Starting phenix.real_space_refine
on Tue Jul 29 05:04:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6of4_20042/07_2025/6of4_20042.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.018 sd=   0.673
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      54      5.16       5
     C    7028      2.51       5
     N    1920      2.21       5
     O    1996      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10998
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1451
          Classifications: {'peptide': 183}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 174}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 4048
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4048
          Classifications: {'peptide': 528}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 52, 'TRANS': 475}
          Unresolved chain links: 1
          Chain breaks: 4
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 23
  Restraints were copied for chains:
    E, D
  Time building chain proxies: 8.55, per 1000 atoms: 0.78
  Number of scatterers: 10998
  At special positions: 0
  Unit cell: (146.88, 89.64, 89.64, 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      54     16.00
     O    1996      8.00
     N    1920      7.00
     C    7028      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: 2.68
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2652

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 10 sheets defined
      40.4% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 4.271A  pdb=" N   LEU A  15 " --> pdb=" O   ASN A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 28
    Processing helix  chain 'A' and resid 41 through 64
    Processing helix  chain 'A' and resid 67 through 84
      removed outlier: 3.500A  pdb=" N   GLU A  71 " --> pdb=" O   PRO A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 115
    Processing helix  chain 'A' and resid 123 through 132
    Processing helix  chain 'A' and resid 134 through 147
      removed outlier: 4.261A  pdb=" N   VAL A 138 " --> pdb=" O   PRO A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 170
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'B' and resid 196 through 202
      removed outlier: 3.935A  pdb=" N   LEU B 200 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU B 202 " --> pdb=" O   GLN B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 211
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 242 through 258
      removed outlier: 3.501A  pdb=" N   ASN B 246 " --> pdb=" O   HIS B 242 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ARG B 258 " --> pdb=" O   THR B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 288
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 4.522A  pdb=" N   SER B 296 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 334
      removed outlier: 3.870A  pdb=" N   CYS B 333 " --> pdb=" O   PRO B 330 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   HIS B 334 " --> pdb=" O   PRO B 331 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 330 through 334'
    Processing helix  chain 'B' and resid 367 through 387
    Processing helix  chain 'B' and resid 403 through 417
    Processing helix  chain 'B' and resid 429 through 443
      removed outlier: 3.633A  pdb=" N   SER B 443 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 484
    Processing helix  chain 'B' and resid 535 through 544
      removed outlier: 4.239A  pdb=" N   SER B 540 " --> pdb=" O   PRO B 536 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ASP B 541 " --> pdb=" O   GLU B 537 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 660
      removed outlier: 3.591A  pdb=" N   LEU B 658 " --> pdb=" O   PRO B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 691
      removed outlier: 4.045A  pdb=" N   VAL B 681 " --> pdb=" O   THR B 677 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY B 683 " --> pdb=" O   ALA B 679 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LEU B 684 " --> pdb=" O   TYR B 680 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS B 691 " --> pdb=" O   LYS B 687 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 23
      removed outlier: 4.271A  pdb=" N   LEU D  15 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 28
    Processing helix  chain 'D' and resid 41 through 64
    Processing helix  chain 'D' and resid 67 through 84
      removed outlier: 3.500A  pdb=" N   GLU D  71 " --> pdb=" O   PRO D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 115
    Processing helix  chain 'D' and resid 123 through 132
    Processing helix  chain 'D' and resid 134 through 147
      removed outlier: 4.261A  pdb=" N   VAL D 138 " --> pdb=" O   PRO D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 170
    Processing helix  chain 'D' and resid 171 through 174
    Processing helix  chain 'E' and resid 196 through 202
      removed outlier: 3.935A  pdb=" N   LEU E 200 " --> pdb=" O   THR E 196 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLU E 202 " --> pdb=" O   GLN E 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 203 through 211
      Proline residue:  E 208  - end of helix
    Processing helix  chain 'E' and resid 242 through 258
      removed outlier: 3.502A  pdb=" N   ASN E 246 " --> pdb=" O   HIS E 242 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG E 258 " --> pdb=" O   THR E 254 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 273 through 288
    Processing helix  chain 'E' and resid 292 through 296
      removed outlier: 4.522A  pdb=" N   SER E 296 " --> pdb=" O   LYS E 293 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 330 through 334
