Starting phenix.real_space_refine
on Wed Mar  4 04:58:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_20042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_20042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_20042.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_20042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6of4_20042/03_2026/6of4_20042.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.018 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
  Restraints were copied for chains:
    D, E
  Time building chain proxies: 3.45, per 1000 atoms: 0.31
  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: 0.90
  Conformation dependent library (CDL) restraints added in 501.0 milliseconds
  

  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: 0.38
  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: 1.43

  Time building geometry restraints manager: 1.23 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}

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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.720
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.670
-------------------------------------------------------------------------------
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 : 11.72
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG A  56 
 TYR   0.034   0.004   TYR E 530 
 PHE   0.026   0.003   PHE A 107 
 TRP   0.035   0.003   TRP B 297 
 HIS   0.008   0.002   HIS D  68 

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

*********************** 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  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ASN cc_start: 0.7377 (t0) cc_final: 0.6946 (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: 0.8585 (tp)
REVERT: B  164 ILE cc_start: 0.8876 (mt) cc_final: 0.8545 (pt)
REVERT: B  183 THR cc_start: 0.7986 (m) cc_final: 0.7720 (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: 0.8848 (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: 0.7932 (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: 0.8019 (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: 0.1165
  time to fit residues: 51.4963
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  : 0.273 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0030
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.100653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.081160 restraints weight = 19286.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 3.15
r_work: 0.2987 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
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:       96 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2703

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= 0.152
  Angle     :  0.825  11.627  15412  Z= 0.412
  Chirality :  0.045   0.277   1726
  Planarity :  0.007   0.058   1978
  Dihedral  :  6.677  85.925   1548
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 10.42 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 13.31 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.23), residues: 1382
  helix:  1.97 (0.22), residues: 478
  sheet: -0.40 (0.33), residues: 256
  loop : -3.31 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 376 
 TYR   0.017   0.002   TYR E 423 
 PHE   0.014   0.002   PHE B 379 
 TRP   0.017   0.001   TRP B 297 
 HIS   0.012   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11296)
  covalent geometry    : angle       0.82518 (15412)
  hydrogen bonds       : bond        0.05675 (  492)
  hydrogen bonds       : angle       4.98415 ( 1392)

*********************** 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
  278 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 236
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: B  156 ILE cc_start: 0.8801 (mt) cc_final: 0.8575 (tt)
REVERT: B  174 HIS cc_start: 0.8033 (t70) cc_final: 0.7134 (t70)
REVERT: B  251 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7940 (tp30)
REVERT: B  272 SER cc_start: 0.8507 (t) cc_final: 0.8273 (m)
REVERT: B  288 ASP cc_start: 0.8345 (t0) cc_final: 0.7972 (p0)
REVERT: B  309 GLN cc_start: 0.9128 (pm20) cc_final: 0.8784 (pm20)
REVERT: B  557 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8638 (tp30)
REVERT: E  109 MET cc_start: 0.5525 (mtm) cc_final: 0.3519 (tmm)
REVERT: E  128 ARG cc_start: 0.6394 (ptt180) cc_final: 0.5886 (ptp-170)
REVERT: E  129 LEU cc_start: 0.7645 (mp) cc_final: 0.7363 (tt)
REVERT: E  156 ILE cc_start: 0.8995 (mt) cc_final: 0.8726 (tt)
REVERT: E  239 LEU cc_start: 0.7543 (tp) cc_final: 0.7253 (tt)
REVERT: E  288 ASP cc_start: 0.8443 (t0) cc_final: 0.7778 (p0)
REVERT: E  417 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7629 (mtp85)
  outliers start: 42
  outliers final: 23
  residues processed: 264
  average time/residue: 0.0831
  time to fit residues: 33.2385
Evaluate side-chains
  215 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
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  430 GLU
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 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 98 optimal weight:    3.9990
   chunk 124 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 126 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 136 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0970
   overall best weight:    0.5978

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.097376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.077757 restraints weight = 19521.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 3.13
r_work: 0.2946 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       96 |
|-----------------------------------------------------------------------------|
|-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:      127 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11296  Z= 0.130
  Angle     :  0.719   9.855  15412  Z= 0.353
  Chirality :  0.043   0.176   1726
  Planarity :  0.006   0.053   1978
  Dihedral  :  5.810  80.879   1528
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  9.91 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.10 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.24), residues: 1382
  helix:  3.04 (0.23), residues: 482
  sheet:  0.07 (0.34), residues: 256
  loop : -2.72 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 160 
 TYR   0.009   0.001   TYR E 482 
 PHE   0.029   0.002   PHE B 332 
 TRP   0.008   0.001   TRP A  60 
 HIS   0.008   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11296)
  covalent geometry    : angle       0.71937 (15412)
  hydrogen bonds       : bond        0.04968 (  492)
  hydrogen bonds       : angle       4.48197 ( 1392)

