Starting phenix.real_space_refine
on Fri Feb  6 05:45:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yfm_72898/02_2026/9yfm_72898.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      96      5.49       5
     S      54      5.16       5
     C    7184      2.51       5
     N    2089      2.21       5
     O    2404      1.98       5
     H   11093      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22920
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 1475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1475
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 6, 'TRANS': 84}
    Chain: "C"
      Number of atoms: 1992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1992
          Classifications: {'peptide': 123}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 115}
    Chain: "E"
      Number of atoms: 1544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1544
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 7, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 1030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 1030
          Classifications: {'peptide': 61}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 55}
    Chain: "G"
      Number of atoms: 2057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2057
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 119}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1001
          Classifications: {'peptide': 59}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
    Chain: "A"
      Number of atoms: 5421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5421
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 14, 'TRANS': 323}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 5305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 5305
          Classifications: {'peptide': 331}
          Link IDs: {'PTRANS': 13, 'TRANS': 317}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 3095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 3095
          Classifications: {'RNA': 96}
          Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 40, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 15, 'rna3p': 80}
          Chain breaks: 6
  Time building chain proxies: 4.31, per 1000 atoms: 0.19
  Number of scatterers: 22920
  At special positions: 0
  Unit cell: (94.392, 115.92, 158.148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P      96     15.00
     O    2404      8.00
     N    2089      7.00
     C    7184      6.00
     H   11093      1.00
    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: 1.96
  Conformation dependent library (CDL) restraints added in 761.0 milliseconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 12 sheets defined
      34.9% alpha, 17.4% beta
      31 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 4.70
  Creating SS restraints...
    Processing helix  chain 'C' and resid 42 through 57
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 90 through 94
    Processing helix  chain 'C' and resid 96 through 105
    Processing helix  chain 'C' and resid 113 through 122
      removed outlier: 3.680A  pdb=" N   ILE C 117 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 137
      No H-bonds generated for 'chain 'C' and resid 135 through 137'
    Processing helix  chain 'C' and resid 138 through 153
    Processing helix  chain 'E' and resid 129 through 133
      removed outlier: 3.532A  pdb=" N   PHE E 133 " --> pdb=" O   ALA E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'F' and resid 41 through 52
    Processing helix  chain 'F' and resid 55 through 59
    Processing helix  chain 'G' and resid 26 through 33
      removed outlier: 3.614A  pdb=" N   CYS G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 42 through 58
      removed outlier: 3.989A  pdb=" N   SER G  58 " --> pdb=" O   LYS G  54 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 59 through 61
      No H-bonds generated for 'chain 'G' and resid 59 through 61'
    Processing helix  chain 'G' and resid 66 through 76
    Processing helix  chain 'G' and resid 90 through 94
    Processing helix  chain 'G' and resid 96 through 105
    Processing helix  chain 'G' and resid 113 through 121
      removed outlier: 3.788A  pdb=" N   ILE G 117 " --> pdb=" O   SER G 113 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 135 through 137
      No H-bonds generated for 'chain 'G' and resid 135 through 137'
    Processing helix  chain 'G' and resid 138 through 151
    Processing helix  chain 'H' and resid 41 through 52
    Processing helix  chain 'H' and resid 55 through 59
    Processing helix  chain 'A' and resid 55 through 59
    Processing helix  chain 'A' and resid 60 through 64
      removed outlier: 3.680A  pdb=" N   LEU A  64 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 3.771A  pdb=" N   ARG A  83 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 91
    Processing helix  chain 'A' and resid 103 through 116
    Processing helix  chain 'A' and resid 140 through 143