      removed outlier: 3.870A  pdb=" N   CYS E 333 " --> pdb=" O   PRO E 330 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   HIS E 334 " --> pdb=" O   PRO E 331 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 330 through 334'
    Processing helix  chain 'E' and resid 367 through 387
    Processing helix  chain 'E' and resid 403 through 417
    Processing helix  chain 'E' and resid 429 through 443
      removed outlier: 3.632A  pdb=" N   SER E 443 " --> pdb=" O   ALA E 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 470 through 484
    Processing helix  chain 'E' and resid 535 through 544
      removed outlier: 4.238A  pdb=" N   SER E 540 " --> pdb=" O   PRO E 536 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   ASP E 541 " --> pdb=" O   GLU E 537 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN E 544 " --> pdb=" O   SER E 540 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 654 through 660
      removed outlier: 3.591A  pdb=" N   LEU E 658 " --> pdb=" O   PRO E 654 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 677 through 691
      removed outlier: 4.045A  pdb=" N   VAL E 681 " --> pdb=" O   THR E 677 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY E 683 " --> pdb=" O   ALA E 679 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LEU E 684 " --> pdb=" O   TYR E 680 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS E 691 " --> pdb=" O   LYS E 687 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349
      removed outlier: 3.672A  pdb=" N   GLU B 646 " --> pdb=" O   SER B 639 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY B 637 " --> pdb=" O   HIS B 648 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU B 650 " --> pdb=" O   ILE B 635 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   ILE B 635 " --> pdb=" O   LEU B 650 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   LEU B 550 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   LEU B 632 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   MET B 548 " --> pdb=" O   LEU B 632 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125
      removed outlier: 3.963A  pdb=" N   ARG B 123 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 130 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358
      removed outlier: 7.026A  pdb=" N   LEU B 320 " --> pdb=" O   VAL B 354 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   MET B 356 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL B 318 " --> pdb=" O   MET B 356 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLU B 420 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349
      removed outlier: 3.672A  pdb=" N   GLU E 646 " --> pdb=" O   SER E 639 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY E 637 " --> pdb=" O   HIS E 648 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU E 650 " --> pdb=" O   ILE E 635 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   ILE E 635 " --> pdb=" O   LEU E 650 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   LEU E 550 " --> pdb=" O   VAL E 630 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   LEU E 632 " --> pdb=" O   MET E 548 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   MET E 548 " --> pdb=" O   LEU E 632 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125
      removed outlier: 3.963A  pdb=" N   ARG E 123 " --> pdb=" O   VAL E 130 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL E 130 " --> pdb=" O   ARG E 123 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161
    Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358
      removed outlier: 7.027A  pdb=" N   LEU E 320 " --> pdb=" O   VAL E 354 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   MET E 356 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL E 318 " --> pdb=" O   MET E 356 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU E 420 " --> pdb=" O   ILE E 263 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1392 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3528
        1.34 -     1.45: 1629
        1.45 -     1.57: 6051
        1.57 -     1.69: 0
        1.69 -     1.80: 88
  Bond restraints: 11296
  Sorted by residual:
  bond pdb=" C   ALA E 535 "
       pdb=" N   PRO E 536 "
    ideal  model  delta    sigma   weight residual
    1.335  1.309  0.026 1.38e-02 5.25e+03 3.49e+00
  bond pdb=" C   ALA B 535 "
       pdb=" N   PRO B 536 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.025 1.38e-02 5.25e+03 3.38e+00
  bond pdb=" CB  TRP A 355 "
       pdb=" CG  TRP A 355 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.04e+00
  bond pdb=" CB  TRP D 355 "
       pdb=" CG  TRP D 355 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.01e+00
  bond pdb=" CB  TRP D  60 "
       pdb=" CG  TRP D  60 "
    ideal  model  delta    sigma   weight residual
    1.498  1.447  0.051 3.10e-02 1.04e+03 2.74e+00
  ... (remaining 11291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 14965
        3.12 -     6.25: 418
        6.25 -     9.37: 25
        9.37 -    12.50: 0
       12.50 -    15.62: 4
  Bond angle restraints: 15412
  Sorted by residual:
  angle pdb=" N   PRO E 455 "
        pdb=" CA  PRO E 455 "
        pdb=" CB  PRO E 455 "
      ideal   model   delta    sigma   weight residual
     103.00  110.52   -7.52 1.10e+00 8.26e-01 4.67e+01
  angle pdb=" N   PRO B 455 "
        pdb=" CA  PRO B 455 "
        pdb=" CB  PRO B 455 "
      ideal   model   delta    sigma   weight residual
     103.00  110.48   -7.48 1.10e+00 8.26e-01 4.62e+01
  angle pdb=" N   ALA B 290 "
        pdb=" CA  ALA B 290 "
        pdb=" C   ALA B 290 "
      ideal   model   delta    sigma   weight residual
     110.80  124.04  -13.24 2.13e+00 2.20e-01 3.86e+01
  angle pdb=" N   ALA E 290 "
        pdb=" CA  ALA E 290 "
