Starting phenix.real_space_refine
on Wed Jul 30 17:56:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y60_33630/07_2025/7y60_33630.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1848 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     216      5.49       5
     S      20      5.16       5
     C    6418      2.51       5
     N    2172      2.21       5
     O    2552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11378
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "G"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 595
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 761
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 591
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "I"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2198
          Classifications: {'DNA': 108}
          Link IDs: {'rna3p': 107}
    Chain: "C"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 732
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "D"
      Number of atoms: 583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 583
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 602
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
    Chain: "J"
      Number of atoms: 2230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 2230
          Classifications: {'DNA': 108}
          Link IDs: {'rna3p': 107}
    Chain: "K"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 99
          Classifications: {'peptide': 20}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 18}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "L"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 1749
          Classifications: {'peptide': 354}
          Incomplete info: {'truncation_to_alanine': 309}
          Link IDs: {'PTRANS': 13, 'TRANS': 340}
          Chain breaks: 4
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 1113
          Unresolved non-hydrogen angles: 1439
          Unresolved non-hydrogen dihedrals: 949
          Unresolved non-hydrogen chiralities: 104
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 18, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 8, 'ASP:plan': 22, 'PHE:plan': 17, 'GLU:plan': 14, 'HIS:plan': 10}
          Unresolved non-hydrogen planarities: 600
  Time building chain proxies: 7.31, per 1000 atoms: 0.64
  Number of scatterers: 11378
  At special positions: 0
  Unit cell: (107, 116, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     216     15.00
     O    2552      8.00
     N    2172      7.00
     C    6418      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: 2.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1896

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      49.4% alpha, 15.4% beta
      97 base pairs and 169 stacking pairs defined.
    Time for finding SS restraints: 5.23
  Creating SS restraints...
    Processing helix  chain 'G' and resid 63 through 79
    Processing helix  chain 'G' and resid 85 through 114
      removed outlier: 3.786A  pdb=" N   ALA G 114 " --> pdb=" O   CYS G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.573A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
    Processing helix  chain 'H' and resid 30 through 42
    Processing helix  chain 'H' and resid 49 through 77
      removed outlier: 4.122A  pdb=" N   ARG H  55 " --> pdb=" O   TYR H  51 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN H  64 " --> pdb=" O   VAL H  60 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL H  65 " --> pdb=" O   PHE H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 94
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.820A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.325A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.735A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 57
      removed outlier: 3.787A  pdb=" N   SER C  57 " --> pdb=" O   ARG C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 77
      removed outlier: 3.736A  pdb=" N   ASP C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 131
      removed outlier: 3.502A  pdb=" N   ILE C 124 " --> pdb=" O   MET C 120 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG C 131 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 29
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.761A  pdb=" N   ARG D  55 " --> pdb=" O   TYR D  51 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLY D  56 " --> pdb=" O   GLU D  52 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL D  57 " --> pdb=" O   GLU D  53 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN D  64 " --> pdb=" O   VAL D  60 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   THR D  71 " --> pdb=" O   ARG D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.736A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.505A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 4.054A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.703A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 4.201A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 703 through 707
      removed outlier: 3.643A  pdb=" N   GLN K 706 " --> pdb=" O   VAL K 703 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.831A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84
      removed outlier: 6.917A  pdb=" N   ARG C  83 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 5
      removed outlier: 6.881A  pdb=" N   PHE L 360 " --> pdb=" O   TRP L 354 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   TRP L 354 " --> pdb=" O   PHE L 360 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA L 362 " --> pdb=" O   ILE L 352 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ILE L 352 " --> pdb=" O   ALA L 362 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER L 364 " --> pdb=" O   SER L 350 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 21
      removed outlier: 6.606A  pdb=" N   ALA L  35 " --> pdb=" O   TYR L  17 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LEU L  19 " --> pdb=" O   ALA L  33 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ALA L  33 " --> pdb=" O   LEU L  19 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   PHE L  21 " --> pdb=" O   ARG L  31 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ARG L  31 " --> pdb=" O   PHE L  21 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL L  41 " --> pdb=" O   ASN L  61 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   ASN L  61 " --> pdb=" O   VAL L  41 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE L  43 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74
