Starting phenix.real_space_refine
on Sun Dec 21 09:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5yys_6859/12_2025/5yys_6859.map"
  }
  resolution = 4.2
  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=   0.000 sd=   0.003
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      88      5.16       5
     C   15312      2.51       5
     N    4148      2.21       5
     O    4496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 24044
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 811, 6011
          Classifications: {'peptide': 811}
          Incomplete info: {'truncation_to_alanine': 83}
          Link IDs: {'CIS': 36, 'PCIS': 2, 'PTRANS': 44, 'TRANS': 728}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 333
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 277
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 10, 'TYR:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 8, 'PHE:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 204
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 6.18, per 1000 atoms: 0.26
  Number of scatterers: 24044
  At special positions: 0
  Unit cell: (115.7, 130, 209.3, 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      88     16.00
     O    4496      8.00
     N    4148      7.00
     C   15312      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 910.6 milliseconds
  

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5968

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 20 sheets defined
      34.4% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 107 through 119
      Proline residue:  A 115  - end of helix
    Processing helix  chain 'A' and resid 162 through 168
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 236 through 245
    Processing helix  chain 'A' and resid 247 through 253
    Processing helix  chain 'A' and resid 275 through 284
      removed outlier: 4.018A  pdb=" N   LEU A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 4.052A  pdb=" N   GLY A 385 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP A 386 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   LEU A 387 " --> pdb=" O   LYS A 384 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ARG A 388 " --> pdb=" O   GLY A 385 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP A 389 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 479
      removed outlier: 3.929A  pdb=" N   ARG A 479 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 491
    Processing helix  chain 'A' and resid 502 through 509
    Processing helix  chain 'A' and resid 516 through 522
    Processing helix  chain 'A' and resid 527 through 545
    Processing helix  chain 'A' and resid 548 through 566
      removed outlier: 3.583A  pdb=" N   ASP A 566 " --> pdb=" O   ASP A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 675
      removed outlier: 3.540A  pdb=" N   ALA A 672 " --> pdb=" O   SER A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 696
    Processing helix  chain 'A' and resid 717 through 734
    Processing helix  chain 'A' and resid 739 through 755
      removed outlier: 3.914A  pdb=" N   LEU A 753 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 766
      removed outlier: 3.573A  pdb=" N   TYR A 764 " --> pdb=" O   TRP A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 824
    Processing helix  chain 'A' and resid 830 through 852
      removed outlier: 3.686A  pdb=" N   ASN A 834 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 871
    Processing helix  chain 'A' and resid 878 through 887
      removed outlier: 3.760A  pdb=" N   GLU A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 887 " --> pdb=" O   ALA A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 925
    Processing helix  chain 'B' and resid 107 through 119
      Proline residue:  B 115  - end of helix
    Processing helix  chain 'B' and resid 162 through 168
    Processing helix  chain 'B' and resid 189 through 195
    Processing helix  chain 'B' and resid 214 through 218
    Processing helix  chain 'B' and resid 236 through 245
    Processing helix  chain 'B' and resid 247 through 253
    Processing helix  chain 'B' and resid 275 through 284
      removed outlier: 4.019A  pdb=" N   LEU B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 389
      removed outlier: 4.053A  pdb=" N   GLY B 385 " --> pdb=" O   VAL B 382 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASP B 386 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   LEU B 387 " --> pdb=" O   LYS B 384 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ARG B 388 " --> pdb=" O   GLY B 385 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP B 389 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 479
      removed outlier: 3.928A  pdb=" N   ARG B 479 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 491
    Processing helix  chain 'B' and resid 502 through 509
    Processing helix  chain 'B' and resid 516 through 522
    Processing helix  chain 'B' and resid 527 through 545
    Processing helix  chain 'B' and resid 548 through 566
      removed outlier: 3.583A  pdb=" N   ASP B 566 " --> pdb=" O   ASP B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 675
      removed outlier: 3.540A  pdb=" N   ALA B 672 " --> pdb=" O   SER B 668 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 696
    Processing helix  chain 'B' and resid 717 through 734
    Processing helix  chain 'B' and resid 739 through 755
      removed outlier: 3.914A  pdb=" N   LEU B 753 " --> pdb=" O   VAL B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 760 through 766
      removed outlier: 3.572A  pdb=" N   TYR B 764 " --> pdb=" O   TRP B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 824
    Processing helix  chain 'B' and resid 830 through 852
      removed outlier: 3.687A  pdb=" N   ASN B 834 " --> pdb=" O   SER B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 854 through 871
    Processing helix  chain 'B' and resid 878 through 887
      removed outlier: 3.760A  pdb=" N   GLU B 882 " --> pdb=" O   PRO B 878 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU B 887 " --> pdb=" O   ALA B 883 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 913 through 925
    Processing helix  chain 'C' and resid 107 through 119
      Proline residue:  C 115  - end of helix
    Processing helix  chain 'C' and resid 162 through 168
    Processing helix  chain 'C' and resid 189 through 195
    Processing helix  chain 'C' and resid 214 through 218
    Processing helix  chain 'C' and resid 236 through 245
    Processing helix  chain 'C' and resid 247 through 253
    Processing helix  chain 'C' and resid 275 through 284
      removed outlier: 4.018A  pdb=" N   LEU C 279 " --> pdb=" O   THR C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 389
      removed outlier: 4.052A  pdb=" N   GLY C 385 " --> pdb=" O   VAL C 382 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ASP C 386 " --> pdb=" O   PHE C 383 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   LEU C 387 " --> pdb=" O   LYS C 384 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ARG C 388 " --> pdb=" O   GLY C 385 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP C 389 " --> pdb=" O   ASP C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 468 through 479
      removed outlier: 3.928A  pdb=" N   ARG C 479 " --> pdb=" O   LEU C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 491
    Processing helix  chain 'C' and resid 502 through 509
    Processing helix  chain 'C' and resid 516 through 522
    Processing helix  chain 'C' and resid 527 through 545
    Processing helix  chain 'C' and resid 548 through 566
      removed outlier: 3.583A  pdb=" N   ASP C 566 " --> pdb=" O   ASP C 562 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 667 through 675
      removed outlier: 3.539A  pdb=" N   ALA C 672 " --> pdb=" O   SER C 668 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 696
    Processing helix  chain 'C' and resid 717 through 734
    Processing helix  chain 'C' and resid 739 through 755
      removed outlier: 3.915A  pdb=" N   LEU C 753 " --> pdb=" O   VAL C 749 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 760 through 766
      removed outlier: 3.572A  pdb=" N   TYR C 764 " --> pdb=" O   TRP C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 817 through 824
    Processing helix  chain 'C' and resid 830 through 852
      removed outlier: 3.686A  pdb=" N   ASN C 834 " --> pdb=" O   SER C 830 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 854 through 871
    Processing helix  chain 'C' and resid 878 through 887
      removed outlier: 3.760A  pdb=" N   GLU C 882 " --> pdb=" O   PRO C 878 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU C 887 " --> pdb=" O   ALA C 883 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 913 through 925
    Processing helix  chain 'D' and resid 107 through 119
      Proline residue:  D 115  - end of helix
    Processing helix  chain 'D' and resid 162 through 168
    Processing helix  chain 'D' and resid 189 through 195
    Processing helix  chain 'D' and resid 214 through 218
    Processing helix  chain 'D' and resid 236 through 245
    Processing helix  chain 'D' and resid 247 through 253
    Processing helix  chain 'D' and resid 275 through 284
      removed outlier: 4.019A  pdb=" N   LEU D 279 " --> pdb=" O   THR D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 381 through 389
      removed outlier: 4.053A  pdb=" N   GLY D 385 " --> pdb=" O   VAL D 382 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASP D 386 " --> pdb=" O   PHE D 383 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   LEU D 387 " --> pdb=" O   LYS D 384 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ARG D 388 " --> pdb=" O   GLY D 385 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP D 389 " --> pdb=" O   ASP D 386 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 468 through 479
      removed outlier: 3.929A  pdb=" N   ARG D 479 " --> pdb=" O   LEU D 475 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 479 through 491
    Processing helix  chain 'D' and resid 502 through 509
    Processing helix  chain 'D' and resid 516 through 522
    Processing helix  chain 'D' and resid 527 through 545
    Processing helix  chain 'D' and resid 548 through 566
      removed outlier: 3.583A  pdb=" N   ASP D 566 " --> pdb=" O   ASP D 562 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 667 through 675
      removed outlier: 3.539A  pdb=" N   ALA D 672 " --> pdb=" O   SER D 668 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 687 through 696
    Processing helix  chain 'D' and resid 717 through 734
    Processing helix  chain 'D' and resid 739 through 755
      removed outlier: 3.914A  pdb=" N   LEU D 753 " --> pdb=" O   VAL D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 760 through 766
      removed outlier: 3.573A  pdb=" N   TYR D 764 " --> pdb=" O   TRP D 760 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 817 through 824
    Processing helix  chain 'D' and resid 830 through 852
      removed outlier: 3.687A  pdb=" N   ASN D 834 " --> pdb=" O   SER D 830 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 854 through 871
    Processing helix  chain 'D' and resid 878 through 887
      removed outlier: 3.760A  pdb=" N   GLU D 882 " --> pdb=" O   PRO D 878 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU D 887 " --> pdb=" O   ALA D 883 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 913 through 925
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 157
      removed outlier: 3.570A  pdb=" N   GLY A 157 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 185
    Processing sheet with id=AA3, first strand: chain 'A' and resid 221 through 223
    Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587
      removed outlier: 3.621A  pdb=" N   VAL A 585 " --> pdb=" O   VAL A 630 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 895 through 896
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 157
      removed outlier: 3.570A  pdb=" N   GLY B 157 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 185
    Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 223
    Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 587
      removed outlier: 3.622A  pdb=" N   VAL B 585 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 895 through 896
    Processing sheet with id=AB2, first strand: chain 'C' and resid 156 through 157
      removed outlier: 3.570A  pdb=" N   GLY C 157 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 183 through 185
    Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 223
    Processing sheet with id=AB5, first strand: chain 'C' and resid 585 through 587
      removed outlier: 3.623A  pdb=" N   VAL C 585 " --> pdb=" O   VAL C 630 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 895 through 896
    Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 157
      removed outlier: 3.569A  pdb=" N   GLY D 157 " --> pdb=" O   LEU D 263 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 183 through 185
    Processing sheet with id=AB9, first strand: chain 'D' and resid 221 through 223
    Processing sheet with id=AC1, first strand: chain 'D' and resid 585 through 587
      removed outlier: 3.622A  pdb=" N   VAL D 585 " --> pdb=" O   VAL D 630 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 895 through 896