        pdb=" C   ALA E 290 "
      ideal   model   delta    sigma   weight residual
     110.80  124.02  -13.22 2.13e+00 2.20e-01 3.85e+01
  angle pdb=" C   HIS A 146 "
        pdb=" N   GLU A 147 "
        pdb=" CA  GLU A 147 "
      ideal   model   delta    sigma   weight residual
     122.15  106.53   15.62 2.83e+00 1.25e-01 3.05e+01
  ... (remaining 15407 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 6128
       17.44 -    34.87: 436
       34.87 -    52.31: 86
       52.31 -    69.75: 78
       69.75 -    87.18: 14
  Dihedral angle restraints: 6742
    sinusoidal: 2650
      harmonic: 4092
  Sorted by residual:
  dihedral pdb=" CA  ARG B 295 "
           pdb=" C   ARG B 295 "
           pdb=" N   SER B 296 "
           pdb=" CA  SER B 296 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.61  -47.39     0      5.00e+00 4.00e-02 8.98e+01
  dihedral pdb=" CA  ARG E 295 "
           pdb=" C   ARG E 295 "
           pdb=" N   SER E 296 "
           pdb=" CA  SER E 296 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.61  -47.39     0      5.00e+00 4.00e-02 8.98e+01
  dihedral pdb=" CA  ALA D  91 "
           pdb=" C   ALA D  91 "
           pdb=" N   GLY D  92 "
           pdb=" CA  GLY D  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.19  -31.81     0      5.00e+00 4.00e-02 4.05e+01
  ... (remaining 6739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1012
       0.048 -    0.096: 511
       0.096 -    0.143: 149
       0.143 -    0.191: 48
       0.191 -    0.239: 6
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CA  ALA B 290 "
            pdb=" N   ALA B 290 "
            pdb=" C   ALA B 290 "
            pdb=" CB  ALA B 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  ALA E 290 "
            pdb=" N   ALA E 290 "
            pdb=" C   ALA E 290 "
            pdb=" CB  ALA E 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  PRO E 455 "
            pdb=" N   PRO E 455 "
            pdb=" C   PRO E 455 "
            pdb=" CB  PRO E 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1723 not shown)

  Planarity restraints: 1978
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 330 "   -0.049 5.00e-02 4.00e+02   7.31e-02 8.56e+00
        pdb=" N   PRO E 331 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO E 331 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO E 331 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 330 "    0.049 5.00e-02 4.00e+02   7.29e-02 8.50e+00
        pdb=" N   PRO B 331 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B 331 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 331 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E 509 "    0.042 5.00e-02 4.00e+02   6.20e-02 6.14e+00
        pdb=" N   PRO E 510 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO E 510 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 510 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1975 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 187
        2.65 -     3.21: 10602
        3.21 -     3.78: 15009
        3.78 -     4.34: 19213
        4.34 -     4.90: 33309
  Nonbonded interactions: 78320
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 272 "
            pdb=" O   MET E 424 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" OG  SER B 272 "
            pdb=" O   MET B 424 "
     model   vdw
     2.091 3.040
  nonbonded pdb=" O   SER B 444 "
            pdb=" OG1 THR B 445 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   SER E 444 "
            pdb=" OG1 THR E 445 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" NH2 ARG E 201 "
            pdb=" OD1 ASN E 215 "
     model   vdw
     2.229 3.120
  ... (remaining 78315 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.20 max=1.00 mean=0.96
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.670
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.680
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
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      :  0.010   0.064  11296  Z= 0.439
  Angle     :  1.187  15.624  15412  Z= 0.643
  Chirality :  0.062   0.239   1726
  Planarity :  0.009   0.073   1978
  Dihedral  : 15.119  87.184   4090
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  3.55 %
    Allowed  : 19.61 %
    Favored  : 76.85 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  6.44 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.47 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.99 (0.17), residues: 1382
  helix: -2.88 (0.15), residues: 456
  sheet: -1.37 (0.33), residues: 202
  loop : -4.37 (0.18), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP B 297 
 HIS   0.008   0.002   HIS D  68 
 PHE   0.026   0.003   PHE A 107 
 TYR   0.034   0.004   TYR E 530 
 ARG   0.005   0.001   ARG A  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18074 (  492)
  hydrogen bonds       : angle       7.80630 ( 1392)
  covalent geometry    : bond        0.01037 (11296)
  covalent geometry    : angle       1.18729 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 301
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ASN cc_start: 0.7377 (t0) cc_final: 0.7076 (t0)
REVERT: B  128 ARG cc_start: 0.6520 (ptt180) cc_final: 0.6009 (ptp-170)
REVERT: B  139 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6937 (m-10)
REVERT: B  156 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8584 (tp)
REVERT: B  164 ILE cc_start: 0.8876 (mt) cc_final: 0.8546 (pt)
REVERT: B  183 THR cc_start: 0.7986 (m) cc_final: 0.7723 (t)
REVERT: B  275 SER cc_start: 0.8651 (m) cc_final: 0.8430 (t)
REVERT: B  557 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8849 (tp30)
REVERT: B  723 VAL cc_start: 0.9126 (t) cc_final: 0.8848 (p)