      removed outlier: 3.753A  pdb=" N   ARG A 143 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 140 through 143'
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 167 through 177
      removed outlier: 3.875A  pdb=" N   VAL A 171 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 240
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 288
    Processing helix  chain 'A' and resid 292 through 296
    Processing helix  chain 'A' and resid 304 through 313
      removed outlier: 4.568A  pdb=" N   ASN A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ALA A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 4.360A  pdb=" N   SER A 389 " --> pdb=" O   PRO A 386 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 64
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.909A  pdb=" N   ARG D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 90
    Processing helix  chain 'D' and resid 103 through 116
    Processing helix  chain 'D' and resid 141 through 149
      removed outlier: 4.602A  pdb=" N   LYS D 146 " --> pdb=" O   ARG D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 177
      removed outlier: 3.756A  pdb=" N   VAL D 171 " --> pdb=" O   ASN D 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 239
    Processing helix  chain 'D' and resid 265 through 279
    Processing helix  chain 'D' and resid 281 through 287
    Processing helix  chain 'D' and resid 292 through 296
      removed outlier: 3.649A  pdb=" N   VAL D 296 " --> pdb=" O   GLY D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 313
      removed outlier: 4.469A  pdb=" N   ASN D 309 " --> pdb=" O   ASP D 305 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ALA D 310 " --> pdb=" O   SER D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 353 through 360
    Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 98
      removed outlier: 6.793A  pdb=" N   PHE B 139 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   TYR B 118 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU B 110 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 91
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65
    Processing sheet with id=AA4, first strand: chain 'E' and resid 97 through 98
      removed outlier: 6.714A  pdb=" N   PHE E 139 " --> pdb=" O   LEU E  70 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ILE E  82 " --> pdb=" O   GLY E  74 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   THR E  76 " --> pdb=" O   ASP E  80 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ASP E  80 " --> pdb=" O   THR E  76 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   TYR E 118 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   PHE E 119 " --> pdb=" O   ILE E 111 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ILE E 111 " --> pdb=" O   PHE E 119 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   SER E 121 " --> pdb=" O   ASP E 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 90 through 91
    Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 16
    Processing sheet with id=AA7, first strand: chain 'G' and resid 63 through 65
    Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 16
    Processing sheet with id=AA9, first strand: chain 'A' and resid 65 through 66
      removed outlier: 6.907A  pdb=" N   PHE A 302 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   TYR A 325 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ARG A 300 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LYS A 299 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLN A 333 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   ILE A 349 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   LEU A 368 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL A 317 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 92 through 97
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 92 through 97
    current: chain 'A' and resid 131 through 138
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 131 through 138
    current: chain 'A' and resid 197 through 210
      removed outlier: 5.781A  pdb=" N   SER A 204 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   SER A 221 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   LEU A 206 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   TRP A 219 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 65 through 66
      removed outlier: 3.510A  pdb=" N   ARG D 324 " --> pdb=" O   PHE D 302 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   LYS D 299 " --> pdb=" O   VAL D 336 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL D 338 " --> pdb=" O   LYS D 299 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ILE D 301 " --> pdb=" O   VAL D 338 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLN D 333 " --> pdb=" O   ALA D 350 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE D 349 " --> pdb=" O   LEU D 368 " (cutoff:3.500A)