      removed outlier: 6.226A  pdb=" N   ILE L  90 " --> pdb=" O   THR L 124 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   THR L 124 " --> pdb=" O   ILE L  90 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU L  92 " --> pdb=" O   VAL L 122 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137
      removed outlier: 6.220A  pdb=" N   ASP L 157 " --> pdb=" O   LYS L 163 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   LYS L 163 " --> pdb=" O   ASP L 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179
      removed outlier: 3.617A  pdb=" N   GLY L 176 " --> pdb=" O   LEU L 189 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU L 195 " --> pdb=" O   ASN L 208 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASN L 208 " --> pdb=" O   LEU L 195 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL L 197 " --> pdb=" O   ALA L 206 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG L 204 " --> pdb=" O   SER L 199 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 211 through 213
    Processing sheet with id=AB1, first strand: chain 'L' and resid 241 through 242
      removed outlier: 3.822A  pdb=" N   ALA L 253 " --> pdb=" O   THR L 265 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   THR L 265 " --> pdb=" O   ALA L 253 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   CYS L 255 " --> pdb=" O   MET L 263 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   MET L 263 " --> pdb=" O   CYS L 255 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA L 279 " --> pdb=" O   VAL L 268 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 288 through 299
      removed outlier: 5.542A  pdb=" N   VAL L 318 " --> pdb=" O   CYS L 294 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   VAL L 296 " --> pdb=" O   ARG L 316 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ARG L 316 " --> pdb=" O   VAL L 296 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   SER L 326 " --> pdb=" O   SER L 323 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      239 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      97 basepair parallelities
      169 stacking parallelities
  Total time for adding SS restraints: 4.89

  Time building geometry restraints manager: 3.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2326
        1.33 -     1.45: 3591
        1.45 -     1.58: 5584
        1.58 -     1.70: 430
        1.70 -     1.82: 32
  Bond restraints: 11963
  Sorted by residual:
  bond pdb=" C   ARG G  63 "
       pdb=" O   ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.234  1.210  0.025 1.20e-02 6.94e+03 4.27e+00
  bond pdb=" N   ARG G  63 "
       pdb=" CA  ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.479 -0.022 1.28e-02 6.10e+03 3.09e+00
  bond pdb=" CD  ARG G  63 "
       pdb=" NE  ARG G  63 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.40e-02 5.10e+03 2.87e+00
  bond pdb=" C   LEU G  65 "
       pdb=" O   LEU G  65 "
    ideal  model  delta    sigma   weight residual
    1.244  1.229  0.014 9.80e-03 1.04e+04 2.17e+00
  bond pdb=" C3'  DC I  79 "
       pdb=" O3'  DC I  79 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.05e+00
  ... (remaining 11958 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 16916
        2.30 -     4.59: 173
        4.59 -     6.89: 26
        6.89 -     9.18: 7
        9.18 -    11.48: 1
  Bond angle restraints: 17123
  Sorted by residual:
  angle pdb=" C   LEU G  65 "
        pdb=" N   PRO G  66 "
        pdb=" CA  PRO G  66 "
      ideal   model   delta    sigma   weight residual
     118.85  127.59   -8.74 1.09e+00 8.42e-01 6.44e+01
  angle pdb=" N   LYS G  64 "
        pdb=" CA  LYS G  64 "
        pdb=" C   LYS G  64 "
      ideal   model   delta    sigma   weight residual
     111.28  119.29   -8.01 1.09e+00 8.42e-01 5.40e+01
  angle pdb=" O3'  DC I  84 "
        pdb=" C3'  DC I  84 "
        pdb=" C2'  DC I  84 "
      ideal   model   delta    sigma   weight residual
     111.50  102.59    8.91 1.50e+00 4.44e-01 3.53e+01
  angle pdb=" CA  LEU G  65 "
        pdb=" C   LEU G  65 "
        pdb=" N   PRO G  66 "
      ideal   model   delta    sigma   weight residual
     120.93  116.13    4.80 1.06e+00 8.90e-01 2.05e+01
  angle pdb=" C   ARG G  63 "
        pdb=" CA  ARG G  63 "
        pdb=" CB  ARG G  63 "
      ideal   model   delta    sigma   weight residual
     109.90  116.83   -6.93 1.56e+00 4.11e-01 1.97e+01
  ... (remaining 17118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.09: 5462
       35.09 -    70.17: 1123
       70.17 -   105.26: 37
      105.26 -   140.34: 0
      140.34 -   175.43: 4
  Dihedral angle restraints: 6626
    sinusoidal: 3721
      harmonic: 2905
  Sorted by residual:
  dihedral pdb=" CA  PHE K 711 "
           pdb=" C   PHE K 711 "
           pdb=" N   LEU K 712 "
           pdb=" CA  LEU K 712 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.46   22.54     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" C4'  DC I  82 "
           pdb=" C3'  DC I  82 "
           pdb=" O3'  DC I  82 "
           pdb=" P    DG I  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.57  175.43     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC I  79 "
           pdb=" C3'  DC I  79 "
           pdb=" O3'  DC I  79 "
           pdb=" P    DC I  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.97 -173.97     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1657
       0.049 -    0.097: 294
       0.097 -    0.146: 66
       0.146 -    0.194: 3
       0.194 -    0.243: 1
  Chirality restraints: 2021
  Sorted by residual:
  chirality pdb=" CA  LYS G  64 "
            pdb=" N   LYS G  64 "
            pdb=" C   LYS G  64 "
            pdb=" CB  LYS G  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CG  LEU F  37 "
            pdb=" CB  LEU F  37 "
            pdb=" CD1 LEU F  37 "
            pdb=" CD2 LEU F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" C3'  DC I  84 "
            pdb=" C4'  DC I  84 "
            pdb=" O3'  DC I  84 "
            pdb=" C2'  DC I  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.38e-01