*********************** 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
  244 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.397 
Fit side-chains
REVERT: B  174 HIS cc_start: 0.7626 (t70) cc_final: 0.6952 (t70)
REVERT: B  251 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7843 (tp30)
REVERT: B  272 SER cc_start: 0.8443 (t) cc_final: 0.8175 (m)
REVERT: B  309 GLN cc_start: 0.9015 (pm20) cc_final: 0.8671 (pm20)
REVERT: B  557 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8654 (tp30)
REVERT: E  109 MET cc_start: 0.5275 (mtm) cc_final: 0.3421 (tmm)
REVERT: E  239 LEU cc_start: 0.7463 (tp) cc_final: 0.7161 (tt)
REVERT: E  272 SER cc_start: 0.8586 (t) cc_final: 0.8254 (m)
REVERT: E  309 GLN cc_start: 0.9063 (pm20) cc_final: 0.8858 (pm20)
REVERT: E  367 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8238 (m-30)
REVERT: E  417 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7596 (mtp85)
REVERT: E  613 LEU cc_start: 0.8669 (tt) cc_final: 0.8397 (tt)
  outliers start: 40
  outliers final: 21
  residues processed: 226
  average time/residue: 0.0761
  time to fit residues: 26.8381
Evaluate side-chains
  211 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  537 GLU
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  351 MET
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  666 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 103 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 129 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.097215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.077783 restraints weight = 19513.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.12
r_work: 0.2942 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      127 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      128 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11296  Z= 0.130
  Angle     :  0.690   9.690  15412  Z= 0.338
  Chirality :  0.043   0.211   1726
  Planarity :  0.006   0.047   1978
  Dihedral  :  5.641  76.092   1528
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  9.12 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.95 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.24), residues: 1382
  helix:  3.12 (0.23), residues: 486
  sheet: -0.08 (0.32), residues: 262
  loop : -2.47 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 128 
 TYR   0.010   0.001   TYR B 423 
 PHE   0.018   0.001   PHE B 332 
 TRP   0.008   0.001   TRP B 400 
 HIS   0.003   0.001   HIS E 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11296)
  covalent geometry    : angle       0.69026 (15412)
  hydrogen bonds       : bond        0.04774 (  492)
  hydrogen bonds       : angle       4.26033 ( 1392)

*********************** 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
  242 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 207
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: B  174 HIS cc_start: 0.7679 (t70) cc_final: 0.7085 (t70)
REVERT: B  251 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7832 (tp30)
REVERT: B  272 SER cc_start: 0.8431 (t) cc_final: 0.8157 (m)
REVERT: B  288 ASP cc_start: 0.8410 (t0) cc_final: 0.7789 (p0)
REVERT: B  309 GLN cc_start: 0.9055 (pm20) cc_final: 0.8631 (pm20)
REVERT: B  319 SER cc_start: 0.8187 (p) cc_final: 0.7894 (p)
REVERT: B  327 ASN cc_start: 0.9372 (t0) cc_final: 0.8992 (t0)
REVERT: B  512 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7480 (ttt90)
REVERT: B  557 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8645 (tp30)
REVERT: E  109 MET cc_start: 0.5164 (mtm) cc_final: 0.3336 (tmm)
REVERT: E  128 ARG cc_start: 0.6256 (ptt180) cc_final: 0.5593 (ptp-170)
REVERT: E  239 LEU cc_start: 0.7517 (tp) cc_final: 0.7196 (tt)
REVERT: E  272 SER cc_start: 0.8547 (t) cc_final: 0.8264 (m)
REVERT: E  288 ASP cc_start: 0.8568 (t0) cc_final: 0.7993 (p0)
REVERT: E  367 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (m-30)
  outliers start: 35
  outliers final: 21
  residues processed: 228
  average time/residue: 0.0798
  time to fit residues: 28.0622
Evaluate side-chains
  221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  445 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  512 ARG
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  367 ASP
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  666 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 133 optimal weight:    0.1980
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 138 optimal weight:    0.0000
   chunk 112 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.3986