REVERT: E  109 MET cc_start: 0.3795 (mtm) cc_final: 0.3156 (tmm)
REVERT: E  156 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8813 (tt)
REVERT: E  183 THR cc_start: 0.8287 (m) cc_final: 0.7934 (t)
REVERT: E  239 LEU cc_start: 0.7453 (tp) cc_final: 0.7247 (tt)
REVERT: E  298 LYS cc_start: 0.8540 (mptt) cc_final: 0.8219 (mmtt)
REVERT: E  349 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6570 (mp0)
REVERT: E  376 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (tpp80)
REVERT: E  557 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8901 (tp30)
REVERT: E  665 GLU cc_start: 0.7645 (pt0) cc_final: 0.7202 (pt0)
  outliers start: 30
  outliers final: 5
  residues processed: 324
  average time/residue: 0.2720
  time to fit residues: 119.5695
Evaluate side-chains
  197 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 188
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain B residue  139 PHE
Chi-restraints excluded: chain B residue  156 ILE
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain E residue  139 PHE
Chi-restraints excluded: chain E residue  156 ILE
Chi-restraints excluded: chain E residue  206 LEU
Chi-restraints excluded: chain E residue  376 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 71 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0050
   chunk 81 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
B 115 GLN
B 144 ASN
B 151 GLN
B 174 HIS
B 327 ASN
D  62 GLN
D 146 HIS
E 115 GLN
E 327 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081080 restraints weight = 19044.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.14
r_work: 0.2986 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2990 r_free = 0.2990    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      102 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  11296  Z= 0.154
  Angle     :  0.825  11.703  15412  Z= 0.411
  Chirality :  0.045   0.278   1726
  Planarity :  0.007   0.058   1978
  Dihedral  :  6.680  86.075   1548
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 10.42 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 13.22 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.23), residues: 1382
  helix:  1.97 (0.22), residues: 478
  sheet: -0.38 (0.33), residues: 256
  loop : -3.29 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 297 
 HIS   0.013   0.001   HIS B 174 
 PHE   0.015   0.002   PHE B 312 
 TYR   0.017   0.002   TYR E 423 
 ARG   0.006   0.001   ARG B 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05807 (  492)
  hydrogen bonds       : angle       5.00471 ( 1392)
  covalent geometry    : bond        0.00322 (11296)
  covalent geometry    : angle       0.82494 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 232
  time to evaluate  : 1.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  156 ILE cc_start: 0.8778 (mt) cc_final: 0.8557 (tt)
REVERT: B  174 HIS cc_start: 0.8014 (t70) cc_final: 0.7106 (t70)
REVERT: B  251 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7936 (tp30)
REVERT: B  272 SER cc_start: 0.8502 (t) cc_final: 0.8270 (m)
REVERT: B  309 GLN cc_start: 0.9118 (pm20) cc_final: 0.8798 (pm20)
REVERT: B  557 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8623 (tp30)
REVERT: B  719 GLU cc_start: 0.8207 (mp0) cc_final: 0.7932 (mp0)
REVERT: E  109 MET cc_start: 0.5431 (mtm) cc_final: 0.3497 (tmm)
REVERT: E  128 ARG cc_start: 0.6372 (ptt180) cc_final: 0.5868 (ptp-170)
REVERT: E  129 LEU cc_start: 0.7597 (mp) cc_final: 0.7313 (tt)
REVERT: E  156 ILE cc_start: 0.8976 (mt) cc_final: 0.8723 (tt)
REVERT: E  239 LEU cc_start: 0.7494 (tp) cc_final: 0.7217 (tt)
REVERT: E  288 ASP cc_start: 0.8333 (t0) cc_final: 0.7671 (p0)
  outliers start: 41
  outliers final: 23
  residues processed: 259
  average time/residue: 0.2207
  time to fit residues: 84.4982
Evaluate side-chains
  214 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain B residue  689 ASN
Chi-restraints excluded: chain D residue   22 PHE
Chi-restraints excluded: chain D residue  351 ASP
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  539 VAL
Chi-restraints excluded: chain E residue  666 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 114 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0670
   chunk 120 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
B 120 ASN
B 207 ASN
B 242 HIS
B 454 GLN
D  62 GLN
E 120 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.093372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.074238 restraints weight = 19879.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 3.08
r_work: 0.2877 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      102 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      124 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11296  Z= 0.200
  Angle     :  0.763  10.769  15412  Z= 0.380
  Chirality :  0.045   0.180   1726
  Planarity :  0.006   0.054   1978
  Dihedral  :  5.947  81.870   1528
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 10.85 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.76 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.24), residues: 1382
  helix:  2.77 (0.23), residues: 480
  sheet: -0.21 (0.33), residues: 260
  loop : -2.73 (0.24), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 297 
 HIS   0.005   0.001   HIS E 648 
 PHE   0.016   0.002   PHE E 332 
 TYR   0.013   0.002   TYR B 626 
 ARG   0.006   0.001   ARG A 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06443 (  492)
  hydrogen bonds       : angle       4.71367 ( 1392)
  covalent geometry    : bond        0.00473 (11296)
  covalent geometry    : angle       0.76297 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 211