      removed outlier: 5.388A  pdb=" N   LEU D 368 " --> pdb=" O   ILE D 349 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 91 through 98
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 91 through 98
    current: chain 'D' and resid 131 through 139
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 131 through 139
    current: chain 'D' and resid 197 through 210
      removed outlier: 5.647A  pdb=" N   SER D 204 " --> pdb=" O   SER D 221 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   SER D 221 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   LEU D 206 " --> pdb=" O   TRP D 219 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   TRP D 219 " --> pdb=" O   LEU D 206 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      164 hydrogen bond angles
      0 basepair planarities
      31 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 5.45

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 11069
        1.03 -     1.22: 46
        1.22 -     1.42: 5071
        1.42 -     1.61: 7089
        1.61 -     1.81: 84
  Bond restraints: 23359
  Sorted by residual:
  bond pdb=" CA  PHE D 159 "
       pdb=" C   PHE D 159 "
    ideal  model  delta    sigma   weight residual
    1.522  1.477  0.046 1.23e-02 6.61e+03 1.38e+01
  bond pdb=" N   ILE E 105 "
       pdb=" CA  ILE E 105 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.033 9.10e-03 1.21e+04 1.30e+01
  bond pdb=" C   VAL C  82 "
       pdb=" O   VAL C  82 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.038 1.07e-02 8.73e+03 1.28e+01
  bond pdb=" C   ARG G  64 "
       pdb=" O   ARG G  64 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.14e-02 7.69e+03 1.17e+01
  bond pdb=" CG  HIS C  59 "
       pdb=" CD2 HIS C  59 "
    ideal  model  delta    sigma   weight residual
    1.354  1.318  0.036 1.10e-02 8.26e+03 1.10e+01
  ... (remaining 23354 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 42045
        3.12 -     6.24: 266
        6.24 -     9.36: 12
        9.36 -    12.49: 0
       12.49 -    15.61: 1
  Bond angle restraints: 42324
  Sorted by residual:
  angle pdb=" N   LEU A 239 "
        pdb=" CA  LEU A 239 "
        pdb=" C   LEU A 239 "
      ideal   model   delta    sigma   weight residual
     111.07  105.11    5.96 1.07e+00 8.73e-01 3.10e+01
  angle pdb=" C   ARG G  64 "
        pdb=" CA  ARG G  64 "
        pdb=" CB  ARG G  64 "
      ideal   model   delta    sigma   weight residual
     110.74  119.11   -8.37 1.61e+00 3.86e-01 2.70e+01
  angle pdb=" N   GLY E 125 "
        pdb=" CA  GLY E 125 "
        pdb=" C   GLY E 125 "
      ideal   model   delta    sigma   weight residual
     112.82  105.70    7.12 1.38e+00 5.25e-01 2.66e+01
  angle pdb=" CA  LEU B  81 "
        pdb=" C   LEU B  81 "
        pdb=" O   LEU B  81 "
      ideal   model   delta    sigma   weight residual
     121.32  115.39    5.93 1.16e+00 7.43e-01 2.61e+01
  angle pdb=" CA  GLY C  80 "
        pdb=" C   GLY C  80 "
        pdb=" O   GLY C  80 "
      ideal   model   delta    sigma   weight residual
     121.05  116.64    4.41 9.00e-01 1.23e+00 2.40e+01
  ... (remaining 42319 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.86: 10419
       34.86 -    69.72: 555
       69.72 -   104.58: 56
      104.58 -   139.44: 1
      139.44 -   174.30: 4
  Dihedral angle restraints: 11035
    sinusoidal: 6900
      harmonic: 4135
  Sorted by residual:
  dihedral pdb=" CD  ARG G  64 "
           pdb=" NE  ARG G  64 "
           pdb=" CZ  ARG G  64 "
           pdb=" NH1 ARG G  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.81  -86.81     1      1.00e+01 1.00e-02 9.07e+01
  dihedral pdb=" O4'   C I  31 "
           pdb=" C1'   C I  31 "
           pdb=" N1    C I  31 "
           pdb=" C2    C I  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.30 -174.30     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   C I 102 "
           pdb=" C1'   C I 102 "
           pdb=" N1    C I 102 "
           pdb=" C2    C I 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   41.39 -169.39     1      1.70e+01 3.46e-03 6.59e+01
  ... (remaining 11032 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1590
       0.047 -    0.095: 239
       0.095 -    0.142: 114
       0.142 -    0.189: 15
       0.189 -    0.237: 11
  Chirality restraints: 1969
  Sorted by residual:
  chirality pdb=" CA  ARG H  43 "
            pdb=" N   ARG H  43 "
            pdb=" C   ARG H  43 "
            pdb=" CB  ARG H  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  ILE C  81 "
            pdb=" N   ILE C  81 "
            pdb=" C   ILE C  81 "
            pdb=" CB  ILE C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  VAL A 241 "
            pdb=" N   VAL A 241 "
            pdb=" C   VAL A 241 "
            pdb=" CB  VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1966 not shown)

  Planarity restraints: 3037
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  95 "   -0.199 2.00e-02 2.50e+03   2.20e-01 7.28e+02
