk 100 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.7238

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.135835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.123295 restraints weight = 12520.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.108564 restraints weight = 21499.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.106762 restraints weight = 19481.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11714  Z= 0.112
  Angle     :  0.531  10.955  15890  Z= 0.263
  Chirality :  0.038   0.137   1834
  Planarity :  0.004   0.045   1994
  Dihedral  :  3.884  17.635   1574
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.54 %
    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:  1.67 (0.22), residues: 1446
  helix:  2.38 (0.17), residues: 918
  sheet: -3.43 (0.89), residues: 24
  loop : -1.14 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 590 
 HIS   0.009   0.001   HIS B 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        0.03584 (  670)
  hydrogen bonds       : angle       3.63902 ( 1980)
  SS BOND              : bond        0.00186 (    6)
  SS BOND              : angle       2.29187 (   12)
  covalent geometry    : bond        0.00263 (11708)
  covalent geometry    : angle       0.52767 (15878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4141.83 seconds
wall clock time: 78 minutes 7.23 seconds (4687.23 seconds total)