  ... (remaining 2018 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G  63 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ARG G  63 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG G  63 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G  64 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G  82 "   -0.008 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   LEU G  82 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU G  82 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG G  83 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU G  65 "   -0.028 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO G  66 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO G  66 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO G  66 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1111
        2.74 -     3.28: 10944
        3.28 -     3.82: 21860
        3.82 -     4.36: 23489
        4.36 -     4.90: 34819
  Nonbonded interactions: 92223
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  56 "
            pdb=" N2   DG J  92 "
     model   vdw
     2.200 2.496
  nonbonded pdb=" N2   DG I  37 "
            pdb=" O2   DC J 111 "
     model   vdw
     2.219 2.496
  nonbonded pdb=" O2   DC I  54 "
            pdb=" N2   DG J  94 "
     model   vdw
     2.231 2.496
  nonbonded pdb=" N2   DG I  67 "
            pdb=" O2   DC J  81 "
     model   vdw
     2.239 2.496
  nonbonded pdb=" OG1 THR E 118 "
            pdb=" NH1 ARG F  45 "
     model   vdw
     2.240 3.120
  ... (remaining 92218 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'B' and resid 26 through 97)
  selection = (chain 'D' and resid 26 through 97)
  selection = (chain 'F' and resid 26 through 97)
  selection = (chain 'H' and resid 26 through 97)
}

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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.240
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.060
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
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      :  0.004   0.043  11963  Z= 0.170
  Angle     :  0.674  11.477  17123  Z= 0.397
  Chirality :  0.040   0.243   2021
  Planarity :  0.004   0.048   1458
  Dihedral  : 28.445 175.426   4730
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 34.39 %
    Favored  : 64.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 974
  helix:  0.66 (0.24), residues: 461
  sheet:  0.40 (0.45), residues: 132
  loop : -1.04 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.009   0.003   HIS C 113 
 PHE   0.022   0.001   PHE G  84 
 TYR   0.019   0.001   TYR C  99 
 ARG   0.014   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14707 (  669)
  hydrogen bonds       : angle       5.61335 ( 1689)
  covalent geometry    : bond        0.00360 (11963)
  covalent geometry    : angle       0.67430 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 236
  time to evaluate  : 0.999 
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: E  109 LEU cc_start: 0.8749 (mt) cc_final: 0.8334 (mp)
REVERT: F   88 TYR cc_start: 0.7381 (m-80) cc_final: 0.6741 (m-80)
REVERT: D   68 ASP cc_start: 0.6511 (p0) cc_final: 0.5584 (p0)
REVERT: D   77 LYS cc_start: 0.7997 (tptp) cc_final: 0.7789 (tppt)
REVERT: A   90 MET cc_start: 0.8241 (mtm) cc_final: 0.7022 (mtm)
  outliers start: 7
  outliers final: 0
  residues processed: 239
  average time/residue: 0.3045
  time to fit residues: 96.0256
Evaluate side-chains
  152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:   40.0000
   chunk 87 optimal weight:   50.0000
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 59 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 105 optimal weight:   50.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.050002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.033409 restraints weight = 87233.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.034466 restraints weight = 48810.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.035148 restraints weight = 34326.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056  11963  Z= 0.374
  Angle     :  0.773   8.557  17123  Z= 0.441
  Chirality :  0.045   0.201   2021
  Planarity :  0.005   0.049   1458
  Dihedral  : 31.243 177.432   3422
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 25.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  8.55 %
    Allowed  : 29.74 %
    Favored  : 61.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 974
  helix:  0.74 (0.23), residues: 476
  sheet:  0.58 (0.45), residues: 131
  loop : -0.90 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.009   0.003   HIS G 113 
 PHE   0.027   0.002   PHE E  67 
 TYR   0.018   0.002   TYR C  99 
 ARG   0.008   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09569 (  669)
  hydrogen bonds       : angle       4.43274 ( 1689)
  covalent geometry    : bond        0.00810 (11963)
  covalent geometry    : angle       0.77304 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 173
  time to evaluate  : 0.936 
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: G   60 LEU cc_start: 0.8892 (pt) cc_final: 0.8632 (pt)
REVERT: G   62 ILE cc_start: 0.9667 (mp) cc_final: 0.9399 (pt)
REVERT: G   70 LEU cc_start: 0.9726 (tp) cc_final: 0.9183 (mt)
REVERT: G   73 GLU cc_start: 0.8068 (tt0) cc_final: 0.7790 (mt-10)
REVERT: G   90 MET cc_start: 0.8668 (tmm) cc_final: 0.8439 (tmm)
REVERT: H   26 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9476 (mm)
REVERT: H   63 GLU cc_start: 0.9084 (pp20) cc_final: 0.8779 (pp20)
REVERT: E   64 LYS cc_start: 0.9631 (mmmm) cc_final: 0.9427 (mmmm)
REVERT: F   31 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9431 (ttmm)
REVERT: F   63 GLU cc_start: 0.9117 (tp30) cc_final: 0.8457 (tp30)
REVERT: F   67 ARG cc_start: 0.8598 (ttm110) cc_final: 0.8082 (ttm110)
REVERT: F   84 MET cc_start: 0.9362 (tpp) cc_final: 0.8863 (tpp)
REVERT: F   88 TYR cc_start: 0.9440 (m-80) cc_final: 0.8811 (m-80)
REVERT: C   54 TYR cc_start: 0.9164 (m-80) cc_final: 0.8882 (m-80)
REVERT: C   80 THR cc_start: 0.9140 (m) cc_final: 0.8696 (m)
REVERT: C   94 GLU cc_start: 0.9384 (tp30) cc_final: 0.8316 (tp30)
REVERT: C  105 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9296 (mm-30)
REVERT: D   25 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8856 (p0)
REVERT: D   77 LYS cc_start: 0.9697 (tptp) cc_final: 0.9470 (tppt)
REVERT: D   84 MET cc_start: 0.9007 (tpp) cc_final: 0.8505 (tmm)
REVERT: A   90 MET cc_start: 0.8858 (mtm) cc_final: 0.8396 (mtm)
REVERT: A   94 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8743 (mm-30)
REVERT: A  120 MET cc_start: 0.8500 (mmt) cc_final: 0.8216 (mmt)
