Starting phenix.real_space_refine
on Sat Oct 11 03:53:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jpj_36481/10_2025/8jpj_36481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jpj_36481/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jpj_36481/10_2025/8jpj_36481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jpj_36481/10_2025/8jpj_36481.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jpj_36481/10_2025/8jpj_36481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jpj_36481/10_2025/8jpj_36481.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'PHE:plan': 1, '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: 4.96, per 1000 atoms: 0.43
  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: 0.88
  Conformation dependent library (CDL) restraints added in 540.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.30
  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: 1.65

  Time building geometry restraints manager: 1.17 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: 0.02
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:             2.200
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.530
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 583 
 TYR   0.012   0.001   TYR A 866 
 PHE   0.012   0.001   PHE B 101 
 TRP   0.008   0.001   TRP A 303 
 HIS   0.002   0.000   HIS A 515 

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

*********************** 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  : 0.430 
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: 0.1352
  time to fit residues: 60.0661
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  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 819 HIS
B 852 ASN
B 859 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.148362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.137831 restraints weight = 12435.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.121431 restraints weight = 20197.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.121199 restraints weight = 18581.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.121068 restraints weight = 18472.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.121138 restraints weight = 17304.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11714  Z= 0.169
  Angle     :  0.650   8.894  15890  Z= 0.335
  Chirality :  0.043   0.155   1834
  Planarity :  0.005   0.044   1994
  Dihedral  :  4.417  18.776   1574
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.39 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.22), residues: 1446
  helix:  1.90 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -0.88 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 861 
 TYR   0.016   0.002   TYR B 806 
 PHE   0.029   0.002   PHE A 473 
 TRP   0.015   0.002   TRP B 272 
 HIS   0.007   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (11708)
  covalent geometry    : angle       0.64922 (15878)
  SS BOND              : bond        0.00098 (    6)
  SS BOND              : angle       1.17362 (   12)
  hydrogen bonds       : bond        0.04437 (  670)
  hydrogen bonds       : angle       3.99235 ( 1980)

*********************** 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
  208 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 182
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7573 (mtt) cc_final: 0.7285 (mtt)
REVERT: A  161 GLU cc_start: 0.6921 (mp0) cc_final: 0.6658 (mp0)
REVERT: A  239 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7906 (ttt180)
REVERT: A  313 ASN cc_start: 0.7797 (p0) cc_final: 0.7511 (p0)
REVERT: A  360 LYS cc_start: 0.8297 (mttt) cc_final: 0.8027 (mtmt)
REVERT: A  573 LYS cc_start: 0.8558 (mttt) cc_final: 0.8068 (mmtm)
REVERT: A  587 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8011 (mp)
REVERT: A  589 GLU cc_start: 0.6965 (pt0) cc_final: 0.6520 (pm20)
REVERT: B   82 MET cc_start: 0.7585 (mtt) cc_final: 0.7303 (mtt)
REVERT: B  161 GLU cc_start: 0.6923 (mp0) cc_final: 0.6665 (mp0)
REVERT: B  239 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7892 (ttt180)
REVERT: B  313 ASN cc_start: 0.7808 (p0) cc_final: 0.7540 (p0)
REVERT: B  360 LYS cc_start: 0.8306 (mttt) cc_final: 0.8060 (mtmt)
REVERT: B  573 LYS cc_start: 0.8570 (mttt) cc_final: 0.8066 (mmtm)
REVERT: B  587 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8018 (mp)
REVERT: B  589 GLU cc_start: 0.6968 (pt0) cc_final: 0.6512 (pm20)
  outliers start: 26
  outliers final: 10
  residues processed: 198
  average time/residue: 0.1241
  time to fit residues: 33.6762
Evaluate side-chains
  154 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  235 ASP
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  235 ASP
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 57 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 135 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
B 355 ASN
B 456 GLN
B 852 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.135168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.125367 restraints weight = 12736.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.119375 restraints weight = 19613.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.104813 restraints weight = 31902.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.104291 restraints weight = 25696.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.104528 restraints weight = 22906.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11714  Z= 0.199
  Angle     :  0.660  16.695  15890  Z= 0.331
  Chirality :  0.044   0.164   1834
  Planarity :  0.005   0.044   1994
  Dihedral  :  4.457  20.663   1574
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 11.31 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.22), residues: 1446
  helix:  1.92 (0.17), residues: 906
  sheet: -2.99 (0.88), residues: 24
  loop : -0.94 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 861 
 TYR   0.016   0.002   TYR B 613 
 PHE   0.023   0.002   PHE A 110 
 TRP   0.010   0.002   TRP B 278 
 HIS   0.007   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (11708)
  covalent geometry    : angle       0.65912 (15878)
  SS BOND              : bond        0.01195 (    6)
  SS BOND              : angle       1.05726 (   12)
  hydrogen bonds       : bond        0.05237 (  670)
  hydrogen bonds       : angle       3.99833 ( 1980)