        pdb=" CG  ASN A  95 "    0.013 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  95 "    0.190 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  95 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN A  95 "   -0.331 2.00e-02 2.50e+03
        pdb="HD22 ASN A  95 "    0.325 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  64 "   -1.120 9.50e-02 1.11e+02   3.74e-01 1.52e+02
        pdb=" NE  ARG G  64 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  64 "    0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  64 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  64 "   -0.017 2.00e-02 2.50e+03
        pdb="HH11 ARG G  64 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG G  64 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG G  64 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG G  64 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  13 "   -0.959 9.50e-02 1.11e+02   3.20e-01 1.12e+02
        pdb=" NE  ARG H  13 "    0.054 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  13 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  13 "   -0.028 2.00e-02 2.50e+03
        pdb="HH11 ARG H  13 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG H  13 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG H  13 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG H  13 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3034 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.31: 6430
        2.31 -     2.89: 51412
        2.89 -     3.46: 59642
        3.46 -     4.03: 84642
        4.03 -     4.60: 124822
  Nonbonded interactions: 326948
  Sorted by model distance:
  nonbonded pdb=" H   THR H  27 "
            pdb=" HG1 THR H  27 "
     model   vdw
     1.742 2.100
  nonbonded pdb="HO2'   G I  16 "
            pdb=" H6    U I  17 "
     model   vdw
     1.825 2.100
  nonbonded pdb=" HD1 PHE A  61 "
            pdb=" HE2 PHE A 302 "
     model   vdw
     1.829 2.100
  nonbonded pdb=" HE1 PHE A 218 "
            pdb=" HG  CYS A 232 "
     model   vdw
     1.841 2.270
  nonbonded pdb=" H   SER C  58 "
            pdb=" HG  SER C  58 "
     model   vdw
     1.842 2.100
  ... (remaining 326943 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' and resid 55 through 389)
  selection = (chain 'D' and (resid 55 through 188 or (resid 194 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ 
 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name  \ 
HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ 
 or resid 195 through 389))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'E' and resid 63 through 153)
}
ncs_group {
  reference = (chain 'C' and (resid 33 through 76 or (resid 79 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ 
 name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 
2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 80 through 152))
  selection = (chain 'G' and ((resid 33 and (name N or name CA or name C or name O or name CB  \ 
or name SG or name HA or name HB2 or name HB3 or name HG )) or resid 34 through  \ 
152))
}
ncs_group {
  reference = (chain 'F' and resid 1 through 59)
  selection = chain 'H'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.140
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     26.590
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:6.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
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      :  0.005   0.056  12266  Z= 0.275
  Angle     :  0.780   8.989  16997  Z= 0.465
  Chirality :  0.046   0.237   1969
  Planarity :  0.019   0.502   1800
  Dihedral  : 20.060 174.296   5310
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.49 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 26.52 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.23), residues: 1203
  helix: -0.07 (0.28), residues: 339
  sheet: -1.64 (0.35), residues: 194
  loop : -0.85 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  13 
 TYR   0.015   0.001   TYR G  26 
 PHE   0.018   0.001   PHE D 218 
 TRP   0.012   0.001   TRP D 219 
 HIS   0.008   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (12266)
  covalent geometry    : angle       0.78011 (16997)
  hydrogen bonds       : bond        0.14165 (  414)
  hydrogen bonds       : angle       7.00395 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 248
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   94 MET cc_start: 0.6962 (ppp) cc_final: 0.6652 (ppp)
REVERT: C  121 MET cc_start: 0.6305 (mmm) cc_final: 0.5898 (mmm)
REVERT: E  110 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: D  110 TRP cc_start: 0.7071 (m-10) cc_final: 0.6811 (m-10)
  outliers start: 21
  outliers final: 9
  residues processed: 261
  average time/residue: 1.2822
  time to fit residues: 363.2457
Evaluate side-chains
  250 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 241
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain E residue   98 PHE
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain G residue  134 GLU