REVERT: A  128 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.8995 (mmm-85)
REVERT: A  133 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8400 (mm-30)
REVERT: B   53 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8754 (mm-30)
  outliers start: 46
  outliers final: 26
  residues processed: 209
  average time/residue: 0.2645
  time to fit residues: 75.5298
Evaluate side-chains
  175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   78 PHE
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  118 THR
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   26 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   31 LYS
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 110 optimal weight:   40.0000
   chunk 65 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 98 optimal weight:   20.0000
   chunk 115 optimal weight:   30.0000
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 91 optimal weight:   50.0000
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.050440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.034145 restraints weight = 87534.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.035250 restraints weight = 47510.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.035960 restraints weight = 32739.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11963  Z= 0.243
  Angle     :  0.696  11.484  17123  Z= 0.395
  Chirality :  0.041   0.171   2021
  Planarity :  0.004   0.042   1458
  Dihedral  : 31.339 176.896   3422
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 33.09 %
    Favored  : 60.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.26), residues: 974
  helix:  0.95 (0.23), residues: 475
  sheet:  0.45 (0.43), residues: 141
  loop : -0.77 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.002   HIS C 113 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.012   0.001   TYR H  88 
 ARG   0.008   0.001   ARG H  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06839 (  669)
  hydrogen bonds       : angle       4.02849 ( 1689)
  covalent geometry    : bond        0.00527 (11963)
  covalent geometry    : angle       0.69566 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.947 
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: G   73 GLU cc_start: 0.8303 (tt0) cc_final: 0.7480 (mt-10)
REVERT: G   84 PHE cc_start: 0.8763 (m-10) cc_final: 0.8496 (m-80)
REVERT: G   97 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8290 (pp20)
REVERT: E   64 LYS cc_start: 0.9639 (mmmm) cc_final: 0.9423 (mmmm)
REVERT: E   68 GLN cc_start: 0.9725 (tt0) cc_final: 0.9345 (tp-100)
REVERT: E  120 MET cc_start: 0.9331 (mmm) cc_final: 0.9053 (mmm)
REVERT: F   63 GLU cc_start: 0.9116 (tp30) cc_final: 0.8719 (tp30)
REVERT: F   84 MET cc_start: 0.9328 (tpp) cc_final: 0.8772 (tpp)
REVERT: F   88 TYR cc_start: 0.9430 (m-80) cc_final: 0.8848 (m-80)
REVERT: C   54 TYR cc_start: 0.9031 (m-80) cc_final: 0.8830 (m-80)
REVERT: C   94 GLU cc_start: 0.8874 (tp30) cc_final: 0.8460 (tp30)
REVERT: C  105 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9151 (mm-30)
REVERT: C  110 CYS cc_start: 0.9760 (m) cc_final: 0.9443 (m)
REVERT: D   25 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8214 (p0)
REVERT: D   63 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9113 (mm-30)
REVERT: D   77 LYS cc_start: 0.9697 (tptp) cc_final: 0.9470 (tppt)
REVERT: D   84 MET cc_start: 0.8969 (tpp) cc_final: 0.8369 (tmm)
REVERT: A   90 MET cc_start: 0.8910 (mtm) cc_final: 0.8417 (mtm)
REVERT: A   94 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8792 (mm-30)
REVERT: A   97 GLU cc_start: 0.9295 (tm-30) cc_final: 0.9016 (pp20)
REVERT: A  120 MET cc_start: 0.8680 (mmt) cc_final: 0.8271 (mmm)
REVERT: A  128 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.8305 (mmm-85)
REVERT: A  133 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8494 (mp0)
REVERT: B   53 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8620 (mm-30)
REVERT: B   64 ASN cc_start: 0.9749 (m110) cc_final: 0.9437 (p0)
  outliers start: 35
  outliers final: 20
  residues processed: 190
  average time/residue: 0.2545
  time to fit residues: 66.4040
Evaluate side-chains
  167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   64 LYS
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain H residue   79 LYS
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 113 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 81 optimal weight:   40.0000
   chunk 63 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
C  55 GLN
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 HIS
D  25 ASN
A  76 GLN
B  64 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.065188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.049858 restraints weight = 109655.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.051181 restraints weight = 53003.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.051973 restraints weight = 34249.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11963  Z= 0.157
  Angle     :  0.662  11.408  17123  Z= 0.374
  Chirality :  0.041   0.251   2021
  Planarity :  0.003   0.032   1458
  Dihedral  : 30.961 175.824   3422
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 34.20 %
    Favored  : 60.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.27), residues: 974
  helix:  1.04 (0.24), residues: 478
  sheet:  0.61 (0.43), residues: 145
  loop : -0.71 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.002   HIS C 113 
 PHE   0.010   0.001   PHE C 104 
 TYR   0.011   0.001   TYR B  72 
 ARG   0.009   0.001   ARG G  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06390 (  669)
  hydrogen bonds       : angle       3.65390 ( 1689)
  covalent geometry    : bond        0.00339 (11963)
  covalent geometry    : angle       0.66220 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.950 
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: G   70 LEU cc_start: 0.9656 (tp) cc_final: 0.9096 (mt)
REVERT: G   73 GLU cc_start: 0.7770 (tt0) cc_final: 0.7299 (mt-10)
REVERT: G   84 PHE cc_start: 0.8655 (m-10) cc_final: 0.7966 (m-80)
REVERT: G  129 ARG cc_start: 0.9436 (tpp80) cc_final: 0.9213 (ttp80)
REVERT: H   39 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8419 (mmm-85)
REVERT: H   44 LYS cc_start: 0.9081 (tptp) cc_final: 0.8812 (tppt)
REVERT: E   64 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9407 (mmmm)
REVERT: E   68 GLN cc_start: 0.9669 (tt0) cc_final: 0.9309 (tp40)
REVERT: E  105 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9068 (mm-30)
