Starting phenix.real_space_refine
on Fri Aug 22 21:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tny_41429/08_2025/8tny_41429.cif"
  }
  resolution = 3.55
  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=   0.002 sd=   0.017
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    5258      2.51       5
     N    1316      2.21       5
     O    1408      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8026
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4008
          Classifications: {'peptide': 545}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 17, 'TRANS': 527}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 284
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 18, 'TYR:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 119
    Chain: "A"
      Number of atoms: 4008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4008
          Classifications: {'peptide': 545}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 17, 'TRANS': 527}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 284
          Unresolved non-hydrogen dihedrals: 186
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 18, 'TYR:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 119
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'SO4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.20, per 1000 atoms: 0.27
  Number of scatterers: 8026
  At special positions: 0
  Unit cell: (118.118, 65.254, 96.642, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1408      8.00
     N    1316      7.00
     C    5258      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.73
  Conformation dependent library (CDL) restraints added in 362.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      70.8% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 114 through 123
      removed outlier: 3.604A  pdb=" N   VAL B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 134
      removed outlier: 4.043A  pdb=" N   ALA B 128 " --> pdb=" O   PRO B 124 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR B 129 " --> pdb=" O   GLN B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 154
      removed outlier: 3.899A  pdb=" N   GLY B 140 " --> pdb=" O   GLU B 136 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B 141 " --> pdb=" O   PRO B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 184
    Processing helix  chain 'B' and resid 214 through 240
    Processing helix  chain 'B' and resid 241 through 247
      removed outlier: 3.619A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TYR B 247 " --> pdb=" O   VAL B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 273
      removed outlier: 4.167A  pdb=" N   LYS B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   TYR B 271 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 296
    Processing helix  chain 'B' and resid 303 through 316
    Processing helix  chain 'B' and resid 335 through 351
    Processing helix  chain 'B' and resid 352 through 356
    Processing helix  chain 'B' and resid 378 through 408
      removed outlier: 4.961A  pdb=" N   VAL B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ASP B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 424
    Processing helix  chain 'B' and resid 427 through 432
      removed outlier: 3.748A  pdb=" N   HIS B 432 " --> pdb=" O   SER B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 447
    Processing helix  chain 'B' and resid 455 through 470
      removed outlier: 3.645A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 475
    Processing helix  chain 'B' and resid 479 through 496
      removed outlier: 3.877A  pdb=" N   LEU B 483 " --> pdb=" O   GLN B 479 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLY B 493 " --> pdb=" O   VAL B 489 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ALA B 494 " --> pdb=" O   ASN B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 499
      No H-bonds generated for 'chain 'B' and resid 497 through 499'
    Processing helix  chain 'B' and resid 500 through 508
    Processing helix  chain 'B' and resid 508 through 524
      removed outlier: 3.522A  pdb=" N   THR B 512 " --> pdb=" O   SER B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 548
      removed outlier: 3.500A  pdb=" N   ILE B 543 " --> pdb=" O   ILE B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 603
    Processing helix  chain 'B' and resid 605 through 616
    Processing helix  chain 'B' and resid 660 through 678
    Processing helix  chain 'B' and resid 687 through 697
    Processing helix  chain 'B' and resid 711 through 724
      removed outlier: 3.586A  pdb=" N   ASN B 724 " --> pdb=" O   GLU B 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 123
      removed outlier: 3.604A  pdb=" N   VAL A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 134
      removed outlier: 4.043A  pdb=" N   ALA A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 154
      removed outlier: 3.899A  pdb=" N   GLY A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 141 " --> pdb=" O   PRO A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 184