    764 hydrogen bonds defined for protein.
    2172 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: 4.09

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 4137
        1.30 -     1.43: 6167
        1.43 -     1.56: 14069
        1.56 -     1.68: 51
        1.68 -     1.81: 148
  Bond restraints: 24572
  Sorted by residual:
  bond pdb=" CA  GLN D 528 "
       pdb=" C   GLN D 528 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.40e-02 5.10e+03 3.36e+01
  bond pdb=" CA  GLN A 528 "
       pdb=" C   GLN A 528 "
    ideal  model  delta    sigma   weight residual
    1.522  1.441  0.081 1.40e-02 5.10e+03 3.34e+01
  bond pdb=" CA  GLN B 528 "
       pdb=" C   GLN B 528 "
    ideal  model  delta    sigma   weight residual
    1.522  1.442  0.080 1.40e-02 5.10e+03 3.28e+01
  bond pdb=" CA  GLN C 528 "
       pdb=" C   GLN C 528 "
    ideal  model  delta    sigma   weight residual
    1.522  1.442  0.080 1.40e-02 5.10e+03 3.26e+01
  bond pdb=" C   ILE C 584 "
       pdb=" N   VAL C 585 "
    ideal  model  delta    sigma   weight residual
    1.329  1.256  0.074 1.32e-02 5.74e+03 3.13e+01
  ... (remaining 24567 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.30: 32193
        5.30 -    10.60: 1057
       10.60 -    15.90: 162
       15.90 -    21.20: 28
       21.20 -    26.50: 8
  Bond angle restraints: 33448
  Sorted by residual:
  angle pdb=" N   LEU D 774 "
        pdb=" CA  LEU D 774 "
        pdb=" C   LEU D 774 "
      ideal   model   delta    sigma   weight residual
     111.28  125.99  -14.71 1.35e+00 5.49e-01 1.19e+02
  angle pdb=" N   LEU C 774 "
        pdb=" CA  LEU C 774 "
        pdb=" C   LEU C 774 "
      ideal   model   delta    sigma   weight residual
     111.28  125.98  -14.70 1.35e+00 5.49e-01 1.19e+02
  angle pdb=" N   LEU A 774 "
        pdb=" CA  LEU A 774 "
        pdb=" C   LEU A 774 "
      ideal   model   delta    sigma   weight residual
     111.28  125.96  -14.68 1.35e+00 5.49e-01 1.18e+02
  angle pdb=" N   LEU B 774 "
        pdb=" CA  LEU B 774 "
        pdb=" C   LEU B 774 "
      ideal   model   delta    sigma   weight residual
     111.28  125.94  -14.66 1.35e+00 5.49e-01 1.18e+02
  angle pdb=" N   LEU C 804 "
        pdb=" CA  LEU C 804 "
        pdb=" C   LEU C 804 "
      ideal   model   delta    sigma   weight residual
     112.68  126.90  -14.22 1.33e+00 5.65e-01 1.14e+02
  ... (remaining 33443 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 12509
       14.89 -    29.79: 1583
       29.79 -    44.68: 448
       44.68 -    59.57: 108
       59.57 -    74.47: 36
  Dihedral angle restraints: 14684
    sinusoidal: 5380
      harmonic: 9304
  Sorted by residual:
  dihedral pdb=" CA  ARG C 931 "
           pdb=" C   ARG C 931 "
           pdb=" N   ALA C 932 "
           pdb=" CA  ALA C 932 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.90   70.10     0      5.00e+00 4.00e-02 1.97e+02
  dihedral pdb=" CA  ARG A 931 "
           pdb=" C   ARG A 931 "
           pdb=" N   ALA A 932 "
           pdb=" CA  ALA A 932 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.93   70.07     0      5.00e+00 4.00e-02 1.96e+02
  dihedral pdb=" CA  ARG D 931 "
           pdb=" C   ARG D 931 "
           pdb=" N   ALA D 932 "
           pdb=" CA  ALA D 932 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.95   70.05     0      5.00e+00 4.00e-02 1.96e+02
  ... (remaining 14681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 3232
       0.122 -    0.243: 454
       0.243 -    0.365: 94
       0.365 -    0.486: 20
       0.486 -    0.608: 12
  Chirality restraints: 3812
  Sorted by residual:
  chirality pdb=" CG  LEU C 804 "
            pdb=" CB  LEU C 804 "
            pdb=" CD1 LEU C 804 "
            pdb=" CD2 LEU C 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.98   -0.61 2.00e-01 2.50e+01 9.24e+00
  chirality pdb=" CG  LEU D 804 "
            pdb=" CB  LEU D 804 "
            pdb=" CD1 LEU D 804 "
            pdb=" CD2 LEU D 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.98   -0.61 2.00e-01 2.50e+01 9.17e+00
  chirality pdb=" CG  LEU A 804 "
            pdb=" CB  LEU A 804 "
            pdb=" CD1 LEU A 804 "
            pdb=" CD2 LEU A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.98   -0.61 2.00e-01 2.50e+01 9.16e+00
  ... (remaining 3809 not shown)