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.075010 restraints weight = 19579.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 3.07
r_work: 0.2898 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      128 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      135 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11296  Z= 0.176
  Angle     :  0.697  10.708  15412  Z= 0.346
  Chirality :  0.044   0.148   1726
  Planarity :  0.006   0.051   1978
  Dihedral  :  5.567  74.487   1528
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.84 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.20 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.24), residues: 1382
  helix:  3.00 (0.23), residues: 486
  sheet: -0.16 (0.31), residues: 262
  loop : -2.39 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 417 
 TYR   0.011   0.002   TYR E 482 
 PHE   0.014   0.002   PHE A 107 
 TRP   0.010   0.001   TRP B 400 
 HIS   0.004   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (11296)
  covalent geometry    : angle       0.69712 (15412)
  hydrogen bonds       : bond        0.05654 (  492)
  hydrogen bonds       : angle       4.33990 ( 1392)

*********************** 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
  251 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 205
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: B  174 HIS cc_start: 0.7809 (t70) cc_final: 0.7388 (t70)
REVERT: B  185 ASN cc_start: 0.7937 (m110) cc_final: 0.7601 (t0)
REVERT: B  251 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7886 (tp30)
REVERT: B  272 SER cc_start: 0.8470 (t) cc_final: 0.8219 (m)
REVERT: B  309 GLN cc_start: 0.9034 (pm20) cc_final: 0.8657 (pm20)
REVERT: B  512 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7509 (ttt90)
REVERT: D  354 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9077 (mm-30)
REVERT: D  362 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8762 (tt)
REVERT: E  109 MET cc_start: 0.4833 (mtm) cc_final: 0.3498 (tmm)
REVERT: E  239 LEU cc_start: 0.7724 (tp) cc_final: 0.7404 (tt)
REVERT: E  272 SER cc_start: 0.8582 (t) cc_final: 0.8365 (m)
REVERT: E  288 ASP cc_start: 0.8599 (t0) cc_final: 0.8398 (p0)
REVERT: E  426 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8508 (tm-30)
REVERT: E  499 GLU cc_start: 0.7746 (tt0) cc_final: 0.7351 (tt0)
REVERT: E  512 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7542 (ttt90)
  outliers start: 46
  outliers final: 33
  residues processed: 229
  average time/residue: 0.0764
  time to fit residues: 27.0867
Evaluate side-chains
  229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 192
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  362 ILE
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  252 LEU
Chi-restraints excluded: chain B residue  256 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  512 ARG
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain B residue  531 ASP
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  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  287 THR
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  397 THR
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  666 LEU
Chi-restraints excluded: chain E residue  674 ASP
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 39 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 110 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0170
   chunk 137 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.097354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.078054 restraints weight = 19408.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 3.12
r_work: 0.2950 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      135 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      137 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11296  Z= 0.118
  Angle     :  0.649   9.186  15412  Z= 0.319
  Chirality :  0.042   0.147   1726
  Planarity :  0.006   0.046   1978
  Dihedral  :  5.243  72.975   1528
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.90 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.97 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.24), residues: 1382
  helix:  3.10 (0.23), residues: 486
  sheet:  0.01 (0.31), residues: 262
  loop : -2.30 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 417 
 TYR   0.012   0.001   TYR B 423 
 PHE   0.013   0.001   PHE B 332 
 TRP   0.009   0.001   TRP B 400 
 HIS   0.004   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11296)
  covalent geometry    : angle       0.64905 (15412)
  hydrogen bonds       : bond        0.04313 (  492)
  hydrogen bonds       : angle       4.13501 ( 1392)