    Processing helix  chain 'A' and resid 214 through 240
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.619A  pdb=" N   VAL A 244 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TYR A 247 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 273
      removed outlier: 4.167A  pdb=" N   LYS A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   TYR A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 296
    Processing helix  chain 'A' and resid 303 through 316
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 352 through 356
    Processing helix  chain 'A' and resid 378 through 408
      removed outlier: 4.961A  pdb=" N   VAL A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ASP A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 424
    Processing helix  chain 'A' and resid 427 through 432
      removed outlier: 3.748A  pdb=" N   HIS A 432 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 447
    Processing helix  chain 'A' and resid 455 through 470
      removed outlier: 3.645A  pdb=" N   VAL A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 475
    Processing helix  chain 'A' and resid 479 through 496
      removed outlier: 3.877A  pdb=" N   LEU A 483 " --> pdb=" O   GLN A 479 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLY A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ALA A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 500 through 508
    Processing helix  chain 'A' and resid 508 through 524
      removed outlier: 3.522A  pdb=" N   THR A 512 " --> pdb=" O   SER A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 548
      removed outlier: 3.501A  pdb=" N   ILE A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 603
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 660 through 678
    Processing helix  chain 'A' and resid 687 through 697
    Processing helix  chain 'A' and resid 711 through 724
      removed outlier: 3.586A  pdb=" N   ASN A 724 " --> pdb=" O   GLU A 720 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 162 through 163
    Processing sheet with id=AA2, first strand: chain 'B' and resid 563 through 565
      removed outlier: 4.779A  pdb=" N   ILE B 580 " --> pdb=" O   LEU B 554 " (cutoff:3.500A)
      removed outlier: 9.061A  pdb=" N   LEU B 556 " --> pdb=" O   ILE B 578 " (cutoff:3.500A)
      removed outlier: 13.115A  pdb=" N   ILE B 578 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS B 579 " --> pdb=" O   VAL B 650 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ASP B 652 " --> pdb=" O   LYS B 579 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   PHE B 581 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   PHE B 709 " --> pdb=" O   VAL B 681 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU B 683 " --> pdb=" O   PHE B 709 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163
    Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 565
      removed outlier: 4.779A  pdb=" N   ILE A 580 " --> pdb=" O   LEU A 554 " (cutoff:3.500A)
      removed outlier: 9.061A  pdb=" N   LEU A 556 " --> pdb=" O   ILE A 578 " (cutoff:3.500A)
      removed outlier: 13.115A  pdb=" N   ILE A 578 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS A 579 " --> pdb=" O   VAL A 650 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   ASP A 652 " --> pdb=" O   LYS A 579 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   PHE A 581 " --> pdb=" O   ASP A 652 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   PHE A 709 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU A 683 " --> pdb=" O   PHE A 709 " (cutoff:3.500A)

    546 hydrogen bonds defined for protein.
    1584 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: 1.26

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1294
        1.32 -     1.44: 2126
        1.44 -     1.57: 4704
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 8184
  Sorted by residual:
  bond pdb=" CA  SER A 126 "
       pdb=" CB  SER A 126 "
    ideal  model  delta    sigma   weight residual
    1.536  1.444  0.091 1.65e-02 3.67e+03 3.06e+01
  bond pdb=" CA  SER B 126 "
       pdb=" CB  SER B 126 "
    ideal  model  delta    sigma   weight residual
    1.536  1.444  0.091 1.65e-02 3.67e+03 3.06e+01
  bond pdb=" O4  SO4 A 801 "
       pdb=" S   SO4 A 801 "
    ideal  model  delta    sigma   weight residual
    1.499  1.430  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" O4  SO4 B 801 "
       pdb=" S   SO4 B 801 "
    ideal  model  delta    sigma   weight residual
    1.499  1.430  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" O3  SO4 B 801 "
       pdb=" S   SO4 B 801 "
    ideal  model  delta    sigma   weight residual
    1.499  1.431  0.068 2.00e-02 2.50e+03 1.15e+01
  ... (remaining 8179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10696
        2.09 -     4.18: 402
        4.18 -     6.27: 40
        6.27 -     8.35: 8
        8.35 -    10.44: 10
  Bond angle restraints: 11156
  Sorted by residual:
  angle pdb=" CA  ILE B 120 "
        pdb=" C   ILE B 120 "
        pdb=" N   LEU B 121 "
      ideal   model   delta    sigma   weight residual
     118.56  111.90    6.66 9.90e-01 1.02e+00 4.53e+01