  time to evaluate  : 1.112 
Fit side-chains
REVERT: B  156 ILE cc_start: 0.8841 (mt) cc_final: 0.8613 (tt)
REVERT: B  174 HIS cc_start: 0.7981 (t70) cc_final: 0.7252 (t70)
REVERT: B  251 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7941 (tp30)
REVERT: B  272 SER cc_start: 0.8631 (t) cc_final: 0.8395 (m)
REVERT: B  306 ASP cc_start: 0.8597 (t70) cc_final: 0.8348 (t70)
REVERT: B  309 GLN cc_start: 0.9029 (pm20) cc_final: 0.8672 (pm20)
REVERT: D   62 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8410 (tp40)
REVERT: E  109 MET cc_start: 0.5336 (mtm) cc_final: 0.3658 (tmm)
REVERT: E  156 ILE cc_start: 0.8972 (mt) cc_final: 0.8750 (tt)
REVERT: E  183 THR cc_start: 0.7826 (m) cc_final: 0.7429 (t)
REVERT: E  239 LEU cc_start: 0.7628 (tp) cc_final: 0.7323 (tt)
REVERT: E  272 SER cc_start: 0.8723 (t) cc_final: 0.8429 (m)
REVERT: E  417 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7721 (mtp85)
REVERT: E  499 GLU cc_start: 0.7697 (tt0) cc_final: 0.7325 (tt0)
  outliers start: 48
  outliers final: 36
  residues processed: 240
  average time/residue: 0.1958
  time to fit residues: 69.9185
Evaluate side-chains
  230 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain D residue   62 GLN
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  167 VAL
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  256 THR
Chi-restraints excluded: chain E residue  351 MET
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  666 LEU
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
B 242 HIS
E 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.090714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.071634 restraints weight = 19877.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 3.05
r_work: 0.2838 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      124 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      152 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  11296  Z= 0.304
  Angle     :  0.813  11.121  15412  Z= 0.413
  Chirality :  0.048   0.242   1726
  Planarity :  0.007   0.053   1978
  Dihedral  :  6.041  77.428   1528
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 11.43 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 17.37 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.24), residues: 1382
  helix:  2.31 (0.23), residues: 488
  sheet: -0.51 (0.32), residues: 260
  loop : -2.64 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 171 
 HIS   0.011   0.002   HIS E 532 
 PHE   0.018   0.002   PHE A 107 
 TYR   0.017   0.002   TYR E 626 
 ARG   0.006   0.001   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07702 (  492)
  hydrogen bonds       : angle       4.83189 ( 1392)
  covalent geometry    : bond        0.00727 (11296)
  covalent geometry    : angle       0.81299 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 199
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 VAL cc_start: 0.7804 (t) cc_final: 0.7553 (m)
REVERT: B  139 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7291 (m-10)
REVERT: B  156 ILE cc_start: 0.8844 (mt) cc_final: 0.8593 (tt)
REVERT: B  174 HIS cc_start: 0.8077 (t70) cc_final: 0.7480 (t70)
REVERT: B  185 ASN cc_start: 0.8365 (m110) cc_final: 0.8047 (t0)
REVERT: B  309 GLN cc_start: 0.9065 (pm20) cc_final: 0.8724 (pm20)
REVERT: B  512 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7470 (ttt90)
REVERT: E  109 MET cc_start: 0.5143 (mtm) cc_final: 0.3709 (tmm)
REVERT: E  156 ILE cc_start: 0.8961 (mt) cc_final: 0.8705 (tt)
REVERT: E  183 THR cc_start: 0.7971 (m) cc_final: 0.7562 (t)
REVERT: E  239 LEU cc_start: 0.7819 (tp) cc_final: 0.7486 (tt)
REVERT: E  272 SER cc_start: 0.8816 (t) cc_final: 0.8597 (m)
REVERT: E  512 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7399 (ttt90)
  outliers start: 53
  outliers final: 39
  residues processed: 234
  average time/residue: 0.1967
  time to fit residues: 68.2528
Evaluate side-chains
  229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  139 PHE
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  167 VAL
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  256 THR
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  351 MET
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  666 LEU
Chi-restraints excluded: chain E residue  674 ASP
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 133 optimal weight:    1.9990
   chunk 89 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0010
   chunk 96 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 132 optimal weight:    2.9990
   overall best weight:    1.2792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.094257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.074928 restraints weight = 19311.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 3.08
r_work: 0.2897 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      152 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      156 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11296  Z= 0.167
  Angle     :  0.714   9.741  15412  Z= 0.354
  Chirality :  0.044   0.167   1726
  Planarity :  0.006   0.049   1978
  Dihedral  :  5.433  47.091   1528
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  9.62 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.31 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1382
  helix:  2.67 (0.24), residues: 486
  sheet: -0.47 (0.32), residues: 262
  loop : -2.47 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 171 
 HIS   0.004   0.001   HIS B 532 
 PHE   0.015   0.002   PHE B 332 
 TYR   0.011   0.001   TYR E 423 
 ARG   0.005   0.001   ARG A 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05813 (  492)
  hydrogen bonds       : angle       4.47132 ( 1392)