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  373 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS
A 101 ASN
A 277 ASN
A 333 GLN
D  65 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.170853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.148393 restraints weight = 51994.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.4113 rms_B_bonded: 2.58
r_work: 0.3992 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.118  12266  Z= 0.273
  Angle     :  0.632   6.074  16997  Z= 0.329
  Chirality :  0.042   0.192   1969
  Planarity :  0.005   0.092   1800
  Dihedral  : 19.778 173.941   2851
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 27.17 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.23), residues: 1203
  helix: -0.32 (0.27), residues: 344
  sheet: -1.92 (0.33), residues: 207
  loop : -1.06 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  13 
 TYR   0.017   0.002   TYR A 155 
 PHE   0.026   0.002   PHE D 218 
 TRP   0.018   0.002   TRP D 219 
 HIS   0.005   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 (12266)
  covalent geometry    : angle       0.63232 (16997)
  hydrogen bonds       : bond        0.04626 (  414)
  hydrogen bonds       : angle       5.67331 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 259
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 ASN cc_start: 0.6766 (p0) cc_final: 0.6435 (p0)
REVERT: B  124 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6903 (tpt)
REVERT: C  121 MET cc_start: 0.6268 (mmm) cc_final: 0.5845 (mmm)
REVERT: E  110 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7465 (mm-30)
REVERT: G  143 ASP cc_start: 0.8296 (m-30) cc_final: 0.7887 (m-30)
REVERT: G  144 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: G  145 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6903 (p)
REVERT: A  318 LEU cc_start: 0.8357 (mt) cc_final: 0.8144 (mm)
REVERT: A  352 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7712 (tmm)
REVERT: D  110 TRP cc_start: 0.7154 (m-10) cc_final: 0.6906 (m-10)
  outliers start: 42
  outliers final: 23
  residues processed: 281
  average time/residue: 1.2188
  time to fit residues: 372.3349
Evaluate side-chains
  281 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 255
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   12 ASP
Chi-restraints excluded: chain F residue   14 GLN
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue  134 GLU
Chi-restraints excluded: chain G residue  145 VAL
Chi-restraints excluded: chain G residue  150 LYS
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  360 CYS
Chi-restraints excluded: chain D residue  373 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 127 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
D 256 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.171858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.149394 restraints weight = 51823.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 2.57
r_work: 0.4007 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  12266  Z= 0.189
  Angle     :  0.578   6.370  16997  Z= 0.297
  Chirality :  0.040   0.168   1969
  Planarity :  0.004   0.039   1800
  Dihedral  : 19.690 175.141   2838
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 28.29 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.23), residues: 1203
  helix: -0.11 (0.27), residues: 343
  sheet: -1.98 (0.32), residues: 209
  loop : -0.91 (0.23), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 185 
 TYR   0.015   0.001   TYR E  73 
 PHE   0.023   0.002   PHE D 218 
 TRP   0.016   0.002   TRP D 219 
 HIS   0.004   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (12266)
  covalent geometry    : angle       0.57800 (16997)
  hydrogen bonds       : bond        0.04058 (  414)
  hydrogen bonds       : angle       5.31007 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 259
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7174 (tpt)
REVERT: C   71 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6364 (tt0)
REVERT: C  102 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7090 (mm-30)
REVERT: C  121 MET cc_start: 0.6120 (mmm) cc_final: 0.5701 (mmm)
REVERT: E  110 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7481 (mm-30)
REVERT: A  185 ARG cc_start: 0.6780 (ttm-80) cc_final: 0.6514 (ttm-80)
REVERT: A  318 LEU cc_start: 0.8353 (mt) cc_final: 0.8148 (mm)
REVERT: A  339 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7399 (p)
REVERT: D  110 TRP cc_start: 0.7139 (m-10) cc_final: 0.6898 (m-10)
  outliers start: 30
  outliers final: 15
  residues processed: 273
  average time/residue: 1.1441
  time to fit residues: 340.2278
Evaluate side-chains
  272 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 254
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue   71 GLN
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   14 GLN
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  339 THR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  333 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0470