*********************** 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
  184 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7701 (mtt) cc_final: 0.7423 (mtt)
REVERT: A  119 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5990 (mp0)
REVERT: A  177 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8157 (tp)
REVERT: A  313 ASN cc_start: 0.7944 (p0) cc_final: 0.7683 (p0)
REVERT: A  360 LYS cc_start: 0.8300 (mttt) cc_final: 0.8053 (mtmt)
REVERT: A  508 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7545 (mttp)
REVERT: A  573 LYS cc_start: 0.8714 (mttt) cc_final: 0.8446 (mtmm)
REVERT: A  587 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8108 (mp)
REVERT: A  589 GLU cc_start: 0.6874 (pt0) cc_final: 0.6452 (pm20)
REVERT: B   82 MET cc_start: 0.7681 (mtt) cc_final: 0.7400 (mtt)
REVERT: B  119 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5985 (mp0)
REVERT: B  177 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (tp)
REVERT: B  313 ASN cc_start: 0.7931 (p0) cc_final: 0.7692 (p0)
REVERT: B  360 LYS cc_start: 0.8321 (mttt) cc_final: 0.8066 (mtmt)
REVERT: B  508 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7554 (mttp)
REVERT: B  573 LYS cc_start: 0.8724 (mttt) cc_final: 0.8457 (mtmm)
REVERT: B  587 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8103 (mp)
REVERT: B  589 GLU cc_start: 0.6879 (pt0) cc_final: 0.6464 (pm20)
  outliers start: 39
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1323
  time to fit residues: 29.9314
Evaluate side-chains
  148 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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  177 LEU
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  394 MET
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  396 LEU
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  662 SER
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  177 LEU
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  394 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  396 LEU
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  616 THR
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 102 optimal weight:    2.9990
   chunk 123 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 138 optimal weight:    0.0270
   chunk 59 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 120 optimal weight:    0.6980
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.5840

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.138410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.128575 restraints weight = 12722.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.110166 restraints weight = 22877.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.108756 restraints weight = 27567.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.108994 restraints weight = 25272.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.109352 restraints weight = 19640.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.5717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11714  Z= 0.110
  Angle     :  0.562  11.774  15890  Z= 0.281
  Chirality :  0.039   0.171   1834
  Planarity :  0.004   0.044   1994
  Dihedral  :  4.103  20.255   1574
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.58 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.22), residues: 1446
  helix:  2.13 (0.17), residues: 910
  sheet: -3.21 (0.88), residues: 24
  loop : -0.91 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 672 
 TYR   0.010   0.001   TYR B 613 
 PHE   0.017   0.001   PHE A 473 
 TRP   0.007   0.001   TRP B 590 
 HIS   0.005   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11708)
  covalent geometry    : angle       0.55596 (15878)
  SS BOND              : bond        0.00123 (    6)
  SS BOND              : angle       3.09208 (   12)
  hydrogen bonds       : bond        0.03775 (  670)
  hydrogen bonds       : angle       3.74285 ( 1980)