  covalent geometry    : bond        0.00390 (11296)
  covalent geometry    : angle       0.71353 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 198
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: B  156 ILE cc_start: 0.8785 (mt) cc_final: 0.8547 (tt)
REVERT: B  174 HIS cc_start: 0.7908 (t70) cc_final: 0.7431 (t70)
REVERT: B  185 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7862 (t0)
REVERT: B  512 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7398 (ttt90)
REVERT: E  156 ILE cc_start: 0.8854 (mt) cc_final: 0.8645 (tt)
REVERT: E  183 THR cc_start: 0.7754 (m) cc_final: 0.7387 (t)
REVERT: E  239 LEU cc_start: 0.7815 (tp) cc_final: 0.7476 (tt)
REVERT: E  272 SER cc_start: 0.8746 (t) cc_final: 0.8432 (m)
REVERT: E  426 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8504 (tm-30)
  outliers start: 54
  outliers final: 34
  residues processed: 234
  average time/residue: 0.2754
  time to fit residues: 97.8489
Evaluate side-chains
  226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 190
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 ASP
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  256 THR
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  432 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  666 LEU
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 138 optimal weight:    0.0050
   chunk 85 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.098031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.078565 restraints weight = 19287.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.13
r_work: 0.2960 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      156 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11296  Z= 0.120
  Angle     :  0.665   9.241  15412  Z= 0.326
  Chirality :  0.042   0.154   1726
  Planarity :  0.006   0.043   1978
  Dihedral  :  5.024  31.493   1528
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.97 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.49 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1382
  helix:  2.87 (0.24), residues: 486
  sheet: -0.25 (0.32), residues: 262
  loop : -2.30 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  60 
 HIS   0.004   0.001   HIS B 532 
 PHE   0.016   0.001   PHE B 312 
 TYR   0.013   0.001   TYR E 423 
 ARG   0.005   0.001   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  492)
  hydrogen bonds       : angle       4.19320 ( 1392)
  covalent geometry    : bond        0.00269 (11296)
  covalent geometry    : angle       0.66529 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 204
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8783 (tt)
REVERT: B  156 ILE cc_start: 0.8735 (mt) cc_final: 0.8533 (tt)
REVERT: B  174 HIS cc_start: 0.7671 (t70) cc_final: 0.7303 (t70)
REVERT: B  185 ASN cc_start: 0.7936 (m110) cc_final: 0.7542 (t0)
REVERT: B  288 ASP cc_start: 0.8563 (t0) cc_final: 0.8322 (p0)
REVERT: B  309 GLN cc_start: 0.9042 (pm20) cc_final: 0.8802 (pm20)
REVERT: B  512 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7353 (ttt90)
REVERT: D  362 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: E  239 LEU cc_start: 0.7841 (tp) cc_final: 0.7504 (tt)
REVERT: E  272 SER cc_start: 0.8705 (t) cc_final: 0.8352 (m)
REVERT: E  288 ASP cc_start: 0.8571 (t0) cc_final: 0.8325 (p0)
REVERT: E  426 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: E  512 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7246 (ttt90)
  outliers start: 43
  outliers final: 25
  residues processed: 229
  average time/residue: 0.1838
  time to fit residues: 63.5565
Evaluate side-chains
  222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain D residue  362 ILE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  387 SER
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  674 ASP
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 130 optimal weight:    0.0770
   chunk 125 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.7938

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
B 454 GLN
E 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.097512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.077895 restraints weight = 19515.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 3.15
r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      165 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11296  Z= 0.127
  Angle     :  0.665   9.172  15412  Z= 0.323
  Chirality :  0.042   0.158   1726
  Planarity :  0.005   0.041   1978
  Dihedral  :  4.912  31.470   1528
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.83 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.10 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.24), residues: 1382
  helix:  2.91 (0.24), residues: 486
  sheet: -0.16 (0.32), residues: 262
  loop : -2.28 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 167 
 HIS   0.003   0.001   HIS B 532 
 PHE   0.013   0.001   PHE B 312 
 TYR   0.011   0.001   TYR E 423 
 ARG   0.004   0.000   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04518 (  492)
  hydrogen bonds       : angle       4.16748 ( 1392)
  covalent geometry    : bond        0.00291 (11296)
  covalent geometry    : angle       0.66532 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 1.136 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9168 (mt) cc_final: 0.8817 (tt)
REVERT: B  156 ILE cc_start: 0.8720 (mt) cc_final: 0.8488 (tt)
REVERT: B  174 HIS cc_start: 0.7645 (t70) cc_final: 0.7308 (t70)
REVERT: B  185 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7467 (t0)
REVERT: B  288 ASP cc_start: 0.8566 (t0) cc_final: 0.7990 (p0)
REVERT: B  309 GLN cc_start: 0.9069 (pm20) cc_final: 0.8745 (pm20)
REVERT: B  420 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7591 (mp0)