*********************** 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
  243 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8735 (tt)
REVERT: B  174 HIS cc_start: 0.7642 (t70) cc_final: 0.7284 (t70)
REVERT: B  185 ASN cc_start: 0.7715 (m110) cc_final: 0.7427 (t0)
REVERT: B  251 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7864 (tp30)
REVERT: B  272 SER cc_start: 0.8406 (t) cc_final: 0.8113 (m)
REVERT: B  288 ASP cc_start: 0.8460 (t0) cc_final: 0.7847 (p0)
REVERT: B  512 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7486 (ttt90)
REVERT: B  649 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7834 (pp)
REVERT: D  362 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8792 (tt)
REVERT: E  109 MET cc_start: 0.5287 (mtm) cc_final: 0.3489 (tmm)
REVERT: E  239 LEU cc_start: 0.7695 (tp) cc_final: 0.7364 (tt)
REVERT: E  272 SER cc_start: 0.8559 (t) cc_final: 0.8287 (m)
REVERT: E  426 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: E  499 GLU cc_start: 0.7737 (tt0) cc_final: 0.7342 (tt0)
REVERT: E  649 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7855 (pp)
  outliers start: 44
  outliers final: 21
  residues processed: 226
  average time/residue: 0.0781
  time to fit residues: 27.3264
Evaluate side-chains
  221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  362 ILE
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  287 THR
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  397 THR
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 B residue  649 LEU
Chi-restraints excluded: chain D residue  362 ILE
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  287 THR
Chi-restraints excluded: chain E residue  328 LEU
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  445 THR
Chi-restraints excluded: chain E residue  640 LEU
Chi-restraints excluded: chain E residue  649 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0370
   chunk 19 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.098155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.078758 restraints weight = 19342.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 3.13
r_work: 0.2961 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      137 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      148 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.4201

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= 0.116
  Angle     :  0.658   9.465  15412  Z= 0.320
  Chirality :  0.042   0.216   1726
  Planarity :  0.005   0.043   1978
  Dihedral  :  5.089  71.624   1528
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.39 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.56 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.24), residues: 1382
  helix:  3.10 (0.24), residues: 486
  sheet:  0.09 (0.31), residues: 262
  loop : -2.21 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 417 
 TYR   0.011   0.001   TYR B 423 
 PHE   0.014   0.001   PHE B 312 
 TRP   0.010   0.001   TRP B 400 
 HIS   0.003   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11296)
  covalent geometry    : angle       0.65835 (15412)
  hydrogen bonds       : bond        0.04105 (  492)
  hydrogen bonds       : angle       4.02982 ( 1392)

*********************** 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
  240 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 201
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9102 (mt) cc_final: 0.8736 (tt)
REVERT: B  174 HIS cc_start: 0.7530 (t70) cc_final: 0.7209 (t70)
REVERT: B  185 ASN cc_start: 0.7658 (m110) cc_final: 0.7367 (t0)
REVERT: B  251 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7920 (tp30)
REVERT: B  272 SER cc_start: 0.8423 (t) cc_final: 0.8113 (m)
REVERT: B  288 ASP cc_start: 0.8478 (t0) cc_final: 0.7812 (p0)
REVERT: B  309 GLN cc_start: 0.9007 (pm20) cc_final: 0.8723 (pm20)
REVERT: B  512 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7481 (ttt90)
REVERT: B  548 MET cc_start: 0.7562 (mtm) cc_final: 0.7319 (mtm)
REVERT: B  649 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7745 (pp)
REVERT: D  362 ILE cc_start: 0.9123 (mt) cc_final: 0.8746 (tt)
REVERT: E  109 MET cc_start: 0.4988 (mtm) cc_final: 0.3189 (tmm)
REVERT: E  128 ARG cc_start: 0.5964 (ptt180) cc_final: 0.5581 (ptp-170)
REVERT: E  239 LEU cc_start: 0.7704 (tp) cc_final: 0.7383 (tt)
REVERT: E  272 SER cc_start: 0.8548 (t) cc_final: 0.8266 (m)
REVERT: E  499 GLU cc_start: 0.7724 (tt0) cc_final: 0.7334 (tt0)
REVERT: E  512 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7538 (ttt90)
REVERT: E  649 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7792 (pp)
  outliers start: 39
  outliers final: 26
  residues processed: 228
  average time/residue: 0.0814
  time to fit residues: 28.1707
Evaluate side-chains
  226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
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  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  397 THR
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  531 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain D residue   22 PHE
Chi-restraints excluded: chain D residue   94 TYR
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  328 LEU
Chi-restraints excluded: chain E residue  397 THR
Chi-restraints excluded: chain E residue  400 TRP
Chi-restraints excluded: chain E residue  445 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 118 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 107 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.097025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.077584 restraints weight = 19484.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.12
r_work: 0.2928 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      148 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      150 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11296  Z= 0.159
  Angle     :  0.678   8.908  15412  Z= 0.332
  Chirality :  0.043   0.200   1726
  Planarity :  0.006   0.043   1978
  Dihedral  :  5.099  71.510   1528
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.77 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.56 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.24), residues: 1382
  helix:  3.05 (0.24), residues: 486
  sheet: -0.03 (0.31), residues: 262
  loop : -2.19 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 417 
 TYR   0.009   0.001   TYR B 482 
 PHE   0.012   0.001   PHE A 107 
 TRP   0.010   0.001   TRP B 400 
 HIS   0.005   0.001   HIS E 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11296)
  covalent geometry    : angle       0.67768 (15412)
  hydrogen bonds       : bond        0.05036 (  492)
  hydrogen bonds       : angle       4.14706 ( 1392)