  Planarity restraints: 4340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 785 "    0.029 2.00e-02 2.50e+03   5.90e-02 3.48e+01
        pdb=" C   LEU C 785 "   -0.102 2.00e-02 2.50e+03
        pdb=" O   LEU C 785 "    0.039 2.00e-02 2.50e+03
        pdb=" N   VAL C 786 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 785 "    0.029 2.00e-02 2.50e+03   5.89e-02 3.47e+01
        pdb=" C   LEU D 785 "   -0.102 2.00e-02 2.50e+03
        pdb=" O   LEU D 785 "    0.039 2.00e-02 2.50e+03
        pdb=" N   VAL D 786 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 785 "   -0.029 2.00e-02 2.50e+03   5.89e-02 3.47e+01
        pdb=" C   LEU B 785 "    0.102 2.00e-02 2.50e+03
        pdb=" O   LEU B 785 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   VAL B 786 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 4337 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 3756
        2.74 -     3.28: 26513
        3.28 -     3.82: 44715
        3.82 -     4.36: 51400
        4.36 -     4.90: 76329
  Nonbonded interactions: 202713
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 580 "
            pdb=" O   ASN C 929 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OH  TYR C 806 "
            pdb=" OG1 THR C 808 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR B 806 "
            pdb=" OG1 THR B 808 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR D 806 "
            pdb=" OG1 THR D 808 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR A 806 "
            pdb=" OG1 THR A 808 "
     model   vdw
     2.211 3.040
  ... (remaining 202708 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     22.270
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
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      :  0.016   0.131  24572  Z= 0.808
  Angle     :  2.273  26.499  33448  Z= 1.217
  Chirality :  0.102   0.608   3812
  Planarity :  0.014   0.113   4340
  Dihedral  : 15.297  74.465   8716
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 22.81
  Ramachandran Plot:
    Outliers :  2.60 %
    Allowed  : 27.32 %
    Favored  : 70.07 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.68 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 3.80 %
    Twisted Proline : 15.22 %
    Twisted General : 8.32 %

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: -5.98 (0.11), residues: 3228
  helix: -3.24 (0.11), residues: 1068
  sheet: -2.32 (0.36), residues: 208
  loop : -4.91 (0.10), residues: 1952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG D 948 
 TYR   0.048   0.008   TYR A 891 
 PHE   0.063   0.007   PHE B 654 
 TRP   0.037   0.007   TRP C 336 
 HIS   0.022   0.005   HIS B 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.01647 (24572)
  covalent geometry    : angle       2.27278 (33448)
  hydrogen bonds       : bond        0.21149 (  764)
  hydrogen bonds       : angle      10.11803 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 268
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  579 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (t)
REVERT: A  595 MET cc_start: 0.6627 (mmt) cc_final: 0.6351 (mmt)
REVERT: A  741 ASN cc_start: 0.9526 (m-40) cc_final: 0.9176 (m-40)
REVERT: B  108 ASN cc_start: 0.9261 (m-40) cc_final: 0.8787 (t0)
REVERT: B  579 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7930 (t)
REVERT: B  595 MET cc_start: 0.6802 (mmt) cc_final: 0.6442 (mmt)
REVERT: B  741 ASN cc_start: 0.9380 (m-40) cc_final: 0.9043 (m-40)
REVERT: C  579 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (t)
REVERT: C  595 MET cc_start: 0.6755 (mmt) cc_final: 0.6435 (mmt)
REVERT: C  741 ASN cc_start: 0.9401 (m-40) cc_final: 0.9073 (m-40)
REVERT: D  108 ASN cc_start: 0.9279 (m-40) cc_final: 0.8889 (t0)
REVERT: D  579 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7776 (t)
REVERT: D  595 MET cc_start: 0.6798 (mmt) cc_final: 0.6474 (mmt)
REVERT: D  741 ASN cc_start: 0.9407 (m-40) cc_final: 0.9080 (m-40)
  outliers start: 56
  outliers final: 20
  residues processed: 320
  average time/residue: 0.1983
  time to fit residues: 93.4051
Evaluate side-chains
  199 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 197 optimal weight:    5.9990
   chunk 215 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 132 optimal weight:    7.9990
   chunk 261 optimal weight:   20.0000
   chunk 248 optimal weight:   20.0000
   chunk 207 optimal weight:    0.9990
   chunk 155 optimal weight:    3.9990
   chunk 244 optimal weight:    2.9990
   chunk 183 optimal weight:    7.9990
   chunk 298 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 GLN
A 167 HIS
A 168 HIS
A 224 HIS
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN
A 763 GLN
A 782 GLN
A 803 HIS
A 828 ASN
A 832 HIS
A 914 GLN
A 926 ASN
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 GLN
B 167 HIS
B 168 HIS
B 224 HIS
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 763 GLN
B 782 GLN
B 803 HIS
B 828 ASN
B 832 HIS
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 914 GLN
B 926 ASN
** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN
C 167 HIS
C 168 HIS
C 224 HIS
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 763 GLN
C 782 GLN
C 803 HIS
C 828 ASN
C 832 HIS
C 914 GLN
C 926 ASN
** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN
D 167 HIS
D 168 HIS
D 224 HIS
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 763 GLN
D 782 GLN
D 803 HIS
D 828 ASN
D 832 HIS
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 914 GLN
D 926 ASN