  angle pdb=" CA  ILE A 120 "
        pdb=" C   ILE A 120 "
        pdb=" N   LEU A 121 "
      ideal   model   delta    sigma   weight residual
     118.56  111.90    6.66 9.90e-01 1.02e+00 4.53e+01
  angle pdb=" C   GLN A 547 "
        pdb=" CA  GLN A 547 "
        pdb=" CB  GLN A 547 "
      ideal   model   delta    sigma   weight residual
     110.79  101.63    9.16 1.66e+00 3.63e-01 3.04e+01
  angle pdb=" C   GLN B 547 "
        pdb=" CA  GLN B 547 "
        pdb=" CB  GLN B 547 "
      ideal   model   delta    sigma   weight residual
     110.79  101.63    9.16 1.66e+00 3.63e-01 3.04e+01
  angle pdb=" N   PRO A 549 "
        pdb=" CD  PRO A 549 "
        pdb=" CG  PRO A 549 "
      ideal   model   delta    sigma   weight residual
     103.20   95.35    7.85 1.50e+00 4.44e-01 2.74e+01
  ... (remaining 11151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 4022
       15.98 -    31.95: 500
       31.95 -    47.93: 176
       47.93 -    63.91: 66
       63.91 -    79.88: 14
  Dihedral angle restraints: 4778
    sinusoidal: 1618
      harmonic: 3160
  Sorted by residual:
  dihedral pdb=" C   GLN A 547 "
           pdb=" N   GLN A 547 "
           pdb=" CA  GLN A 547 "
           pdb=" CB  GLN A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.08   -9.52     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" C   GLN B 547 "
           pdb=" N   GLN B 547 "
           pdb=" CA  GLN B 547 "
           pdb=" CB  GLN B 547 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.08   -9.52     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" C   TYR A 129 "
           pdb=" N   TYR A 129 "
           pdb=" CA  TYR A 129 "
           pdb=" CB  TYR A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.51    8.91     0      2.50e+00 1.60e-01 1.27e+01
  ... (remaining 4775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1024
       0.050 -    0.100: 262
       0.100 -    0.151: 66
       0.151 -    0.201: 32
       0.201 -    0.251: 6
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  ILE A 164 "
            pdb=" N   ILE A 164 "
            pdb=" C   ILE A 164 "
            pdb=" CB  ILE A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  ILE B 164 "
            pdb=" N   ILE B 164 "
            pdb=" C   ILE B 164 "
            pdb=" CB  ILE B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  LYS A 548 "
            pdb=" N   LYS A 548 "
            pdb=" C   LYS A 548 "
            pdb=" CB  LYS A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1387 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 120 "   -0.017 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   ILE A 120 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ILE A 120 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 121 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 120 "    0.017 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   ILE B 120 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   ILE B 120 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B 121 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 548 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.72e+00
        pdb=" C   LYS B 548 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LYS B 548 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO B 549 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 156
        2.67 -     3.23: 8355
        3.23 -     3.79: 12938
        3.79 -     4.34: 16351
        4.34 -     4.90: 27075
  Nonbonded interactions: 64875
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 226 "
            pdb=" O   PHE B 434 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG1 THR A 226 "
            pdb=" O   PHE A 434 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" O   LEU B 122 "
            pdb=" OG  SER B 126 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   LEU A 122 "
            pdb=" OG  SER A 126 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OH  TYR A 142 "
            pdb=" O   THR A 366 "
     model   vdw
     2.267 3.040
  ... (remaining 64870 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 'B'
  selection = chain 'A'
}

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:             2.120
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.180
  Find NCS groups from input model:        0.060
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
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      :  0.006   0.091   8184  Z= 0.386
  Angle     :  0.857  10.443  11156  Z= 0.566
  Chirality :  0.055   0.251   1390
  Planarity :  0.005   0.046   1360
  Dihedral  : 17.953  79.881   2734
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.25 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 32.97 %
    Favored  : 62.01 %
  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:  0.96 (0.27), residues: 1066
  helix:  1.54 (0.20), residues: 718
  sheet: -1.34 (0.62), residues: 64
  loop : -1.18 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 582 
 TYR   0.018   0.002   TYR A 139 
 PHE   0.013   0.001   PHE A 368 