REVERT: B  512 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7327 (ttt90)
REVERT: B  649 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7814 (pp)
REVERT: D  354 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9076 (mm-30)
REVERT: D  362 ILE cc_start: 0.9160 (mt) cc_final: 0.8810 (tt)
REVERT: E  272 SER cc_start: 0.8729 (t) cc_final: 0.8337 (m)
REVERT: E  512 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7247 (ttt90)
REVERT: E  649 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7813 (pp)
  outliers start: 35
  outliers final: 26
  residues processed: 215
  average time/residue: 0.1850
  time to fit residues: 60.0801
Evaluate side-chains
  222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  404 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  649 LEU
Chi-restraints excluded: chain E residue  666 LEU
Chi-restraints excluded: chain E residue  674 ASP
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 137 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 124 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
E 144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.098242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.078589 restraints weight = 19314.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.15
r_work: 0.2961 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      165 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      171 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11296  Z= 0.122
  Angle     :  0.662   9.123  15412  Z= 0.321
  Chirality :  0.042   0.230   1726
  Planarity :  0.005   0.042   1978
  Dihedral  :  4.863  31.222   1528
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.76 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.53 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1382
  helix:  2.93 (0.24), residues: 486
  sheet: -0.09 (0.32), residues: 262
  loop : -2.24 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 167 
 HIS   0.003   0.001   HIS B 532 
 PHE   0.013   0.001   PHE B 312 
 TYR   0.011   0.001   TYR E 423 
 ARG   0.003   0.000   ARG D 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  492)
  hydrogen bonds       : angle       4.11392 ( 1392)
  covalent geometry    : bond        0.00277 (11296)
  covalent geometry    : angle       0.66207 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9176 (mt) cc_final: 0.8847 (tt)
REVERT: B  156 ILE cc_start: 0.8726 (mt) cc_final: 0.8501 (tt)
REVERT: B  174 HIS cc_start: 0.7615 (t70) cc_final: 0.7297 (t70)
REVERT: B  185 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7428 (t0)
REVERT: B  309 GLN cc_start: 0.9062 (pm20) cc_final: 0.8787 (pm20)
REVERT: B  512 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7363 (ttt90)
REVERT: B  649 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7859 (pp)
REVERT: D  354 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9035 (mm-30)
REVERT: D  362 ILE cc_start: 0.9164 (mt) cc_final: 0.8843 (tt)
REVERT: E  499 GLU cc_start: 0.7786 (tt0) cc_final: 0.7298 (tt0)
REVERT: E  512 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7291 (ttt90)
REVERT: E  649 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7839 (pp)
  outliers start: 32
  outliers final: 24
  residues processed: 213
  average time/residue: 0.1917
  time to fit residues: 63.1285
Evaluate side-chains
  213 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  404 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  649 LEU
Chi-restraints excluded: chain E residue  674 ASP
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 122 optimal weight:    0.0980
   chunk 35 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0010
   chunk 43 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 121 optimal weight:    0.6980
   chunk 97 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
E 144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.099767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.079939 restraints weight = 19278.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.17
r_work: 0.2983 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      171 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      173 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11296  Z= 0.115
  Angle     :  0.659   8.998  15412  Z= 0.321
  Chirality :  0.042   0.208   1726
  Planarity :  0.005   0.042   1978
  Dihedral  :  4.778  31.041   1528
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.03 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.69 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.24), residues: 1382
  helix:  3.00 (0.24), residues: 486
  sheet:  0.04 (0.32), residues: 264
  loop : -2.16 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 167 
 HIS   0.002   0.001   HIS E 648 
 PHE   0.015   0.001   PHE B 312 
 TYR   0.012   0.001   TYR E 423 
 ARG   0.005   0.000   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  492)
  hydrogen bonds       : angle       3.98708 ( 1392)
  covalent geometry    : bond        0.00253 (11296)
  covalent geometry    : angle       0.65925 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 1.315 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9153 (mt) cc_final: 0.8826 (tt)
REVERT: B  109 MET cc_start: 0.2950 (OUTLIER) cc_final: 0.1300 (tmm)
REVERT: B  156 ILE cc_start: 0.8670 (mt) cc_final: 0.8444 (tt)
REVERT: B  174 HIS cc_start: 0.7474 (t70) cc_final: 0.7190 (t70)
REVERT: B  185 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7326 (t0)
REVERT: B  309 GLN cc_start: 0.9064 (pm20) cc_final: 0.8744 (pm20)
REVERT: B  512 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7330 (ttt90)