Total number of N/Q/H flips: 45

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.100798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.066315 restraints weight = 92185.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.065711 restraints weight = 82765.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.065541 restraints weight = 77323.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.065594 restraints weight = 78768.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.065697 restraints weight = 75440.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  24572  Z= 0.231
  Angle     :  1.317  15.439  33448  Z= 0.670
  Chirality :  0.063   0.423   3812
  Planarity :  0.009   0.093   4340
  Dihedral  : 12.346  55.710   3456
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 30.47
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 23.36 %
    Favored  : 75.46 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.55 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.33 %
    Twisted Proline : 10.87 %
    Twisted General : 3.80 %

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: -5.03 (0.12), residues: 3228
  helix: -1.70 (0.14), residues: 1080
  sheet: -2.47 (0.34), residues: 160
  loop : -4.72 (0.11), residues: 1988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 920 
 TYR   0.031   0.003   TYR C 891 
 PHE   0.036   0.002   PHE A 654 
 TRP   0.025   0.003   TRP A 336 
 HIS   0.008   0.002   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (24572)
  covalent geometry    : angle       1.31712 (33448)
  hydrogen bonds       : bond        0.05296 (  764)
  hydrogen bonds       : angle       7.62184 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 288
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 MET cc_start: 0.7372 (mmm) cc_final: 0.7168 (mmm)
REVERT: A  608 TYR cc_start: 0.8751 (t80) cc_final: 0.8198 (t80)
REVERT: A  626 LEU cc_start: 0.9408 (mp) cc_final: 0.9101 (mp)
REVERT: A  799 TYR cc_start: 0.8015 (m-80) cc_final: 0.7244 (p90)
REVERT: A  820 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8780 (mp0)
REVERT: B  232 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7000 (tptt)
REVERT: B  741 ASN cc_start: 0.9601 (m-40) cc_final: 0.9008 (p0)
REVERT: B  799 TYR cc_start: 0.8105 (m-80) cc_final: 0.7057 (p90)
REVERT: C  232 LYS cc_start: 0.8131 (mmtt) cc_final: 0.6933 (tptt)
REVERT: C  741 ASN cc_start: 0.9598 (m-40) cc_final: 0.9010 (p0)
REVERT: C  799 TYR cc_start: 0.8124 (m-80) cc_final: 0.7087 (p90)
REVERT: D  232 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7035 (tptt)
REVERT: D  741 ASN cc_start: 0.9589 (m-40) cc_final: 0.8982 (p0)
REVERT: D  799 TYR cc_start: 0.8077 (m-80) cc_final: 0.7065 (p90)
  outliers start: 12
  outliers final: 4
  residues processed: 300
  average time/residue: 0.1879
  time to fit residues: 84.9306
Evaluate side-chains
  198 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 194
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 221 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 164 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 150 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 202 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 283 optimal weight:    9.9990
   chunk 298 optimal weight:    2.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 ASN
** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 877 ASN
A 914 GLN
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 621 ASN
** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 877 ASN
B 914 GLN
** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 914 GLN
** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 621 ASN
** D 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 914 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.094032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.063651 restraints weight = 94368.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.063419 restraints weight = 83868.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.063233 restraints weight = 79293.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.063206 restraints weight = 75852.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.063220 restraints weight = 72705.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  24572  Z= 0.323
  Angle     :  1.325  14.765  33448  Z= 0.683
  Chirality :  0.064   0.395   3812
  Planarity :  0.009   0.107   4340
  Dihedral  : 11.953  55.430   3456
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 38.99
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  : 25.46 %
    Favored  : 73.64 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.51 %
    Favored  : 92.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.29 %
    Twisted Proline : 8.70 %
    Twisted General : 3.41 %

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: -4.77 (0.13), residues: 3228
  helix: -1.31 (0.16), residues: 1064
  sheet: -2.17 (0.33), residues: 184
  loop : -4.68 (0.11), residues: 1980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 852 
 TYR   0.031   0.003   TYR A 138 
 PHE   0.035   0.003   PHE A 654 
 TRP   0.026   0.003   TRP A 336 
 HIS   0.008   0.002   HIS C 842 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 (24572)
  covalent geometry    : angle       1.32547 (33448)
  hydrogen bonds       : bond        0.05605 (  764)
  hydrogen bonds       : angle       7.53685 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 208
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  608 TYR cc_start: 0.8395 (t80) cc_final: 0.8192 (t80)
REVERT: A  648 MET cc_start: 0.7554 (mtt) cc_final: 0.6779 (tpp)
REVERT: A  727 LEU cc_start: 0.9561 (mt) cc_final: 0.9353 (mt)
REVERT: B  232 LYS cc_start: 0.8110 (mmtt) cc_final: 0.6828 (tptt)
REVERT: B  727 LEU cc_start: 0.9550 (mt) cc_final: 0.9344 (mt)
REVERT: C  232 LYS cc_start: 0.8109 (mmtt) cc_final: 0.6832 (tptt)
REVERT: C  648 MET cc_start: 0.7614 (mtt) cc_final: 0.6928 (mtt)
REVERT: C  727 LEU cc_start: 0.9518 (mt) cc_final: 0.9311 (mt)
REVERT: D  232 LYS cc_start: 0.8107 (mmtt) cc_final: 0.6845 (tptt)
REVERT: D  727 LEU cc_start: 0.9528 (mt) cc_final: 0.9317 (mt)
  outliers start: 4
  outliers final: 4
  residues processed: 212
  average time/residue: 0.1695
  time to fit residues: 56.9151
Evaluate side-chains
  161 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 31 optimal weight:    0.3980
   chunk 114 optimal weight:    2.9990
   chunk 206 optimal weight:    3.9990
   chunk 284 optimal weight:    6.9990
   chunk 148 optimal weight:    0.3980
   chunk 99 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 274 optimal weight:    0.4980
   chunk 197 optimal weight:    0.0570
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 287 GLN
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 GLN
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 745 GLN
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 851 GLN
C 287 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 745 GLN
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
D 287 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 745 GLN
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.112552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.085036 restraints weight = 160136.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.084335 restraints weight = 131603.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.084840 restraints weight = 103961.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.084946 restraints weight = 81569.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.086069 restraints weight = 69794.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.5086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  24572  Z= 0.209
  Angle     :  1.211  13.399  33448  Z= 0.615
  Chirality :  0.061   0.379   3812
  Planarity :  0.008   0.101   4340
  Dihedral  : 10.761  49.620   3456
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 28.17
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 21.81 %
    Favored  : 77.57 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.93 %
    Favored  : 93.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.39 %
    Twisted Proline : 6.52 %
    Twisted General : 2.95 %