 TRP   0.009   0.001   TRP B 376 
 HIS   0.002   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 8184)
  covalent geometry    : angle       0.85735 (11156)
  hydrogen bonds       : bond        0.14107 (  546)
  hydrogen bonds       : angle       5.73169 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 234
  time to evaluate  : 0.296 
Fit side-chains
REVERT: B  356 TYR cc_start: 0.6737 (t80) cc_final: 0.6384 (t80)
REVERT: B  431 PHE cc_start: 0.8529 (m-10) cc_final: 0.8249 (m-10)
REVERT: B  466 LEU cc_start: 0.8447 (mm) cc_final: 0.7966 (tp)
REVERT: B  504 MET cc_start: 0.6848 (mtp) cc_final: 0.6349 (mtp)
REVERT: B  548 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7726 (mttm)
REVERT: A  356 TYR cc_start: 0.6732 (t80) cc_final: 0.6382 (t80)
REVERT: A  431 PHE cc_start: 0.8527 (m-10) cc_final: 0.8248 (m-10)
REVERT: A  466 LEU cc_start: 0.8444 (mm) cc_final: 0.7962 (tp)
REVERT: A  504 MET cc_start: 0.6852 (mtp) cc_final: 0.6351 (mtp)
REVERT: A  548 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (mttm)
  outliers start: 41
  outliers final: 12
  residues processed: 261
  average time/residue: 0.0719
  time to fit residues: 26.8875
Evaluate side-chains
  187 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  548 LYS
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  659 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  548 LYS
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  659 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
B 268 GLN
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 ASN
B 547 GLN
B 573 GLN
B 680 GLN
B 696 ASN
A 159 HIS
A 268 GLN
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
A 547 GLN
A 573 GLN
A 680 GLN
A 696 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.164867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132517 restraints weight = 12460.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136711 restraints weight = 6595.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.139380 restraints weight = 4463.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.141037 restraints weight = 3549.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.141936 restraints weight = 3107.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8184  Z= 0.165
  Angle     :  0.624   7.986  11156  Z= 0.317
  Chirality :  0.043   0.174   1390
  Planarity :  0.004   0.031   1360
  Dihedral  :  5.916  50.608   1174
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 29.90 %
    Favored  : 62.13 %
  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:  1.36 (0.26), residues: 1066
  helix:  1.83 (0.19), residues: 724
  sheet: -1.61 (0.55), residues: 64
  loop : -0.91 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 671 
 TYR   0.012   0.001   TYR A 247 
 PHE   0.015   0.002   PHE A 152 
 TRP   0.009   0.001   TRP B 515 
 HIS   0.006   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8184)
  covalent geometry    : angle       0.62383 (11156)
  hydrogen bonds       : bond        0.04656 (  546)
  hydrogen bonds       : angle       4.25745 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 190
  time to evaluate  : 0.322 
Fit side-chains
REVERT: B  153 LEU cc_start: 0.7701 (mm) cc_final: 0.7497 (mt)
REVERT: B  431 PHE cc_start: 0.8683 (m-10) cc_final: 0.8430 (m-80)
REVERT: B  442 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (mttp)
REVERT: B  504 MET cc_start: 0.6580 (mtp) cc_final: 0.6111 (mtp)
REVERT: A  153 LEU cc_start: 0.7712 (mm) cc_final: 0.7495 (mt)
REVERT: A  431 PHE cc_start: 0.8693 (m-10) cc_final: 0.8438 (m-80)
REVERT: A  442 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7729 (mttp)
REVERT: A  504 MET cc_start: 0.6574 (mtp) cc_final: 0.6106 (mtp)
  outliers start: 65
  outliers final: 36
  residues processed: 225
  average time/residue: 0.0616
  time to fit residues: 21.4046
Evaluate side-chains
  206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  296 ASN
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain B residue  680 GLN
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  680 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 ASN
B 353 HIS
B 573 GLN
B 680 GLN
A 159 HIS
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
A 353 HIS
A 573 GLN
A 680 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.165346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132472 restraints weight = 12539.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.136545 restraints weight = 6696.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.139221 restraints weight = 4572.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140683 restraints weight = 3632.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141704 restraints weight = 3211.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8184  Z= 0.144
  Angle     :  0.581   7.744  11156  Z= 0.299
  Chirality :  0.042   0.156   1390
  Planarity :  0.004   0.031   1360
  Dihedral  :  4.564  46.817   1160
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  8.09 %
    Allowed  : 29.29 %
    Favored  : 62.62 %
  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:  1.53 (0.26), residues: 1066