*********************** 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
  151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7635 (mtt) cc_final: 0.7365 (mtt)
REVERT: A  119 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6052 (mp0)
REVERT: A  360 LYS cc_start: 0.8281 (mttt) cc_final: 0.7941 (mtmm)
REVERT: A  508 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7532 (mttp)
REVERT: A  573 LYS cc_start: 0.8630 (mttt) cc_final: 0.8105 (mmtm)
REVERT: A  587 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (mp)
REVERT: A  589 GLU cc_start: 0.6872 (pt0) cc_final: 0.6457 (pm20)
REVERT: B   82 MET cc_start: 0.7657 (mtt) cc_final: 0.7392 (mtt)
REVERT: B  119 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6048 (mp0)
REVERT: B  360 LYS cc_start: 0.8292 (mttt) cc_final: 0.7955 (mtmm)
REVERT: B  508 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7535 (mttp)
REVERT: B  573 LYS cc_start: 0.8642 (mttt) cc_final: 0.8127 (mmtm)
REVERT: B  587 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8192 (mp)
REVERT: B  589 GLU cc_start: 0.6890 (pt0) cc_final: 0.6476 (pm20)
  outliers start: 28
  outliers final: 14
  residues processed: 137
  average time/residue: 0.1459
  time to fit residues: 27.6120
Evaluate side-chains
  136 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
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  131 LEU
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 90 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 127 optimal weight:    6.9990
   chunk 125 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.133248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.107282 restraints weight = 12642.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.106229 restraints weight = 14201.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.106001 restraints weight = 16050.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.105996 restraints weight = 15085.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.105981 restraints weight = 14843.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.6158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11714  Z= 0.204
  Angle     :  0.646  12.176  15890  Z= 0.327
  Chirality :  0.044   0.213   1834
  Planarity :  0.005   0.045   1994
  Dihedral  :  4.381  20.822   1574
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.22), residues: 1446
  helix:  1.89 (0.17), residues: 916
  sheet: -3.12 (0.88), residues: 24
  loop : -1.07 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 861 
 TYR   0.014   0.002   TYR B 613 
 PHE   0.021   0.002   PHE A 110 
 TRP   0.010   0.002   TRP A 278 
 HIS   0.007   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (11708)
  covalent geometry    : angle       0.63666 (15878)
  SS BOND              : bond        0.00440 (    6)
  SS BOND              : angle       4.04377 (   12)
  hydrogen bonds       : bond        0.04711 (  670)
  hydrogen bonds       : angle       3.99485 ( 1980)

*********************** 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
  150 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 112
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7634 (mtt) cc_final: 0.7365 (mtt)
REVERT: A  119 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.6018 (mp0)
REVERT: A  177 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8244 (tp)
REVERT: A  360 LYS cc_start: 0.8310 (mttt) cc_final: 0.8011 (mtmm)
REVERT: A  573 LYS cc_start: 0.8765 (mttt) cc_final: 0.8377 (mmtm)
REVERT: A  587 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8124 (mp)
REVERT: A  589 GLU cc_start: 0.6902 (pt0) cc_final: 0.6519 (pm20)
REVERT: B   82 MET cc_start: 0.7664 (mtt) cc_final: 0.7402 (mtt)
REVERT: B  119 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.6012 (mp0)
REVERT: B  177 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8258 (tp)
REVERT: B  360 LYS cc_start: 0.8316 (mttt) cc_final: 0.8010 (mtmm)
REVERT: B  573 LYS cc_start: 0.8768 (mttt) cc_final: 0.8382 (mmtm)
REVERT: B  587 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8108 (mp)
REVERT: B  589 GLU cc_start: 0.6905 (pt0) cc_final: 0.6518 (pm20)
  outliers start: 38
  outliers final: 28
  residues processed: 137
  average time/residue: 0.1307
  time to fit residues: 25.0284
Evaluate side-chains
  140 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
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  125 CYS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 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  639 ASN
Chi-restraints excluded: chain A residue  662 SER
Chi-restraints excluded: chain A residue  761 SER
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  177 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0970
   chunk 18 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0980
   chunk 42 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.137737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.111554 restraints weight = 12545.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.110802 restraints weight = 14484.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.110662 restraints weight = 15395.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.110590 restraints weight = 15619.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.110476 restraints weight = 14947.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.6176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11714  Z= 0.104
  Angle     :  0.524  10.101  15890  Z= 0.264
  Chirality :  0.038   0.139   1834
  Planarity :  0.004   0.047   1994
  Dihedral  :  4.058  19.728   1574
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.14 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.22), residues: 1446
  helix:  2.23 (0.17), residues: 914
  sheet: -3.27 (0.88), residues: 24
  loop : -1.04 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 861 
 TYR   0.009   0.001   TYR B 613 
 PHE   0.017   0.001   PHE B 429 
 TRP   0.008   0.001   TRP B 590 
 HIS   0.007   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (11708)
  covalent geometry    : angle       0.52012 (15878)
  SS BOND              : bond        0.00515 (    6)
  SS BOND              : angle       2.27903 (   12)
  hydrogen bonds       : bond        0.03585 (  670)
  hydrogen bonds       : angle       3.73893 ( 1980)