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: -4.44 (0.13), residues: 3228
  helix: -0.59 (0.17), residues: 1044
  sheet: -2.17 (0.34), residues: 188
  loop : -4.72 (0.11), residues: 1996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 918 
 TYR   0.024   0.003   TYR D 891 
 PHE   0.024   0.002   PHE A 698 
 TRP   0.016   0.002   TRP B 760 
 HIS   0.007   0.001   HIS D 796 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (24572)
  covalent geometry    : angle       1.21072 (33448)
  hydrogen bonds       : bond        0.04210 (  764)
  hydrogen bonds       : angle       6.92034 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 253
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7424 (tptt)
REVERT: A  707 LEU cc_start: 0.9324 (tt) cc_final: 0.8899 (mp)
REVERT: B  204 MET cc_start: 0.2949 (tpt) cc_final: 0.2691 (tpt)
REVERT: B  232 LYS cc_start: 0.8452 (mmtt) cc_final: 0.7646 (tptt)
REVERT: B  294 ARG cc_start: 0.8687 (mmp80) cc_final: 0.8470 (mmp-170)
REVERT: B  707 LEU cc_start: 0.9345 (tt) cc_final: 0.8910 (mp)
REVERT: B  799 TYR cc_start: 0.7228 (m-80) cc_final: 0.6982 (p90)
REVERT: B  804 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6593 (pp)
REVERT: B  846 MET cc_start: 0.9036 (tpp) cc_final: 0.8819 (tpp)
REVERT: C  232 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7662 (tptt)
REVERT: C  294 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8457 (mmp-170)
REVERT: C  648 MET cc_start: 0.8284 (mtp) cc_final: 0.7511 (mtt)
REVERT: C  707 LEU cc_start: 0.9324 (tt) cc_final: 0.8783 (mp)
REVERT: C  799 TYR cc_start: 0.7270 (m-80) cc_final: 0.6994 (p90)
REVERT: D  204 MET cc_start: 0.2931 (tpt) cc_final: 0.2651 (tpt)
REVERT: D  232 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7660 (tptt)
REVERT: D  294 ARG cc_start: 0.8708 (mmp80) cc_final: 0.8495 (mmp-170)
REVERT: D  707 LEU cc_start: 0.9346 (tt) cc_final: 0.8910 (mp)
REVERT: D  799 TYR cc_start: 0.7281 (m-80) cc_final: 0.7000 (p90)
REVERT: D  804 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6571 (pp)
  outliers start: 5
  outliers final: 0
  residues processed: 258
  average time/residue: 0.1749
  time to fit residues: 69.4147
Evaluate side-chains
  189 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 288 optimal weight:    0.9980
   chunk 266 optimal weight:   20.0000
   chunk 59 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 92 optimal weight:   30.0000
   chunk 1 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 124 optimal weight:    9.9990
   chunk 316 optimal weight:    3.9990
   chunk 211 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 GLN
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 GLN
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 146 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.112049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.084805 restraints weight = 160160.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.084033 restraints weight = 154505.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.084344 restraints weight = 116300.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.084906 restraints weight = 89887.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.084912 restraints weight = 77173.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.5600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  24572  Z= 0.203
  Angle     :  1.175  13.052  33448  Z= 0.601
  Chirality :  0.059   0.348   3812
  Planarity :  0.008   0.107   4340
  Dihedral  : 10.145  52.199   3456
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 27.77
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 23.02 %
    Favored  : 76.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.46 %
    Twisted Proline : 6.52 %
    Twisted General : 2.20 %

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: -4.34 (0.14), residues: 3228
  helix: -0.53 (0.17), residues: 1068
  sheet: -2.70 (0.36), residues: 180
  loop : -4.61 (0.11), residues: 1980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 918 
 TYR   0.024   0.002   TYR C 138 
 PHE   0.032   0.002   PHE C 944 
 TRP   0.022   0.002   TRP A 866 
 HIS   0.007   0.001   HIS B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (24572)
  covalent geometry    : angle       1.17518 (33448)
  hydrogen bonds       : bond        0.04064 (  764)
  hydrogen bonds       : angle       6.58908 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7293 (tptt)
REVERT: A  294 ARG cc_start: 0.8764 (mmp80) cc_final: 0.8539 (mmp-170)
REVERT: A  707 LEU cc_start: 0.9333 (tt) cc_final: 0.8846 (mp)
REVERT: A  792 HIS cc_start: 0.8255 (t-90) cc_final: 0.8013 (t-90)
REVERT: B  232 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7481 (tptt)
REVERT: B  294 ARG cc_start: 0.8780 (mmp80) cc_final: 0.8577 (mmp-170)
REVERT: B  616 LEU cc_start: 0.8812 (pp) cc_final: 0.8477 (pp)
REVERT: B  648 MET cc_start: 0.7794 (mmt) cc_final: 0.7521 (mmt)
REVERT: B  707 LEU cc_start: 0.9374 (tt) cc_final: 0.8826 (mp)
REVERT: B  799 TYR cc_start: 0.7558 (m-80) cc_final: 0.7161 (p90)
REVERT: B  846 MET cc_start: 0.9141 (tpp) cc_final: 0.8924 (tpp)
REVERT: C  204 MET cc_start: 0.2629 (tpt) cc_final: 0.2349 (tpt)
REVERT: C  232 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7435 (tptt)
REVERT: C  616 LEU cc_start: 0.8667 (pp) cc_final: 0.8335 (pp)
REVERT: C  707 LEU cc_start: 0.9354 (tt) cc_final: 0.8711 (mp)
REVERT: C  799 TYR cc_start: 0.7569 (m-80) cc_final: 0.7170 (p90)
REVERT: C  846 MET cc_start: 0.9198 (tpp) cc_final: 0.8951 (tpp)
REVERT: D  204 MET cc_start: 0.3121 (tpt) cc_final: 0.2860 (tpt)
REVERT: D  232 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7369 (tptt)
REVERT: D  294 ARG cc_start: 0.8753 (mmp80) cc_final: 0.8549 (mmp-170)
REVERT: D  616 LEU cc_start: 0.8771 (pp) cc_final: 0.8473 (pp)
REVERT: D  707 LEU cc_start: 0.9336 (tt) cc_final: 0.8841 (mp)
REVERT: D  799 TYR cc_start: 0.7570 (m-80) cc_final: 0.7179 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1643
  time to fit residues: 60.7271
Evaluate side-chains
  184 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 125 optimal weight:    0.9980
   chunk 165 optimal weight:    0.9990
   chunk 185 optimal weight:   20.0000
   chunk 126 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 307 optimal weight:   10.0000
   chunk 151 optimal weight:    0.8980
   chunk 104 optimal weight:   20.0000
   chunk 202 optimal weight:    9.9990
   chunk 99 optimal weight:    0.3980
   chunk 303 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 752 GLN
A 763 GLN
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 869 ASN
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 752 GLN
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 869 ASN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 752 GLN
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
C 869 ASN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 752 GLN
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 869 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.113834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.085857 restraints weight = 159747.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.085989 restraints weight = 135909.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.086230 restraints weight = 110070.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.086375 restraints weight = 89724.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.086317 restraints weight = 86496.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.6136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  24572  Z= 0.197
  Angle     :  1.145  13.498  33448  Z= 0.583
  Chirality :  0.059   0.431   3812
  Planarity :  0.007   0.102   4340
  Dihedral  :  9.641  47.998   3456
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 26.31
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 22.00 %
    Favored  : 77.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.46 %
    Twisted Proline : 6.52 %
    Twisted General : 1.61 %