REVERT: B  649 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7762 (pp)
REVERT: D  354 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: D  362 ILE cc_start: 0.9134 (mt) cc_final: 0.8813 (tt)
REVERT: E  499 GLU cc_start: 0.7747 (tt0) cc_final: 0.7271 (tt0)
REVERT: E  512 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7234 (ttt90)
REVERT: E  649 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7767 (pp)
  outliers start: 32
  outliers final: 20
  residues processed: 218
  average time/residue: 0.1900
  time to fit residues: 63.5188
Evaluate side-chains
  214 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 188
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  351 MET
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain E residue  144 ASN
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  381 TYR
Chi-restraints excluded: chain E residue  387 SER
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  649 LEU
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   chunk 109 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0070
   chunk 112 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.099506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.079681 restraints weight = 19287.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 3.17
r_work: 0.2981 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2982
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      173 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2982 r_free = 0.2982    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      177 |
|-----------------------------------------------------------------------------|
r_final: 0.2982
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11296  Z= 0.119
  Angle     :  0.662   8.956  15412  Z= 0.320
  Chirality :  0.042   0.200   1726
  Planarity :  0.005   0.041   1978
  Dihedral  :  4.724  30.936   1528
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.18 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.20 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1382
  helix:  2.99 (0.24), residues: 488
  sheet:  0.04 (0.32), residues: 264
  loop : -2.08 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 167 
 HIS   0.003   0.001   HIS B 532 
 PHE   0.014   0.001   PHE B 312 
 TYR   0.021   0.001   TYR E 145 
 ARG   0.003   0.000   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  492)
  hydrogen bonds       : angle       3.96598 ( 1392)
  covalent geometry    : bond        0.00270 (11296)
  covalent geometry    : angle       0.66237 (15412)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 1.273 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9153 (mt) cc_final: 0.8830 (tt)
REVERT: B  109 MET cc_start: 0.2948 (OUTLIER) cc_final: 0.1373 (tmm)
REVERT: B  156 ILE cc_start: 0.8680 (mt) cc_final: 0.8462 (tt)
REVERT: B  174 HIS cc_start: 0.7452 (t70) cc_final: 0.7189 (t70)
REVERT: B  185 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7313 (t0)
REVERT: B  309 GLN cc_start: 0.9077 (pm20) cc_final: 0.8747 (pm20)
REVERT: B  512 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7329 (ttt90)
REVERT: B  560 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7619 (ttp80)
REVERT: B  649 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (pp)
REVERT: D  354 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8970 (mm-30)
REVERT: D  362 ILE cc_start: 0.9134 (mt) cc_final: 0.8816 (tt)
REVERT: E  131 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7775 (pp)
REVERT: E  499 GLU cc_start: 0.7764 (tt0) cc_final: 0.7282 (tt0)
REVERT: E  512 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7243 (ttt90)
REVERT: E  649 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7742 (pp)
  outliers start: 27
  outliers final: 18
  residues processed: 211
  average time/residue: 0.1895
  time to fit residues: 60.7479
Evaluate side-chains
  218 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  381 TYR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  485 LEU
Chi-restraints excluded: chain E residue  512 ARG
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  649 LEU
Chi-restraints excluded: chain E residue  666 LEU
Chi-restraints excluded: chain E residue  723 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0770
   chunk 105 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
E 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.099591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.079873 restraints weight = 19029.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.14
r_work: 0.2982 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      177 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      178 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.148  11296  Z= 0.224
  Angle     :  0.936  59.200  15412  Z= 0.520
  Chirality :  0.046   0.777   1726
  Planarity :  0.005   0.048   1978
  Dihedral  :  4.864  47.086   1528
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.10 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 22.71 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.24), residues: 1382
  helix:  2.98 (0.24), residues: 488
  sheet:  0.01 (0.32), residues: 264
  loop : -2.08 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 297 
 HIS   0.003   0.001   HIS B 532 
 PHE   0.014   0.001   PHE B 277 
 TYR   0.020   0.001   TYR E 145 
 ARG   0.003   0.000   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  492)
  hydrogen bonds       : angle       3.96945 ( 1392)
  covalent geometry    : bond        0.00429 (11296)
  covalent geometry    : angle       0.93594 (15412)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4906.33 seconds
wall clock time: 87 minutes 2.81 seconds (5222.81 seconds total)