*********************** 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
  144 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7618 (mtt) cc_final: 0.7364 (mtt)
REVERT: A  360 LYS cc_start: 0.8256 (mttt) cc_final: 0.8043 (mtmt)
REVERT: A  573 LYS cc_start: 0.8617 (mttt) cc_final: 0.8141 (mmtm)
REVERT: A  589 GLU cc_start: 0.6883 (pt0) cc_final: 0.6470 (pm20)
REVERT: B   82 MET cc_start: 0.7631 (mtt) cc_final: 0.7378 (mtt)
REVERT: B  573 LYS cc_start: 0.8619 (mttt) cc_final: 0.8176 (mmtm)
REVERT: B  589 GLU cc_start: 0.6905 (pt0) cc_final: 0.6493 (pm20)
REVERT: B  670 GLU cc_start: 0.8091 (tp30) cc_final: 0.7724 (tp30)
  outliers start: 27
  outliers final: 20
  residues processed: 132
  average time/residue: 0.1339
  time to fit residues: 24.8113
Evaluate side-chains
  128 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  849 THR
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
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 115 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 138 optimal weight:    9.9990
   chunk 137 optimal weight:    0.0170
   chunk 0 optimal weight:    8.9990
   chunk 106 optimal weight:    0.9990
   chunk 112 optimal weight:    0.6980
   chunk 116 optimal weight:    1.9990
   overall best weight:    0.9222

-------------------------------------------------------------------------------
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 = 0.136302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.122872 restraints weight = 12529.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.107091 restraints weight = 21437.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.106765 restraints weight = 19368.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.106519 restraints weight = 19435.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.107036 restraints weight = 16684.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.6305

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= 0.126
  Angle     :  0.542   9.872  15890  Z= 0.273
  Chirality :  0.039   0.136   1834
  Planarity :  0.004   0.046   1994
  Dihedral  :  4.040  18.656   1574
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.18 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.93 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.22), residues: 1446
  helix:  2.27 (0.17), residues: 916
  sheet: -3.32 (0.88), residues: 24
  loop : -1.09 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 861 
 TYR   0.010   0.001   TYR A 613 
 PHE   0.014   0.001   PHE A 473 
 TRP   0.008   0.001   TRP A 278 
 HIS   0.006   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11708)
  covalent geometry    : angle       0.53604 (15878)
  SS BOND              : bond        0.00378 (    6)
  SS BOND              : angle       2.98739 (   12)
  hydrogen bonds       : bond        0.03807 (  670)
  hydrogen bonds       : angle       3.72212 ( 1980)