*********************** 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
  233 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 198
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9140 (mt) cc_final: 0.8760 (tt)
REVERT: B  174 HIS cc_start: 0.7669 (t70) cc_final: 0.7332 (t70)
REVERT: B  185 ASN cc_start: 0.7775 (m110) cc_final: 0.7462 (t0)
REVERT: B  272 SER cc_start: 0.8484 (t) cc_final: 0.8199 (m)
REVERT: B  288 ASP cc_start: 0.8593 (t0) cc_final: 0.8004 (p0)
REVERT: B  309 GLN cc_start: 0.9025 (pm20) cc_final: 0.8728 (pm20)
REVERT: B  512 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7519 (ttt90)
REVERT: B  640 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7641 (mt)
REVERT: B  649 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7740 (pp)
REVERT: D  362 ILE cc_start: 0.9161 (mt) cc_final: 0.8814 (tt)
REVERT: E  109 MET cc_start: 0.4644 (mtm) cc_final: 0.3151 (tmm)
REVERT: E  239 LEU cc_start: 0.7759 (tp) cc_final: 0.7414 (tt)
REVERT: E  272 SER cc_start: 0.8657 (t) cc_final: 0.8420 (m)
REVERT: E  512 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7529 (ttt90)
REVERT: E  649 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7758 (pp)
  outliers start: 35
  outliers final: 25
  residues processed: 219
  average time/residue: 0.0792
  time to fit residues: 26.6877
Evaluate side-chains
  223 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
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  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  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  531 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  256 THR
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  328 LEU
Chi-restraints excluded: chain E residue  397 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 127 optimal weight:    3.9990
   chunk 126 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.097184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.077897 restraints weight = 19395.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 3.11
r_work: 0.2950 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      150 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      156 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11296  Z= 0.148
  Angle     :  0.674   9.747  15412  Z= 0.328
  Chirality :  0.042   0.185   1726
  Planarity :  0.006   0.042   1978
  Dihedral  :  4.831  35.358   1528
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.12 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.47 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.24), residues: 1382
  helix:  3.01 (0.24), residues: 486
  sheet: -0.07 (0.31), residues: 264
  loop : -2.13 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 417 
 TYR   0.009   0.001   TYR E 482 
 PHE   0.012   0.001   PHE B 312 
 TRP   0.010   0.001   TRP B 400 
 HIS   0.005   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11296)
  covalent geometry    : angle       0.67379 (15412)
  hydrogen bonds       : bond        0.04789 (  492)
  hydrogen bonds       : angle       4.14298 ( 1392)

*********************** 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
  239 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 200
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9163 (mt) cc_final: 0.8785 (tt)
REVERT: B  174 HIS cc_start: 0.7626 (t70) cc_final: 0.7314 (t70)
REVERT: B  185 ASN cc_start: 0.7770 (m110) cc_final: 0.7412 (t0)
REVERT: B  272 SER cc_start: 0.8525 (t) cc_final: 0.8252 (m)
REVERT: B  288 ASP cc_start: 0.8562 (t0) cc_final: 0.8004 (p0)
REVERT: B  309 GLN cc_start: 0.9036 (pm20) cc_final: 0.8739 (pm20)
REVERT: B  512 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7533 (ttt90)
REVERT: B  640 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7692 (mt)
REVERT: B  649 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7751 (pp)
REVERT: D  362 ILE cc_start: 0.9154 (mt) cc_final: 0.8814 (tt)
REVERT: E  109 MET cc_start: 0.4616 (mtm) cc_final: 0.3179 (tmm)
REVERT: E  272 SER cc_start: 0.8699 (t) cc_final: 0.8440 (m)
REVERT: E  512 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7562 (ttt90)
REVERT: E  649 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7754 (pp)
  outliers start: 39
  outliers final: 29
  residues processed: 224
  average time/residue: 0.0759
  time to fit residues: 26.4354
Evaluate side-chains
  229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
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  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  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  512 ARG
Chi-restraints excluded: chain B residue  531 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain D residue   94 TYR
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  287 THR
Chi-restraints excluded: chain E residue  381 TYR
Chi-restraints excluded: chain E residue  397 THR
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  658 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0020
   chunk 46 optimal weight:    0.5980
   chunk 134 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0980
   chunk 115 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 110 optimal weight:    0.0030
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.3398