REVERT: F   74 GLU cc_start: 0.8586 (pp20) cc_final: 0.8322 (pp20)
REVERT: F   84 MET cc_start: 0.9139 (tpp) cc_final: 0.8459 (tpp)
REVERT: F   88 TYR cc_start: 0.9369 (m-80) cc_final: 0.8700 (m-80)
REVERT: C   94 GLU cc_start: 0.8812 (tp30) cc_final: 0.8249 (tp30)
REVERT: C   97 GLU cc_start: 0.8134 (pp20) cc_final: 0.7848 (pp20)
REVERT: C  110 CYS cc_start: 0.9700 (m) cc_final: 0.9484 (m)
REVERT: D   25 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (p0)
REVERT: D   63 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9014 (mm-30)
REVERT: D   77 LYS cc_start: 0.9681 (tptp) cc_final: 0.9476 (tppt)
REVERT: D   84 MET cc_start: 0.8858 (tpp) cc_final: 0.8441 (tmm)
REVERT: D   85 ASP cc_start: 0.8827 (m-30) cc_final: 0.8541 (t0)
REVERT: D   91 LYS cc_start: 0.9285 (tttp) cc_final: 0.8947 (mmtm)
REVERT: A   90 MET cc_start: 0.9033 (mtm) cc_final: 0.8700 (mtt)
REVERT: A   94 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8645 (mm-30)
REVERT: A   97 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8980 (pp20)
REVERT: A  120 MET cc_start: 0.8632 (mmt) cc_final: 0.8166 (mmm)
REVERT: A  128 ARG cc_start: 0.9330 (mmm-85) cc_final: 0.8748 (mmm-85)
REVERT: B   52 GLU cc_start: 0.9303 (pm20) cc_final: 0.9036 (pm20)
REVERT: B   53 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8843 (mm-30)
REVERT: B   55 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8469 (mmm-85)
  outliers start: 28
  outliers final: 12
  residues processed: 188
  average time/residue: 0.2626
  time to fit residues: 66.9534
Evaluate side-chains
  167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:   30.0000
   chunk 105 optimal weight:   40.0000
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 87 optimal weight:   50.0000
   chunk 68 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0770
   overall best weight:    4.2146

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN
A  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.059623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.044813 restraints weight = 110564.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.046015 restraints weight = 54879.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.046734 restraints weight = 35767.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  11963  Z= 0.267
  Angle     :  0.706  13.249  17123  Z= 0.398
  Chirality :  0.042   0.256   2021
  Planarity :  0.004   0.027   1458
  Dihedral  : 31.330 178.844   3422
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 21.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 35.13 %
    Favored  : 58.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.27), residues: 974
  helix:  1.07 (0.24), residues: 475
  sheet:  0.77 (0.44), residues: 141
  loop : -0.56 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.011   0.002   PHE E  67 
 TYR   0.011   0.001   TYR H  88 
 ARG   0.007   0.001   ARG G  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07285 (  669)
  hydrogen bonds       : angle       3.94343 ( 1689)
  covalent geometry    : bond        0.00583 (11963)
  covalent geometry    : angle       0.70649 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 153
  time to evaluate  : 0.910 
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: G   70 LEU cc_start: 0.9667 (tp) cc_final: 0.9069 (mt)
REVERT: G   73 GLU cc_start: 0.7897 (tt0) cc_final: 0.7274 (mt-10)
REVERT: H   39 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8579 (mmm-85)
REVERT: H   67 ARG cc_start: 0.9194 (ttm110) cc_final: 0.8974 (ttm110)
REVERT: E   64 LYS cc_start: 0.9626 (mmmm) cc_final: 0.9418 (mmmm)
REVERT: F   63 GLU cc_start: 0.8832 (tp30) cc_final: 0.8504 (tp30)
REVERT: F   74 GLU cc_start: 0.8723 (pp20) cc_final: 0.8494 (pp20)
REVERT: F   84 MET cc_start: 0.9237 (tpp) cc_final: 0.8664 (tpp)
REVERT: F   88 TYR cc_start: 0.9430 (m-80) cc_final: 0.8908 (m-80)
REVERT: C   54 TYR cc_start: 0.8886 (m-80) cc_final: 0.8676 (m-80)
REVERT: C   94 GLU cc_start: 0.8991 (tp30) cc_final: 0.8401 (tp30)
REVERT: C   97 GLU cc_start: 0.8233 (pp20) cc_final: 0.7976 (pp20)
REVERT: C  105 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9129 (mm-30)
REVERT: D   25 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8664 (p0)
REVERT: D   26 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9434 (tp)
REVERT: D   63 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9057 (mm-30)
REVERT: D   84 MET cc_start: 0.8925 (tpp) cc_final: 0.8318 (tmm)
REVERT: A   78 PHE cc_start: 0.9371 (t80) cc_final: 0.9137 (t80)
REVERT: A   90 MET cc_start: 0.9089 (mtm) cc_final: 0.8419 (mtm)
REVERT: A   94 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8650 (mm-30)
REVERT: A  120 MET cc_start: 0.8782 (mmt) cc_final: 0.8264 (mmm)
REVERT: A  128 ARG cc_start: 0.9421 (mmm-85) cc_final: 0.9115 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9668 (tp30) cc_final: 0.9361 (tm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 178
  average time/residue: 0.2589
  time to fit residues: 63.1384
Evaluate side-chains
  168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  119 ILE
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 28 optimal weight:    0.2980
   chunk 95 optimal weight:   50.0000
   chunk 112 optimal weight:    0.0670
   chunk 90 optimal weight:   50.0000
   chunk 68 optimal weight:    7.9990
   chunk 58 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    2.4724

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.062198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.046727 restraints weight = 112696.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.048008 restraints weight = 54987.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.048775 restraints weight = 35694.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11963  Z= 0.193
  Angle     :  0.677  12.440  17123  Z= 0.382
  Chirality :  0.040   0.203   2021
  Planarity :  0.004   0.033   1458
  Dihedral  : 31.273 176.704   3422
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 34.39 %
    Favored  : 59.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 974
  helix:  1.11 (0.24), residues: 478
  sheet:  0.71 (0.44), residues: 144
  loop : -0.62 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.027   0.001   TYR E  54 
 ARG   0.005   0.000   ARG H  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06295 (  669)
  hydrogen bonds       : angle       3.78570 ( 1689)