*********************** 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
  147 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7628 (mtt) cc_final: 0.7380 (mtt)
REVERT: A  360 LYS cc_start: 0.8210 (mttt) cc_final: 0.7964 (mtmt)
REVERT: A  573 LYS cc_start: 0.8636 (mttt) cc_final: 0.8141 (mmtm)
REVERT: A  587 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8171 (mp)
REVERT: B   82 MET cc_start: 0.7648 (mtt) cc_final: 0.7396 (mtt)
REVERT: B  573 LYS cc_start: 0.8638 (mttt) cc_final: 0.8122 (mmtm)
REVERT: B  587 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8196 (mp)
REVERT: B  670 GLU cc_start: 0.8121 (tp30) cc_final: 0.7723 (tp30)
  outliers start: 31
  outliers final: 24
  residues processed: 135
  average time/residue: 0.1313
  time to fit residues: 24.9212
Evaluate side-chains
  136 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
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  396 LEU
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  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  395 VAL
Chi-restraints excluded: chain B residue  396 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 115 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 135 optimal weight:    7.9990
   chunk 102 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 140 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.9386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.130995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.117421 restraints weight = 12815.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.099382 restraints weight = 32675.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.099025 restraints weight = 26605.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.099490 restraints weight = 24679.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.099860 restraints weight = 20042.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.6680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11714  Z= 0.207
  Angle     :  0.638  10.682  15890  Z= 0.322
  Chirality :  0.043   0.166   1834
  Planarity :  0.005   0.045   1994
  Dihedral  :  4.484  21.258   1574
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.49 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.22), residues: 1446
  helix:  1.94 (0.17), residues: 918
  sheet: -3.26 (0.88), residues: 24
  loop : -1.28 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 239 
 TYR   0.015   0.002   TYR B 613 
 PHE   0.022   0.002   PHE B 110 
 TRP   0.010   0.002   TRP A 303 
 HIS   0.008   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (11708)
  covalent geometry    : angle       0.63452 (15878)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       2.53953 (   12)
  hydrogen bonds       : bond        0.04777 (  670)
  hydrogen bonds       : angle       3.97310 ( 1980)

*********************** 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
  147 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7631 (mtt) cc_final: 0.7369 (mtt)
REVERT: A  360 LYS cc_start: 0.8260 (mttt) cc_final: 0.7897 (mtmm)
REVERT: A  573 LYS cc_start: 0.8689 (mttt) cc_final: 0.8334 (mmtm)
REVERT: A  587 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8126 (mp)
REVERT: B   82 MET cc_start: 0.7662 (mtt) cc_final: 0.7409 (mtt)
REVERT: B  573 LYS cc_start: 0.8686 (mttt) cc_final: 0.8315 (mmtm)
REVERT: B  587 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8148 (mp)
  outliers start: 31
  outliers final: 27
  residues processed: 136
  average time/residue: 0.1262
  time to fit residues: 24.3490
Evaluate side-chains
  144 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  396 LEU
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  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  396 LEU
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 28 optimal weight:    0.0670
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0040
   chunk 74 optimal weight:    3.9990
   chunk 105 optimal weight:    0.5980
   chunk 56 optimal weight:    6.9990
   chunk 140 optimal weight:    0.6980
   chunk 115 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.4530

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.136747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.123355 restraints weight = 12409.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 96)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.108905 restraints weight = 21083.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.108927 restraints weight = 18188.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.108858 restraints weight = 17360.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.109060 restraints weight = 16027.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.6646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11714  Z= 0.103
  Angle     :  0.506   9.358  15890  Z= 0.255
  Chirality :  0.037   0.139   1834
  Planarity :  0.004   0.047   1994
  Dihedral  :  3.988  19.612   1574
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.53 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.22), residues: 1446
  helix:  2.34 (0.17), residues: 916
  sheet: -3.40 (0.89), residues: 24
  loop : -1.20 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 861 
 TYR   0.008   0.001   TYR B 613 
 PHE   0.014   0.001   PHE A 473 
 TRP   0.010   0.001   TRP B 590 
 HIS   0.010   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (11708)
  covalent geometry    : angle       0.50359 (15878)
  SS BOND              : bond        0.00183 (    6)
  SS BOND              : angle       1.80490 (   12)
  hydrogen bonds       : bond        0.03454 (  670)
  hydrogen bonds       : angle       3.67364 ( 1980)