  helix:  1.92 (0.19), residues: 724
  sheet: -1.40 (0.59), residues: 64
  loop : -0.77 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 545 
 TYR   0.012   0.001   TYR B 139 
 PHE   0.019   0.002   PHE A 152 
 TRP   0.007   0.001   TRP B 515 
 HIS   0.002   0.001   HIS B 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8184)
  covalent geometry    : angle       0.58126 (11156)
  hydrogen bonds       : bond        0.04189 (  546)
  hydrogen bonds       : angle       4.04388 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 176
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B  179 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7957 (tp30)
REVERT: B  418 MET cc_start: 0.7883 (ttp) cc_final: 0.7682 (ttp)
REVERT: B  431 PHE cc_start: 0.8591 (m-10) cc_final: 0.8330 (m-10)
REVERT: B  504 MET cc_start: 0.6560 (mtp) cc_final: 0.6065 (mtp)
REVERT: B  580 ILE cc_start: 0.9217 (mp) cc_final: 0.8969 (mt)
REVERT: A  179 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7959 (tp30)
REVERT: A  431 PHE cc_start: 0.8628 (m-10) cc_final: 0.8367 (m-10)
REVERT: A  504 MET cc_start: 0.6549 (mtp) cc_final: 0.6050 (mtp)
REVERT: A  580 ILE cc_start: 0.9215 (mp) cc_final: 0.8974 (mt)
  outliers start: 66
  outliers final: 37
  residues processed: 214
  average time/residue: 0.0550
  time to fit residues: 18.5240
Evaluate side-chains
  202 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0030
   chunk 80 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
B 301 ASN
B 680 GLN
A 159 HIS
A 301 ASN
A 680 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.165677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.132958 restraints weight = 12774.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.137148 restraints weight = 6703.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.139685 restraints weight = 4511.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.141314 restraints weight = 3593.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.141881 restraints weight = 3140.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8184  Z= 0.125
  Angle     :  0.561  10.107  11156  Z= 0.286
  Chirality :  0.041   0.143   1390
  Planarity :  0.004   0.032   1360
  Dihedral  :  3.904  27.397   1148
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 29.04 %
    Favored  : 63.73 %
  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:  1.78 (0.27), residues: 1066
  helix:  2.07 (0.19), residues: 724
  sheet: -0.60 (0.69), residues: 52
  loop : -0.75 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 545 
 TYR   0.012   0.001   TYR B 151 
 PHE   0.019   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 515 
 HIS   0.002   0.001   HIS B 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8184)
  covalent geometry    : angle       0.56126 (11156)
  hydrogen bonds       : bond        0.03741 (  546)
  hydrogen bonds       : angle       3.86321 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 168
  time to evaluate  : 0.223 
Fit side-chains
REVERT: B  179 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8039 (tp30)
REVERT: B  275 LEU cc_start: 0.7732 (tp) cc_final: 0.7411 (mm)
REVERT: B  418 MET cc_start: 0.7824 (ttp) cc_final: 0.7610 (ttp)
REVERT: B  431 PHE cc_start: 0.8562 (m-10) cc_final: 0.8305 (m-10)
REVERT: B  504 MET cc_start: 0.6571 (mtp) cc_final: 0.6275 (mtm)
REVERT: A  179 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8056 (tp30)
REVERT: A  275 LEU cc_start: 0.7728 (tp) cc_final: 0.7410 (mm)
REVERT: A  431 PHE cc_start: 0.8600 (m-10) cc_final: 0.8310 (m-80)
REVERT: A  504 MET cc_start: 0.6559 (mtp) cc_final: 0.6270 (mtm)
  outliers start: 59
  outliers final: 44
  residues processed: 200
  average time/residue: 0.0551
  time to fit residues: 17.4198
Evaluate side-chains
  201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 157
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain B residue  680 GLN
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  573 GLN
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  680 GLN
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 19 optimal weight:    7.9990
   chunk 107 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
B 680 GLN
A 159 HIS
A 680 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.165385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132625 restraints weight = 12661.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.136679 restraints weight = 6737.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.139277 restraints weight = 4578.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.140870 restraints weight = 3642.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.141659 restraints weight = 3188.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8184  Z= 0.126
  Angle     :  0.569  11.021  11156  Z= 0.285
  Chirality :  0.040   0.144   1390
  Planarity :  0.003   0.033   1360
  Dihedral  :  3.731  27.158   1146
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 29.78 %
    Favored  : 62.25 %
  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:  1.77 (0.27), residues: 1066