  covalent geometry    : bond        0.00424 (11963)
  covalent geometry    : angle       0.67714 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 0.950 
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: G   70 LEU cc_start: 0.9643 (tp) cc_final: 0.9071 (mt)
REVERT: G   73 GLU cc_start: 0.7747 (tt0) cc_final: 0.7155 (mt-10)
REVERT: G   82 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7912 (mm)
REVERT: G   84 PHE cc_start: 0.8787 (m-10) cc_final: 0.8569 (m-10)
REVERT: G   97 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8447 (pp20)
REVERT: G  120 MET cc_start: 0.9096 (mmt) cc_final: 0.8850 (mmm)
REVERT: H   39 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8572 (mmm-85)
REVERT: H   67 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8921 (ttm110)
REVERT: E   64 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9330 (mmmm)
REVERT: F   63 GLU cc_start: 0.8858 (tp30) cc_final: 0.8472 (tp30)
REVERT: F   74 GLU cc_start: 0.8696 (pp20) cc_final: 0.8429 (pp20)
REVERT: F   84 MET cc_start: 0.9193 (tpp) cc_final: 0.8547 (tpp)
REVERT: F   88 TYR cc_start: 0.9409 (m-80) cc_final: 0.8884 (m-80)
REVERT: C   94 GLU cc_start: 0.8980 (tp30) cc_final: 0.8286 (tp30)
REVERT: C   97 GLU cc_start: 0.8166 (pp20) cc_final: 0.7881 (pp20)
REVERT: C  105 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9223 (mm-30)
REVERT: C  110 CYS cc_start: 0.9706 (m) cc_final: 0.9405 (m)
REVERT: D   25 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8207 (p0)
REVERT: D   26 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9357 (tp)
REVERT: D   63 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9019 (mm-30)
REVERT: D   84 MET cc_start: 0.8894 (tpp) cc_final: 0.8432 (tmm)
REVERT: D   85 ASP cc_start: 0.8824 (m-30) cc_final: 0.8545 (t0)
REVERT: A   78 PHE cc_start: 0.9372 (t80) cc_final: 0.9094 (t80)
REVERT: A   90 MET cc_start: 0.9123 (mtm) cc_final: 0.8730 (mmm)
REVERT: A   94 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8614 (mm-30)
REVERT: A   97 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8978 (pp20)
REVERT: A  120 MET cc_start: 0.8666 (mmt) cc_final: 0.8198 (mmm)
REVERT: B   55 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8670 (mmm-85)
REVERT: B   63 GLU cc_start: 0.9610 (tp30) cc_final: 0.9286 (tm-30)
  outliers start: 33
  outliers final: 19
  residues processed: 180
  average time/residue: 0.2595
  time to fit residues: 64.4983
Evaluate side-chains
  169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   78 PHE
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue   96 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 103 optimal weight:   50.0000
   chunk 23 optimal weight:    0.6980
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.063334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.047980 restraints weight = 112060.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.049263 restraints weight = 54639.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.050091 restraints weight = 35350.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11963  Z= 0.163
  Angle     :  0.671  12.482  17123  Z= 0.376
  Chirality :  0.041   0.242   2021
  Planarity :  0.003   0.035   1458
  Dihedral  : 31.121 177.554   3422
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 36.43 %
    Favored  : 58.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 974
  helix:  1.11 (0.24), residues: 480
  sheet:  0.79 (0.44), residues: 148
  loop : -0.55 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.013   0.001   TYR C  54 
 ARG   0.008   0.001   ARG D  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06096 (  669)
  hydrogen bonds       : angle       3.66293 ( 1689)
  covalent geometry    : bond        0.00358 (11963)
  covalent geometry    : angle       0.67086 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 GLU cc_start: 0.7684 (tt0) cc_final: 0.7063 (mt-10)
REVERT: G   84 PHE cc_start: 0.8653 (m-10) cc_final: 0.8397 (m-10)
REVERT: G   97 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8460 (pp20)
REVERT: G  120 MET cc_start: 0.9129 (mmt) cc_final: 0.8868 (mmm)
REVERT: G  126 LEU cc_start: 0.9673 (tt) cc_final: 0.9373 (pp)
REVERT: G  129 ARG cc_start: 0.9448 (tpp80) cc_final: 0.9247 (ttp80)
REVERT: H   39 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8520 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9242 (mmmm)
REVERT: E  105 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8933 (mm-30)
REVERT: F   63 GLU cc_start: 0.8876 (tp30) cc_final: 0.8491 (tp30)
REVERT: F   74 GLU cc_start: 0.8672 (pp20) cc_final: 0.8398 (pp20)
REVERT: F   84 MET cc_start: 0.9164 (tpp) cc_final: 0.8467 (tpp)
REVERT: F   88 TYR cc_start: 0.9400 (m-80) cc_final: 0.8825 (m-80)
REVERT: C   94 GLU cc_start: 0.8996 (tp30) cc_final: 0.8175 (tp30)
REVERT: C   97 GLU cc_start: 0.8218 (pp20) cc_final: 0.7911 (pp20)
REVERT: C  105 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9181 (mm-30)
REVERT: C  110 CYS cc_start: 0.9694 (m) cc_final: 0.9461 (m)
REVERT: D   25 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8349 (p0)
REVERT: D   26 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9317 (tp)
REVERT: D   52 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8806 (pp20)
REVERT: D   63 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9031 (mm-30)
REVERT: D   84 MET cc_start: 0.8876 (tpp) cc_final: 0.8430 (tmm)
REVERT: D   85 ASP cc_start: 0.8795 (m-30) cc_final: 0.8580 (t0)
REVERT: D   91 LYS cc_start: 0.9224 (tttp) cc_final: 0.8913 (mmtp)
REVERT: A   78 PHE cc_start: 0.9354 (t80) cc_final: 0.9050 (t80)
REVERT: A   90 MET cc_start: 0.9121 (mtm) cc_final: 0.8689 (mmm)
REVERT: A   94 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8566 (mm-30)
REVERT: A   97 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8991 (pp20)
REVERT: A  120 MET cc_start: 0.8709 (mmt) cc_final: 0.8094 (mmt)
REVERT: A  129 ARG cc_start: 0.9784 (ptm160) cc_final: 0.9541 (ptm-80)
REVERT: B   52 GLU cc_start: 0.9336 (pm20) cc_final: 0.8799 (pm20)
REVERT: B   53 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8919 (mm-30)
REVERT: B   55 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8691 (mmm-85)
REVERT: B   64 ASN cc_start: 0.9713 (m-40) cc_final: 0.9407 (p0)
  outliers start: 27
  outliers final: 16
  residues processed: 174
  average time/residue: 0.2695
  time to fit residues: 65.6888
Evaluate side-chains
  165 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   75 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:   50.0000