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: -4.32 (0.14), residues: 3228
  helix: -0.43 (0.17), residues: 1052
  sheet: -2.69 (0.33), residues: 220
  loop : -4.65 (0.11), residues: 1956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 249 
 TYR   0.024   0.002   TYR B 891 
 PHE   0.024   0.002   PHE A 654 
 TRP   0.019   0.002   TRP A 866 
 HIS   0.008   0.001   HIS D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (24572)
  covalent geometry    : angle       1.14461 (33448)
  hydrogen bonds       : bond        0.03911 (  764)
  hydrogen bonds       : angle       6.55317 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7484 (tptt)
REVERT: A  616 LEU cc_start: 0.8650 (pp) cc_final: 0.8195 (pp)
REVERT: A  707 LEU cc_start: 0.9319 (tt) cc_final: 0.8832 (mp)
REVERT: A  908 MET cc_start: 0.5294 (ttt) cc_final: 0.4762 (tpp)
REVERT: B  204 MET cc_start: 0.2854 (tpt) cc_final: 0.2575 (tpt)
REVERT: B  232 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7560 (tptt)
REVERT: B  616 LEU cc_start: 0.8536 (pp) cc_final: 0.8121 (pp)
REVERT: B  648 MET cc_start: 0.8080 (mmt) cc_final: 0.7878 (mmt)
REVERT: B  707 LEU cc_start: 0.9349 (tt) cc_final: 0.8853 (mp)
REVERT: B  782 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8621 (tp40)
REVERT: B  846 MET cc_start: 0.9106 (tpp) cc_final: 0.8885 (tpt)
REVERT: C  204 MET cc_start: 0.2781 (tpt) cc_final: 0.2522 (tpt)
REVERT: C  232 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7540 (tptt)
REVERT: C  616 LEU cc_start: 0.8608 (pp) cc_final: 0.8149 (pp)
REVERT: C  707 LEU cc_start: 0.9339 (tt) cc_final: 0.8719 (mp)
REVERT: C  782 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8640 (tp40)
REVERT: C  846 MET cc_start: 0.9085 (tpp) cc_final: 0.8864 (tpp)
REVERT: D  204 MET cc_start: 0.2820 (tpt) cc_final: 0.2590 (tpt)
REVERT: D  232 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7581 (tptt)
REVERT: D  616 LEU cc_start: 0.8517 (pp) cc_final: 0.8131 (pp)
REVERT: D  707 LEU cc_start: 0.9323 (tt) cc_final: 0.8838 (mp)
REVERT: D  782 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8597 (tp40)
REVERT: D  846 MET cc_start: 0.9092 (tpp) cc_final: 0.8818 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1629
  time to fit residues: 66.4819
Evaluate side-chains
  183 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 160 optimal weight:    2.9990
   chunk 102 optimal weight:   30.0000
   chunk 228 optimal weight:    5.9990
   chunk 177 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 273 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0270
   chunk 171 optimal weight:    8.9990
   chunk 151 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   chunk 314 optimal weight:    4.9990
   overall best weight:    1.9442

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 ASN
** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 851 GLN
C 287 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.104313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.071704 restraints weight = 86491.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.070550 restraints weight = 77840.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.070324 restraints weight = 87493.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.070289 restraints weight = 88680.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.070214 restraints weight = 85778.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.6418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  24572  Z= 0.207
  Angle     :  1.130  12.153  33448  Z= 0.579
  Chirality :  0.059   0.363   3812
  Planarity :  0.007   0.109   4340
  Dihedral  :  9.428  52.177   3456
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 29.72
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 23.20 %
    Favored  : 76.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.46 %
    Twisted Proline : 6.52 %
    Twisted General : 1.57 %

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: -4.17 (0.14), residues: 3228
  helix: -0.26 (0.17), residues: 1052
  sheet: -2.71 (0.36), residues: 180
  loop : -4.55 (0.11), residues: 1996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 920 
 TYR   0.020   0.002   TYR A 891 
 PHE   0.026   0.002   PHE A 654 
 TRP   0.021   0.002   TRP A 866 
 HIS   0.008   0.001   HIS C 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (24572)
  covalent geometry    : angle       1.13049 (33448)
  hydrogen bonds       : bond        0.03843 (  764)
  hydrogen bonds       : angle       6.40707 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LYS cc_start: 0.7794 (mmtt) cc_final: 0.6701 (tptt)
REVERT: A  294 ARG cc_start: 0.8331 (mmp80) cc_final: 0.8129 (mmp-170)
REVERT: A  616 LEU cc_start: 0.8696 (pp) cc_final: 0.8282 (pp)
REVERT: A  648 MET cc_start: 0.7944 (mtt) cc_final: 0.6303 (mtt)
REVERT: A  707 LEU cc_start: 0.9322 (tt) cc_final: 0.8849 (mp)
REVERT: A  908 MET cc_start: 0.5269 (ttt) cc_final: 0.4974 (tpp)
REVERT: B  204 MET cc_start: 0.3450 (tpt) cc_final: 0.3178 (tpt)
REVERT: B  232 LYS cc_start: 0.7887 (mmtt) cc_final: 0.6884 (tptt)
REVERT: B  616 LEU cc_start: 0.8553 (pp) cc_final: 0.8145 (pp)
REVERT: B  707 LEU cc_start: 0.9356 (tt) cc_final: 0.8831 (mp)
REVERT: B  846 MET cc_start: 0.9007 (tpp) cc_final: 0.8788 (tpt)
REVERT: B  908 MET cc_start: 0.8462 (mpp) cc_final: 0.8048 (tpp)
REVERT: C  204 MET cc_start: 0.3421 (tpt) cc_final: 0.3148 (tpt)
REVERT: C  232 LYS cc_start: 0.7932 (mmtt) cc_final: 0.6927 (tptt)
REVERT: C  616 LEU cc_start: 0.8644 (pp) cc_final: 0.8356 (pp)
REVERT: C  648 MET cc_start: 0.7720 (mtt) cc_final: 0.7469 (mtt)
REVERT: C  707 LEU cc_start: 0.9417 (tt) cc_final: 0.8756 (mp)
REVERT: C  727 LEU cc_start: 0.9514 (mt) cc_final: 0.9297 (mt)
REVERT: C  846 MET cc_start: 0.9008 (tpp) cc_final: 0.8750 (tpt)
REVERT: D  204 MET cc_start: 0.3601 (tpt) cc_final: 0.3327 (tpt)
REVERT: D  232 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7017 (tptt)
REVERT: D  616 LEU cc_start: 0.8556 (pp) cc_final: 0.8128 (pp)
REVERT: D  707 LEU cc_start: 0.9373 (tt) cc_final: 0.8854 (mp)
REVERT: D  846 MET cc_start: 0.9010 (tpp) cc_final: 0.8732 (tpt)
REVERT: D  908 MET cc_start: 0.8524 (mpp) cc_final: 0.8050 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1688
  time to fit residues: 66.0877
Evaluate side-chains
  185 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 126 optimal weight:    4.9990
   chunk 272 optimal weight:   20.0000
   chunk 303 optimal weight:    0.0980
   chunk 131 optimal weight:    6.9990
   chunk 285 optimal weight:    6.9990
   chunk 178 optimal weight:    5.9990
   chunk 108 optimal weight:   30.0000
   chunk 229 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 GLN
** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 GLN
B 310 GLN
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 851 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
D 186 GLN
D 287 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.111991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.083480 restraints weight = 161266.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.083158 restraints weight = 133091.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.083409 restraints weight = 106316.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.084285 restraints weight = 84149.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.084030 restraints weight = 66534.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.6557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  24572  Z= 0.215
  Angle     :  1.149  12.205  33448  Z= 0.586
  Chirality :  0.060   0.407   3812
  Planarity :  0.007   0.108   4340
  Dihedral  :  9.304  49.431   3456
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 30.06
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 23.79 %
    Favored  : 75.71 %
  Rotamer:
    Outliers :  0.04 %
    Allowed  :  2.13 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.59 %
    Twisted Proline : 6.52 %
    Twisted General : 1.51 %