  helix:  2.09 (0.19), residues: 716
  sheet: -0.53 (0.72), residues: 52
  loop : -0.80 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 545 
 TYR   0.010   0.001   TYR B 151 
 PHE   0.017   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 515 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8184)
  covalent geometry    : angle       0.56905 (11156)
  hydrogen bonds       : bond        0.03743 (  546)
  hydrogen bonds       : angle       3.81331 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 163
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B  179 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8068 (tp30)
REVERT: B  286 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7989 (tp)
REVERT: B  431 PHE cc_start: 0.8537 (m-10) cc_final: 0.8274 (m-10)
REVERT: B  707 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8431 (mt)
REVERT: A  179 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8064 (tp30)
REVERT: A  286 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7990 (tp)
REVERT: A  431 PHE cc_start: 0.8583 (m-10) cc_final: 0.8297 (m-80)
REVERT: A  707 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8419 (mt)
  outliers start: 65
  outliers final: 45
  residues processed: 196
  average time/residue: 0.0517
  time to fit residues: 16.2502
Evaluate side-chains
  214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 165
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  590 ILE
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
B 680 GLN
A 159 HIS
A 680 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.146071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112579 restraints weight = 12913.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.116265 restraints weight = 6988.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118602 restraints weight = 4818.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.119850 restraints weight = 3876.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.120733 restraints weight = 3451.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   8184  Z= 0.247
  Angle     :  0.657   7.625  11156  Z= 0.339
  Chirality :  0.044   0.156   1390
  Planarity :  0.004   0.033   1360
  Dihedral  :  3.866  16.240   1146
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  9.07 %
    Allowed  : 28.06 %
    Favored  : 62.87 %
  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:  1.41 (0.27), residues: 1066
  helix:  1.77 (0.19), residues: 722
  sheet: -1.31 (0.66), residues: 60
  loop : -0.66 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 496 
 TYR   0.014   0.002   TYR B 139 
 PHE   0.017   0.002   PHE A 394 
 TRP   0.011   0.001   TRP B 515 
 HIS   0.002   0.001   HIS B 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 ( 8184)
  covalent geometry    : angle       0.65718 (11156)
  hydrogen bonds       : bond        0.04727 (  546)
  hydrogen bonds       : angle       4.06618 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 176
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B  179 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7930 (tp30)
REVERT: B  275 LEU cc_start: 0.7845 (tp) cc_final: 0.7565 (mm)
REVERT: B  431 PHE cc_start: 0.8730 (m-10) cc_final: 0.8506 (m-10)
REVERT: B  504 MET cc_start: 0.6974 (mtm) cc_final: 0.6703 (mtp)
REVERT: A  179 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7879 (tp30)
REVERT: A  275 LEU cc_start: 0.7842 (tp) cc_final: 0.7556 (mm)
REVERT: A  431 PHE cc_start: 0.8728 (m-10) cc_final: 0.8516 (m-10)
REVERT: A  504 MET cc_start: 0.6970 (mtm) cc_final: 0.6708 (mtp)
  outliers start: 74
  outliers final: 58
  residues processed: 210
  average time/residue: 0.0546
  time to fit residues: 18.4461
Evaluate side-chains
  222 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 164
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  220 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  462 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain B residue  680 GLN
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  481 SER
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  680 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0070
   chunk 91 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 HIS
A 680 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.159701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126764 restraints weight = 12618.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.130712 restraints weight = 6638.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.133162 restraints weight = 4516.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.134702 restraints weight = 3621.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135373 restraints weight = 3191.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8184  Z= 0.128
  Angle     :  0.578   8.529  11156  Z= 0.291
  Chirality :  0.041   0.150   1390
  Planarity :  0.004   0.034   1360
  Dihedral  :  3.771  18.193   1146
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 31.62 %
    Favored  : 61.89 %
  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 (0.27), residues: 1066