   chunk 112 optimal weight:   50.0000
   chunk 64 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 107 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.063024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.047642 restraints weight = 111743.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.048929 restraints weight = 54781.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.049714 restraints weight = 35672.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11963  Z= 0.174
  Angle     :  0.687  13.189  17123  Z= 0.381
  Chirality :  0.040   0.244   2021
  Planarity :  0.004   0.034   1458
  Dihedral  : 31.138 178.496   3422
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 37.36 %
    Favored  : 57.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 974
  helix:  1.05 (0.24), residues: 477
  sheet:  0.78 (0.44), residues: 144
  loop : -0.50 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E 104 
 TYR   0.010   0.001   TYR E  54 
 ARG   0.008   0.000   ARG D  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06116 (  669)
  hydrogen bonds       : angle       3.68054 ( 1689)
  covalent geometry    : bond        0.00385 (11963)
  covalent geometry    : angle       0.68673 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9665 (tp) cc_final: 0.9126 (mt)
REVERT: G   73 GLU cc_start: 0.7698 (tt0) cc_final: 0.7075 (mt-10)
REVERT: G   84 PHE cc_start: 0.8677 (m-10) cc_final: 0.7921 (m-80)
REVERT: G   97 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8424 (pp20)
REVERT: G  120 MET cc_start: 0.9181 (mmt) cc_final: 0.8926 (mmm)
REVERT: H   39 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8513 (mmm-85)
REVERT: E   64 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9250 (mmmm)
REVERT: E  105 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8931 (mm-30)
REVERT: F   63 GLU cc_start: 0.8870 (tp30) cc_final: 0.8453 (tp30)
REVERT: F   74 GLU cc_start: 0.8687 (pp20) cc_final: 0.8412 (pp20)
REVERT: F   84 MET cc_start: 0.9154 (tpp) cc_final: 0.8492 (tpp)
REVERT: F   88 TYR cc_start: 0.9430 (m-80) cc_final: 0.8937 (m-80)
REVERT: C   94 GLU cc_start: 0.9015 (tp30) cc_final: 0.8192 (tp30)
REVERT: C   97 GLU cc_start: 0.8246 (pp20) cc_final: 0.7933 (pp20)
REVERT: C  105 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9148 (mm-30)
REVERT: C  110 CYS cc_start: 0.9676 (m) cc_final: 0.9454 (m)
REVERT: D   25 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8245 (p0)
REVERT: D   26 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9344 (tp)
REVERT: D   52 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8839 (pp20)
REVERT: D   63 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: D   84 MET cc_start: 0.8848 (tpp) cc_final: 0.8404 (tmm)
REVERT: D   85 ASP cc_start: 0.8769 (m-30) cc_final: 0.8534 (t0)
REVERT: A   78 PHE cc_start: 0.9356 (t80) cc_final: 0.9053 (t80)
REVERT: A   90 MET cc_start: 0.9111 (mtm) cc_final: 0.8698 (mmm)
REVERT: A   94 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8552 (mm-30)
REVERT: A   97 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8995 (pp20)
REVERT: A  100 LEU cc_start: 0.9779 (tp) cc_final: 0.9495 (tt)
REVERT: A  118 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8543 (p)
REVERT: A  120 MET cc_start: 0.8728 (mmt) cc_final: 0.8160 (mmt)
REVERT: A  129 ARG cc_start: 0.9781 (ptm160) cc_final: 0.9513 (ptm-80)
REVERT: B   53 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8945 (mm-30)
REVERT: B   55 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8703 (mmm-85)
  outliers start: 25
  outliers final: 18
  residues processed: 165
  average time/residue: 0.2612
  time to fit residues: 59.1313
Evaluate side-chains
  163 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   96 CYS
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.064074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.048838 restraints weight = 109986.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.050144 restraints weight = 54116.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.050939 restraints weight = 35091.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11963  Z= 0.158
  Angle     :  0.690  13.248  17123  Z= 0.379
  Chirality :  0.041   0.475   2021
  Planarity :  0.004   0.042   1458
  Dihedral  : 31.018 178.499   3422
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 38.10 %
    Favored  : 57.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.27), residues: 974
  helix:  1.10 (0.24), residues: 477
  sheet:  0.85 (0.44), residues: 148
  loop : -0.51 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.015   0.001   PHE A  67 
 TYR   0.009   0.001   TYR F  72 
 ARG   0.007   0.001   ARG D  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06088 (  669)
  hydrogen bonds       : angle       3.65540 ( 1689)
  covalent geometry    : bond        0.00349 (11963)
  covalent geometry    : angle       0.68986 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9639 (tp) cc_final: 0.9085 (mt)
REVERT: G   73 GLU cc_start: 0.7695 (tt0) cc_final: 0.7051 (mt-10)
REVERT: G   84 PHE cc_start: 0.8638 (m-10) cc_final: 0.7832 (m-80)
REVERT: G  120 MET cc_start: 0.9164 (mmt) cc_final: 0.8774 (mpp)
REVERT: H   39 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8505 (mmm-85)
REVERT: H   59 LYS cc_start: 0.9632 (tppt) cc_final: 0.9425 (mmtt)
REVERT: H   67 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8858 (mpt90)
REVERT: E   64 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9290 (mmmm)
REVERT: E   93 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.9336 (tm-30)
REVERT: E  105 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8882 (mm-30)
REVERT: F   63 GLU cc_start: 0.8901 (tp30) cc_final: 0.8491 (tp30)
REVERT: F   74 GLU cc_start: 0.8606 (pp20) cc_final: 0.8327 (pp20)
REVERT: F   84 MET cc_start: 0.9121 (tpp) cc_final: 0.8391 (tpp)
REVERT: F   88 TYR cc_start: 0.9416 (m-80) cc_final: 0.8966 (m-80)
REVERT: C   94 GLU cc_start: 0.8999 (tp30) cc_final: 0.8204 (tp30)
REVERT: C   97 GLU cc_start: 0.8210 (pp20) cc_final: 0.7893 (pp20)
REVERT: D   25 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8265 (p0)
REVERT: D   26 ILE cc_start: 0.9626 (OUTLIER) cc_final: 0.9268 (tp)
REVERT: D   52 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8811 (pp20)
REVERT: D   63 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9030 (mm-30)
REVERT: D   84 MET cc_start: 0.8767 (tpp) cc_final: 0.8359 (tmm)