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.102134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.082264 restraints weight = 19055.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.17
r_work: 0.3021 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      156 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.4641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  11296  Z= 0.106
  Angle     :  0.652   9.533  15412  Z= 0.314
  Chirality :  0.041   0.182   1726
  Planarity :  0.005   0.044   1978
  Dihedral  :  4.702  31.490   1528
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.74 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.32 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.24), residues: 1382
  helix:  3.10 (0.24), residues: 486
  sheet:  0.30 (0.32), residues: 256
  loop : -2.03 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 417 
 TYR   0.012   0.001   TYR E 423 
 PHE   0.014   0.001   PHE B 312 
 TRP   0.009   0.001   TRP B 400 
 HIS   0.004   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (11296)
  covalent geometry    : angle       0.65231 (15412)
  hydrogen bonds       : bond        0.03389 (  492)
  hydrogen bonds       : angle       3.96687 ( 1392)

********************** 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
  225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 196
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  362 ILE cc_start: 0.9058 (mt) cc_final: 0.8699 (tt)
REVERT: B  185 ASN cc_start: 0.7495 (m110) cc_final: 0.7169 (t0)
REVERT: B  272 SER cc_start: 0.8451 (t) cc_final: 0.8179 (m)
REVERT: B  288 ASP cc_start: 0.8517 (t0) cc_final: 0.8012 (p0)
REVERT: B  309 GLN cc_start: 0.9053 (pm20) cc_final: 0.8757 (pm20)
REVERT: B  649 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7638 (pp)
REVERT: D  362 ILE cc_start: 0.9090 (mt) cc_final: 0.8722 (tt)
REVERT: E  109 MET cc_start: 0.4714 (mtm) cc_final: 0.3224 (tmm)
REVERT: E  128 ARG cc_start: 0.5809 (ptt180) cc_final: 0.5590 (ptp-170)
REVERT: E  272 SER cc_start: 0.8657 (t) cc_final: 0.8378 (m)
REVERT: E  649 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7670 (pp)
  outliers start: 29
  outliers final: 19
  residues processed: 211
  average time/residue: 0.0718
  time to fit residues: 23.8621
Evaluate side-chains
  209 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 188
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  381 TYR
Chi-restraints excluded: chain B residue  397 THR
Chi-restraints excluded: chain B residue  400 TRP
Chi-restraints excluded: chain B residue  531 ASP
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  666 LEU
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain E residue  180 VAL
Chi-restraints excluded: chain E residue  287 THR
Chi-restraints excluded: chain E residue  328 LEU
Chi-restraints excluded: chain E residue  397 THR
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  649 LEU
Chi-restraints excluded: chain E residue  674 ASP
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 14 optimal weight:    0.9990
   chunk 100 optimal weight:    0.4980
   chunk 115 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 132 optimal weight:    8.9990
   chunk 129 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.099429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.079835 restraints weight = 19206.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.13
r_work: 0.2979 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| 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:      161 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      169 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11296  Z= 0.128
  Angle     :  0.656   9.616  15412  Z= 0.317
  Chirality :  0.041   0.173   1726
  Planarity :  0.005   0.043   1978
  Dihedral  :  4.610  30.933   1528
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.39 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.92 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.24), residues: 1382
  helix:  3.08 (0.24), residues: 488
  sheet:  0.19 (0.32), residues: 260
  loop : -2.02 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 417 
 TYR   0.009   0.001   TYR E 423 
 PHE   0.013   0.001   PHE B 312 
 TRP   0.011   0.001   TRP B 400 
 HIS   0.004   0.001   HIS B 532 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11296)
  covalent geometry    : angle       0.65613 (15412)
  hydrogen bonds       : bond        0.04197 (  492)
  hydrogen bonds       : angle       3.97000 ( 1392)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2123.90 seconds
wall clock time: 37 minutes 6.47 seconds (2226.47 seconds total)