  helix:  2.01 (0.20), residues: 720
  sheet: -0.40 (0.77), residues: 48
  loop : -0.86 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 545 
 TYR   0.013   0.001   TYR B 139 
 PHE   0.014   0.001   PHE A 152 
 TRP   0.006   0.001   TRP B 515 
 HIS   0.002   0.000   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8184)
  covalent geometry    : angle       0.57793 (11156)
  hydrogen bonds       : bond        0.03850 (  546)
  hydrogen bonds       : angle       3.86835 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 154
  time to evaluate  : 0.306 
Fit side-chains
REVERT: B  431 PHE cc_start: 0.8690 (m-10) cc_final: 0.8458 (m-10)
REVERT: B  504 MET cc_start: 0.6970 (mtm) cc_final: 0.6663 (mtp)
REVERT: B  580 ILE cc_start: 0.9235 (mp) cc_final: 0.8936 (mt)
REVERT: A  431 PHE cc_start: 0.8648 (m-10) cc_final: 0.8429 (m-10)
REVERT: A  504 MET cc_start: 0.6974 (mtm) cc_final: 0.6674 (mtp)
REVERT: A  580 ILE cc_start: 0.9234 (mp) cc_final: 0.8938 (mt)
  outliers start: 53
  outliers final: 43
  residues processed: 187
  average time/residue: 0.0541
  time to fit residues: 16.3759
Evaluate side-chains
  192 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  220 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  481 SER
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0370
   chunk 90 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
B 680 GLN
A 159 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.160732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.127677 restraints weight = 12724.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.131575 restraints weight = 6695.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.134116 restraints weight = 4558.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135597 restraints weight = 3640.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136589 restraints weight = 3202.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8184  Z= 0.124
  Angle     :  0.571   8.064  11156  Z= 0.288
  Chirality :  0.041   0.144   1390
  Planarity :  0.004   0.034   1360
  Dihedral  :  3.646  17.846   1146
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 32.48 %
    Favored  : 60.54 %
  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:  1.66 (0.27), residues: 1066
  helix:  2.01 (0.20), residues: 716
  sheet: -0.34 (0.78), residues: 48
  loop : -0.89 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 295 
 TYR   0.011   0.001   TYR B 139 
 PHE   0.014   0.001   PHE A 394 
 TRP   0.006   0.001   TRP A 515 
 HIS   0.002   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8184)
  covalent geometry    : angle       0.57111 (11156)
  hydrogen bonds       : bond        0.03655 (  546)
  hydrogen bonds       : angle       3.81962 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 155
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B  431 PHE cc_start: 0.8666 (m-10) cc_final: 0.8432 (m-10)
REVERT: B  504 MET cc_start: 0.6993 (mtm) cc_final: 0.6671 (mtp)
REVERT: A  431 PHE cc_start: 0.8647 (m-10) cc_final: 0.8420 (m-10)
REVERT: A  504 MET cc_start: 0.6995 (mtm) cc_final: 0.6686 (mtp)
  outliers start: 57
  outliers final: 45
  residues processed: 185
  average time/residue: 0.0548
  time to fit residues: 16.3944
Evaluate side-chains
  192 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 147
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  220 MET
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  481 SER
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
A 159 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.161160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128017 restraints weight = 12655.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131978 restraints weight = 6676.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.134527 restraints weight = 4551.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.135901 restraints weight = 3645.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136811 restraints weight = 3231.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8184  Z= 0.124
  Angle     :  0.577   8.036  11156  Z= 0.289
  Chirality :  0.041   0.143   1390
  Planarity :  0.004   0.034   1360
  Dihedral  :  3.614  17.900   1146
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 32.72 %
    Favored  : 60.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.75 (0.27), residues: 1066
  helix:  2.08 (0.20), residues: 716
  sheet: -0.22 (0.79), residues: 48
  loop : -0.86 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 545 
 TYR   0.011   0.001   TYR B 139 
 PHE   0.012   0.001   PHE A 152 
 TRP   0.006   0.000   TRP A 515 
 HIS   0.001   0.000   HIS B 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8184)
  covalent geometry    : angle       0.57727 (11156)
  hydrogen bonds       : bond        0.03638 (  546)
  hydrogen bonds       : angle       3.78241 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 147
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  431 PHE cc_start: 0.8664 (m-10) cc_final: 0.8430 (m-10)
REVERT: B  504 MET cc_start: 0.6970 (mtm) cc_final: 0.6648 (mtp)