REVERT: A   78 PHE cc_start: 0.9343 (t80) cc_final: 0.9034 (t80)
REVERT: A   90 MET cc_start: 0.9089 (mtm) cc_final: 0.8702 (mmm)
REVERT: A   94 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8520 (mm-30)
REVERT: A   97 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8944 (pp20)
REVERT: A  118 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.8558 (p)
REVERT: A  120 MET cc_start: 0.8690 (mmt) cc_final: 0.8121 (mmt)
REVERT: B   53 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8934 (mm-30)
REVERT: B   55 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8556 (mmm-85)
  outliers start: 23
  outliers final: 17
  residues processed: 170
  average time/residue: 0.2644
  time to fit residues: 61.3972
Evaluate side-chains
  166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  117 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   25 ASN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   chunk 97 optimal weight:   50.0000
   chunk 68 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   chunk 15 optimal weight:    0.5980
   chunk 71 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.064587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.049424 restraints weight = 109553.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.050756 restraints weight = 54315.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.051559 restraints weight = 35190.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.5121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11963  Z= 0.158
  Angle     :  0.710  13.790  17123  Z= 0.388
  Chirality :  0.041   0.433   2021
  Planarity :  0.004   0.051   1458
  Dihedral  : 30.967 179.155   3422
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 38.29 %
    Favored  : 57.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 974
  helix:  1.03 (0.24), residues: 482
  sheet:  0.89 (0.43), residues: 148
  loop : -0.42 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.042   0.002   PHE A  67 
 TYR   0.009   0.001   TYR E  54 
 ARG   0.011   0.001   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06175 (  669)
  hydrogen bonds       : angle       3.61824 ( 1689)
  covalent geometry    : bond        0.00350 (11963)
  covalent geometry    : angle       0.70997 (17123)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   70 LEU cc_start: 0.9632 (tp) cc_final: 0.9095 (mt)
REVERT: G   73 GLU cc_start: 0.7622 (tt0) cc_final: 0.6984 (mt-10)
REVERT: G   84 PHE cc_start: 0.8614 (m-10) cc_final: 0.7814 (m-80)
REVERT: G  120 MET cc_start: 0.9168 (mmt) cc_final: 0.8799 (mpp)
REVERT: H   39 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8529 (mmm-85)
REVERT: H   67 ARG cc_start: 0.9328 (ttm110) cc_final: 0.8824 (mpt90)
REVERT: E   64 LYS cc_start: 0.9595 (mmmm) cc_final: 0.9295 (mmmm)
REVERT: E   93 GLN cc_start: 0.9550 (OUTLIER) cc_final: 0.9341 (tm-30)
REVERT: E  105 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8904 (mm-30)
REVERT: F   63 GLU cc_start: 0.8888 (tp30) cc_final: 0.8474 (tp30)
REVERT: F   74 GLU cc_start: 0.8586 (pp20) cc_final: 0.8299 (pp20)
REVERT: F   84 MET cc_start: 0.9107 (tpp) cc_final: 0.8351 (tpp)
REVERT: F   88 TYR cc_start: 0.9416 (m-80) cc_final: 0.8955 (m-80)
REVERT: C   94 GLU cc_start: 0.9018 (tp30) cc_final: 0.8203 (tp30)
REVERT: C   97 GLU cc_start: 0.8186 (pp20) cc_final: 0.7860 (pp20)
REVERT: C  105 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9121 (mm-30)
REVERT: D   26 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9184 (tp)
REVERT: D   52 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8853 (pp20)
REVERT: D   63 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9069 (mm-30)
REVERT: D   84 MET cc_start: 0.8718 (tpp) cc_final: 0.8436 (tmm)
REVERT: D   91 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8534 (mmtm)
REVERT: A   78 PHE cc_start: 0.9361 (t80) cc_final: 0.9061 (t80)
REVERT: A   90 MET cc_start: 0.9095 (mtm) cc_final: 0.8720 (mmm)
REVERT: A   94 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8476 (mm-30)
REVERT: A   97 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8926 (pp20)
REVERT: A  118 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8570 (p)
REVERT: A  120 MET cc_start: 0.8694 (mmt) cc_final: 0.8196 (mmt)
REVERT: B   55 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8520 (mmt180)
  outliers start: 22
  outliers final: 15
  residues processed: 164
  average time/residue: 0.2725
  time to fit residues: 60.8229
Evaluate side-chains
  161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue  104 PHE
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain C residue  125 GLN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   88 TYR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   55 ARG
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   95 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 95 optimal weight:   50.0000
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 102 optimal weight:   20.0000
   chunk 106 optimal weight:    0.0980
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    1.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.051713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.035788 restraints weight = 84830.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.036894 restraints weight = 46745.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.037659 restraints weight = 31944.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.5255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11963  Z= 0.181
  Angle     :  0.727  13.575  17123  Z= 0.398
  Chirality :  0.041   0.426   2021
  Planarity :  0.004   0.063   1458
  Dihedral  : 31.056 179.341   3422
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 37.17 %
    Favored  : 57.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 974
  helix:  1.07 (0.24), residues: 479
  sheet:  0.81 (0.43), residues: 146
  loop : -0.34 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP K 690 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.051   0.002   PHE A  67 
 TYR   0.010   0.001   TYR C  99 
 ARG   0.014   0.001   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06199 (  669)
  hydrogen bonds       : angle       3.75550 ( 1689)
  covalent geometry    : bond        0.00405 (11963)
  covalent geometry    : angle       0.72656 (17123)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4499.27 seconds
wall clock time: 77 minutes 49.31 seconds (4669.31 seconds total)