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: -4.09 (0.14), residues: 3228
  helix: -0.05 (0.17), residues: 1020
  sheet: -2.98 (0.31), residues: 220
  loop : -4.50 (0.11), residues: 1988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 918 
 TYR   0.019   0.002   TYR C 138 
 PHE   0.024   0.002   PHE D 654 
 TRP   0.022   0.002   TRP B 760 
 HIS   0.008   0.001   HIS B 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (24572)
  covalent geometry    : angle       1.14937 (33448)
  hydrogen bonds       : bond        0.03791 (  764)
  hydrogen bonds       : angle       6.40969 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 MET cc_start: 0.0172 (ppp) cc_final: -0.0095 (ttp)
REVERT: A  616 LEU cc_start: 0.8619 (pp) cc_final: 0.8378 (pp)
REVERT: A  648 MET cc_start: 0.7686 (mtt) cc_final: 0.6245 (mtt)
REVERT: A  764 TYR cc_start: 0.8574 (m-10) cc_final: 0.8352 (m-10)
REVERT: B  204 MET cc_start: 0.2680 (tpt) cc_final: 0.2395 (tpt)
REVERT: B  232 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7827 (tptt)
REVERT: B  595 MET cc_start: 0.7276 (mmp) cc_final: 0.7040 (mmm)
REVERT: B  707 LEU cc_start: 0.9356 (tt) cc_final: 0.8856 (mp)
REVERT: C  204 MET cc_start: 0.2632 (tpt) cc_final: 0.2346 (tpt)
REVERT: C  232 LYS cc_start: 0.8558 (mmtt) cc_final: 0.7914 (tptt)
REVERT: C  294 ARG cc_start: 0.8843 (mmp80) cc_final: 0.8631 (mmp80)
REVERT: C  648 MET cc_start: 0.7407 (mtt) cc_final: 0.7166 (mtt)
REVERT: D  204 MET cc_start: 0.2649 (tpt) cc_final: 0.2354 (tpt)
REVERT: D  232 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7935 (tptt)
REVERT: D  616 LEU cc_start: 0.8567 (pp) cc_final: 0.8208 (pp)
REVERT: D  707 LEU cc_start: 0.9356 (tt) cc_final: 0.8866 (mp)
REVERT: D  782 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8471 (tp40)
REVERT: D  846 MET cc_start: 0.9049 (tpp) cc_final: 0.8740 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1663
  time to fit residues: 57.2125
Evaluate side-chains
  173 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 298 optimal weight:    5.9990
   chunk 0 optimal weight:   50.0000
   chunk 272 optimal weight:   10.0000
   chunk 274 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 287 optimal weight:    0.0470
   chunk 206 optimal weight:    5.9990
   chunk 256 optimal weight:   10.0000
   chunk 285 optimal weight:    6.9990
   chunk 308 optimal weight:    0.9990
   chunk 271 optimal weight:    5.9990
   overall best weight:    3.0086

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 GLN
** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 851 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.099746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.067580 restraints weight = 89974.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.066828 restraints weight = 80681.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.066430 restraints weight = 83084.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.066430 restraints weight = 82549.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.066430 restraints weight = 82549.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  24572  Z= 0.226
  Angle     :  1.149  12.334  33448  Z= 0.586
  Chirality :  0.060   0.346   3812
  Planarity :  0.007   0.106   4340
  Dihedral  :  9.278  47.938   3456
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 31.33
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 24.01 %
    Favored  : 75.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.59 %
    Twisted Proline : 5.98 %
    Twisted General : 1.28 %

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: -4.11 (0.14), residues: 3228
  helix: -0.11 (0.17), residues: 1044
  sheet: -2.60 (0.31), residues: 240
  loop : -4.60 (0.11), residues: 1944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 592 
 TYR   0.035   0.002   TYR A 660 
 PHE   0.024   0.002   PHE A 383 
 TRP   0.025   0.002   TRP A 866 
 HIS   0.011   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (24572)
  covalent geometry    : angle       1.14865 (33448)
  hydrogen bonds       : bond        0.03951 (  764)
  hydrogen bonds       : angle       6.40105 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  595 MET cc_start: 0.7933 (mmp) cc_final: 0.7552 (mmm)
REVERT: A  648 MET cc_start: 0.7851 (mtt) cc_final: 0.6454 (mtt)
REVERT: A  707 LEU cc_start: 0.9338 (tt) cc_final: 0.8915 (mp)
REVERT: B  204 MET cc_start: 0.3358 (tpt) cc_final: 0.3102 (tpt)
REVERT: B  232 LYS cc_start: 0.7938 (mmtt) cc_final: 0.6867 (tptt)
REVERT: B  294 ARG cc_start: 0.8539 (mmp80) cc_final: 0.8235 (mmp80)
REVERT: B  727 LEU cc_start: 0.9582 (mt) cc_final: 0.9370 (mt)
REVERT: B  852 ARG cc_start: 0.8950 (ttm170) cc_final: 0.8672 (ttm170)
REVERT: C  232 LYS cc_start: 0.7863 (mmtt) cc_final: 0.6776 (tptt)
REVERT: C  294 ARG cc_start: 0.8530 (mmp80) cc_final: 0.8228 (mmp80)
REVERT: C  307 MET cc_start: 0.3000 (ptm) cc_final: 0.2690 (ptm)
REVERT: C  595 MET cc_start: 0.7812 (mmp) cc_final: 0.7581 (mmm)
REVERT: C  648 MET cc_start: 0.7583 (mtt) cc_final: 0.7198 (mtt)
REVERT: C  707 LEU cc_start: 0.9366 (tt) cc_final: 0.8882 (mp)
REVERT: C  727 LEU cc_start: 0.9534 (mt) cc_final: 0.9299 (mt)
REVERT: C  852 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8681 (ttm170)
REVERT: D  232 LYS cc_start: 0.7840 (mmtt) cc_final: 0.6751 (tptt)
REVERT: D  307 MET cc_start: 0.2938 (ptm) cc_final: 0.2617 (ptm)
REVERT: D  727 LEU cc_start: 0.9534 (mt) cc_final: 0.9307 (mt)
REVERT: D  846 MET cc_start: 0.9052 (tpp) cc_final: 0.8659 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1649
  time to fit residues: 56.4346
Evaluate side-chains
  174 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 109 optimal weight:    0.1980
   chunk 266 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 221 optimal weight:    0.0270
   chunk 188 optimal weight:    9.9990
   chunk 258 optimal weight:   20.0000
   chunk 229 optimal weight:   10.0000
   chunk 264 optimal weight:    5.9990
   chunk 32 optimal weight:   40.0000
   overall best weight:    2.6444