REVERT: A  431 PHE cc_start: 0.8642 (m-10) cc_final: 0.8414 (m-10)
REVERT: A  466 LEU cc_start: 0.8425 (mm) cc_final: 0.7925 (tp)
REVERT: A  504 MET cc_start: 0.6973 (mtm) cc_final: 0.6664 (mtp)
  outliers start: 52
  outliers final: 46
  residues processed: 176
  average time/residue: 0.0550
  time to fit residues: 15.7788
Evaluate side-chains
  191 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  220 MET
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  481 SER
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0770
   chunk 59 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 102 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
B 159 HIS
A  59 GLN
A 159 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.161780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.128208 restraints weight = 12631.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132485 restraints weight = 6443.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.135099 restraints weight = 4282.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.136486 restraints weight = 3398.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.137570 restraints weight = 3002.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8184  Z= 0.123
  Angle     :  0.571   8.655  11156  Z= 0.286
  Chirality :  0.041   0.143   1390
  Planarity :  0.004   0.034   1360
  Dihedral  :  3.567  17.822   1146
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 32.60 %
    Favored  : 61.15 %
  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:  1.75 (0.27), residues: 1066
  helix:  2.07 (0.20), residues: 716
  sheet: -0.11 (0.79), residues: 48
  loop : -0.85 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 295 
 TYR   0.011   0.001   TYR B 139 
 PHE   0.019   0.001   PHE A 152 
 TRP   0.006   0.001   TRP A 515 
 HIS   0.001   0.000   HIS B 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8184)
  covalent geometry    : angle       0.57149 (11156)
  hydrogen bonds       : bond        0.03574 (  546)
  hydrogen bonds       : angle       3.77632 ( 1584)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 145
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B  431 PHE cc_start: 0.8649 (m-10) cc_final: 0.8420 (m-10)
REVERT: B  466 LEU cc_start: 0.8382 (mm) cc_final: 0.7926 (tp)
REVERT: B  504 MET cc_start: 0.6978 (mtm) cc_final: 0.6491 (mtp)
REVERT: A  431 PHE cc_start: 0.8628 (m-10) cc_final: 0.8402 (m-10)
REVERT: A  466 LEU cc_start: 0.8390 (mm) cc_final: 0.7934 (tp)
REVERT: A  504 MET cc_start: 0.6986 (mtm) cc_final: 0.6509 (mtp)
  outliers start: 51
  outliers final: 49
  residues processed: 171
  average time/residue: 0.0550
  time to fit residues: 15.2496
Evaluate side-chains
  193 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 144
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  220 MET
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  476 TYR
Chi-restraints excluded: chain B residue  477 SER
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  588 TYR
Chi-restraints excluded: chain B residue  611 VAL
Chi-restraints excluded: chain B residue  648 THR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  220 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  476 TYR
Chi-restraints excluded: chain A residue  477 SER
Chi-restraints excluded: chain A residue  481 SER
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  588 TYR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  648 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 21 optimal weight:    9.9990
   chunk 97 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
B 159 HIS
A 159 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.161105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127755 restraints weight = 12557.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.131691 restraints weight = 6646.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.134194 restraints weight = 4560.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.135575 restraints weight = 3663.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.136644 restraints weight = 3245.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8184  Z= 0.130
  Angle     :  0.574   7.823  11156  Z= 0.288
  Chirality :  0.041   0.144   1390
  Planarity :  0.004   0.035   1360
  Dihedral  :  3.543  17.511   1146
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  6.99 %
    Allowed  : 31.99 %
    Favored  : 61.03 %
  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:  1.73 (0.27), residues: 1066
  helix:  2.05 (0.20), residues: 716
  sheet: -0.08 (0.79), residues: 48
  loop : -0.86 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 545 
 TYR   0.011   0.001   TYR A 139 
 PHE   0.013   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A 515 
 HIS   0.001   0.000   HIS B 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8184)
  covalent geometry    : angle       0.57414 (11156)
  hydrogen bonds       : bond        0.03639 (  546)
  hydrogen bonds       : angle       3.77516 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1495.45 seconds
wall clock time: 26 minutes 36.66 seconds (1596.66 seconds total)