*********************** 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: 23
    poor density    : 122
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A  360 LYS cc_start: 0.8224 (mttt) cc_final: 0.7990 (mtmt)
REVERT: A  573 LYS cc_start: 0.8612 (mttt) cc_final: 0.8199 (mmtm)
REVERT: A  587 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8105 (mp)
REVERT: A  670 GLU cc_start: 0.8234 (tp30) cc_final: 0.7683 (tp30)
REVERT: B  573 LYS cc_start: 0.8612 (mttt) cc_final: 0.8214 (mmtm)
REVERT: B  587 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8134 (mp)
REVERT: B  670 GLU cc_start: 0.8127 (tp30) cc_final: 0.7766 (tp30)
  outliers start: 23
  outliers final: 21
  residues processed: 137
  average time/residue: 0.1103
  time to fit residues: 21.5886
Evaluate side-chains
  135 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  396 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   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  396 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  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 137 optimal weight:    0.6980
   chunk 125 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.135639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.121878 restraints weight = 12515.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.119186 restraints weight = 22844.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.104299 restraints weight = 27738.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.105280 restraints weight = 23360.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.104932 restraints weight = 22568.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.6710

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= 0.119
  Angle     :  0.531   9.785  15890  Z= 0.269
  Chirality :  0.038   0.155   1834
  Planarity :  0.004   0.047   1994
  Dihedral  :  4.011  18.318   1574
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.61 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.22), residues: 1446
  helix:  2.34 (0.17), residues: 916
  sheet: -3.43 (0.88), residues: 24
  loop : -1.18 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 861 
 TYR   0.010   0.001   TYR A 435 
 PHE   0.015   0.001   PHE A 110 
 TRP   0.008   0.001   TRP B 278 
 HIS   0.009   0.001   HIS A 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11708)
  covalent geometry    : angle       0.52928 (15878)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       1.68375 (   12)
  hydrogen bonds       : bond        0.03650 (  670)
  hydrogen bonds       : angle       3.68740 ( 1980)

********************** 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
  138 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  360 LYS cc_start: 0.8224 (mttt) cc_final: 0.7973 (mtmt)
REVERT: A  573 LYS cc_start: 0.8627 (mttt) cc_final: 0.8201 (mmtm)
REVERT: A  587 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: A  670 GLU cc_start: 0.8167 (tp30) cc_final: 0.7611 (tp30)
REVERT: B  573 LYS cc_start: 0.8613 (mttt) cc_final: 0.8190 (mmtm)
REVERT: B  587 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: B  670 GLU cc_start: 0.8118 (tp30) cc_final: 0.7731 (tp30)
  outliers start: 25
  outliers final: 23
  residues processed: 130
  average time/residue: 0.1290
  time to fit residues: 23.5857
Evaluate side-chains
  131 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
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  396 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  591 GLU
Chi-restraints excluded: chain A residue  618 ILE
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   84 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  396 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  623 SER
Chi-restraints excluded: chain B residue  662 SER
Chi-restraints excluded: chain B residue  761 SER
Chi-restraints excluded: chain B residue  847 ILE
Chi-restraints excluded: chain B residue  849 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 140 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.137245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.123623 restraints weight = 12417.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.109514 restraints weight = 24791.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.108858 restraints weight = 21710.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.108929 restraints weight = 20482.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.109131 restraints weight = 18316.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.6762

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= 0.111
  Angle     :  0.513   9.266  15890  Z= 0.260
  Chirality :  0.038   0.140   1834
  Planarity :  0.004   0.046   1994
  Dihedral  :  3.915  17.906   1574
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.76 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.22), residues: 1446
  helix:  2.39 (0.17), residues: 920
  sheet: -3.44 (0.88), residues: 24
  loop : -1.16 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 861 
 TYR   0.008   0.001   TYR A 613 
 PHE   0.014   0.001   PHE A 473 
 TRP   0.007   0.001   TRP A 278 
 HIS   0.009   0.001   HIS B 865 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (11708)
  covalent geometry    : angle       0.51183 (15878)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       1.56140 (   12)
  hydrogen bonds       : bond        0.03486 (  670)
  hydrogen bonds       : angle       3.62745 ( 1980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1883.95 seconds
wall clock time: 33 minutes 24.70 seconds (2004.70 seconds total)