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 851 GLN
** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.100175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.068376 restraints weight = 89107.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.067277 restraints weight = 80579.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.067011 restraints weight = 86625.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.067006 restraints weight = 88506.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.066912 restraints weight = 87614.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.6916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  24572  Z= 0.215
  Angle     :  1.152  13.527  33448  Z= 0.585
  Chirality :  0.060   0.395   3812
  Planarity :  0.007   0.101   4340
  Dihedral  :  9.146  47.385   3456
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 29.93
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 23.64 %
    Favored  : 75.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.46 %
    Twisted Proline : 5.98 %
    Twisted General : 1.51 %

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: -4.05 (0.14), residues: 3228
  helix:  0.08 (0.17), residues: 1044
  sheet: -2.67 (0.33), residues: 196
  loop : -4.61 (0.11), residues: 1988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 315 
 TYR   0.023   0.002   TYR A 660 
 PHE   0.025   0.002   PHE D 654 
 TRP   0.024   0.002   TRP C 599 
 HIS   0.012   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (24572)
  covalent geometry    : angle       1.15165 (33448)
  hydrogen bonds       : bond        0.03801 (  764)
  hydrogen bonds       : angle       6.39205 ( 2172)

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

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

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6456 Ramachandran restraints generated.
    3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 ARG cc_start: 0.8436 (mmp80) cc_final: 0.8231 (mmp-170)
REVERT: A  595 MET cc_start: 0.8161 (mmp) cc_final: 0.7717 (mmm)
REVERT: A  707 LEU cc_start: 0.9375 (tt) cc_final: 0.8938 (mp)
REVERT: B  204 MET cc_start: 0.3608 (tpt) cc_final: 0.3340 (tpt)
REVERT: B  232 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7400 (mmtt)
REVERT: B  307 MET cc_start: 0.3210 (ptm) cc_final: 0.2966 (ptm)
REVERT: B  707 LEU cc_start: 0.9324 (tt) cc_final: 0.8915 (mp)
REVERT: B  727 LEU cc_start: 0.9518 (mt) cc_final: 0.9308 (mt)
REVERT: B  846 MET cc_start: 0.8976 (tpp) cc_final: 0.8666 (tpp)
REVERT: B  852 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8690 (ttm170)
REVERT: C  204 MET cc_start: 0.3617 (tpt) cc_final: 0.3349 (tpt)
REVERT: C  232 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7482 (mmtt)
REVERT: C  294 ARG cc_start: 0.8392 (mmp80) cc_final: 0.8189 (mmp80)
REVERT: C  297 MET cc_start: 0.1264 (ptp) cc_final: 0.0933 (ptt)
REVERT: C  307 MET cc_start: 0.3096 (ptm) cc_final: 0.2769 (ptm)
REVERT: C  707 LEU cc_start: 0.9384 (tt) cc_final: 0.8925 (mp)
REVERT: C  727 LEU cc_start: 0.9530 (mt) cc_final: 0.9294 (mt)
REVERT: C  846 MET cc_start: 0.8988 (tpp) cc_final: 0.8661 (tpp)
REVERT: C  944 PHE cc_start: 0.7821 (p90) cc_final: 0.7126 (p90)
REVERT: D  232 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7431 (mmtt)
REVERT: D  297 MET cc_start: 0.1447 (ptp) cc_final: 0.1129 (ptt)
REVERT: D  307 MET cc_start: 0.3035 (ptm) cc_final: 0.2708 (ptm)
REVERT: D  616 LEU cc_start: 0.8395 (pp) cc_final: 0.7555 (pp)
REVERT: D  707 LEU cc_start: 0.9374 (tt) cc_final: 0.8937 (mp)
REVERT: D  727 LEU cc_start: 0.9540 (mt) cc_final: 0.9316 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1608
  time to fit residues: 55.8980
Evaluate side-chains
  179 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 324
   random chunks:
   chunk 282 optimal weight:    0.9990
   chunk 257 optimal weight:   40.0000
   chunk 291 optimal weight:    0.0040
   chunk 318 optimal weight:    2.9990
   chunk 311 optimal weight:    0.8980
   chunk 166 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 262 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 190 optimal weight:   20.0000
   overall best weight:    1.7798

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

Flipped N/Q/H residues before XYZ refinement:
** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 GLN
** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 763 GLN
** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 186 GLN
C 310 GLN
** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 851 GLN
D 310 GLN
** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.102937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.070149 restraints weight = 85277.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.069285 restraints weight = 84398.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.068892 restraints weight = 82013.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.068791 restraints weight = 86643.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.068790 restraints weight = 79978.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.7217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  24572  Z= 0.203
  Angle     :  1.137  13.134  33448  Z= 0.577
  Chirality :  0.060   0.434   3812
  Planarity :  0.007   0.098   4340
  Dihedral  :  8.949  46.909   3456
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 28.83
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 23.48 %
    Favored  : 76.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.03 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 4.55 %
    Twisted Proline : 4.35 %
    Twisted General : 1.21 %

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: -3.97 (0.14), residues: 3228
  helix:  0.41 (0.18), residues: 996
  sheet: -2.03 (0.37), residues: 196
  loop : -4.69 (0.10), residues: 2036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 592 
 TYR   0.025   0.002   TYR A 660 
 PHE   0.021   0.002   PHE A 944 
 TRP   0.024   0.002   TRP D 599 
 HIS   0.014   0.001   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (24572)
  covalent geometry    : angle       1.13688 (33448)
  hydrogen bonds       : bond        0.03702 (  764)
  hydrogen bonds       : angle       6.28611 ( 2172)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4614.45 seconds
wall clock time: 80 minutes 36.36 seconds (4836.36 seconds total)