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 GLN
D 256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.173861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.151363 restraints weight = 51875.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 2.58
r_work: 0.4039 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12266  Z= 0.119
  Angle     :  0.540   6.434  16997  Z= 0.273
  Chirality :  0.039   0.155   1969
  Planarity :  0.004   0.043   1800
  Dihedral  : 19.546 175.861   2830
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 27.36 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.23), residues: 1203
  helix:  0.39 (0.28), residues: 343
  sheet: -1.99 (0.32), residues: 207
  loop : -0.79 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 113 
 TYR   0.016   0.001   TYR D  88 
 PHE   0.018   0.001   PHE D 218 
 TRP   0.011   0.001   TRP D 219 
 HIS   0.003   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12266)
  covalent geometry    : angle       0.54012 (16997)
  hydrogen bonds       : bond        0.03540 (  414)
  hydrogen bonds       : angle       4.94026 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 257
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6851 (tpt)
REVERT: C  121 MET cc_start: 0.6061 (mmm) cc_final: 0.5671 (mmm)
REVERT: E  110 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: G  143 ASP cc_start: 0.8173 (m-30) cc_final: 0.7745 (m-30)
REVERT: A  352 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7718 (tmm)
REVERT: D  110 TRP cc_start: 0.7154 (m-10) cc_final: 0.6897 (m-10)
  outliers start: 34
  outliers final: 20
  residues processed: 268
  average time/residue: 1.1594
  time to fit residues: 338.5286
Evaluate side-chains
  274 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 252
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  333 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
F  14 GLN
F  31 HIS
A 277 ASN
D 256 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.171777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.149489 restraints weight = 51686.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4125 rms_B_bonded: 2.55
r_work: 0.4011 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  12266  Z= 0.196
  Angle     :  0.590   8.010  16997  Z= 0.301
  Chirality :  0.040   0.173   1969
  Planarity :  0.005   0.050   1800
  Dihedral  : 19.581 176.168   2830
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 28.76 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.23), residues: 1203
  helix:  0.28 (0.28), residues: 343
  sheet: -1.93 (0.32), residues: 217
  loop : -0.96 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 285 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.025   0.002   PHE D 218 
 TRP   0.014   0.002   TRP D 219 
 HIS   0.004   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (12266)
  covalent geometry    : angle       0.58980 (16997)
  hydrogen bonds       : bond        0.03867 (  414)
  hydrogen bonds       : angle       5.03408 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 252
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7163 (tpt)
REVERT: C  102 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7079 (mm-30)
REVERT: C  121 MET cc_start: 0.6093 (mmm) cc_final: 0.5682 (mmm)
REVERT: E  110 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: G  143 ASP cc_start: 0.8218 (m-30) cc_final: 0.7777 (m-30)
REVERT: D  110 TRP cc_start: 0.7148 (m-10) cc_final: 0.6891 (m-10)
  outliers start: 34
  outliers final: 21
  residues processed: 268
  average time/residue: 1.1699
  time to fit residues: 341.1563
Evaluate side-chains
  274 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 252
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue   40 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  359 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 120 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS
A 277 ASN
D 256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.171565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.149261 restraints weight = 51966.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.57
r_work: 0.4008 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091  12266  Z= 0.206
  Angle     :  0.597   7.280  16997  Z= 0.305
  Chirality :  0.040   0.175   1969
  Planarity :  0.004   0.051   1800
  Dihedral  : 19.599 175.566   2830
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 29.04 %
    Favored  : 67.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.23), residues: 1203
  helix:  0.17 (0.28), residues: 344
  sheet: -1.94 (0.32), residues: 218
  loop : -1.01 (0.23), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 113 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.029   0.002   PHE D 218 
 TRP   0.014   0.002   TRP D 219 
 HIS   0.004   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (12266)
  covalent geometry    : angle       0.59720 (16997)
  hydrogen bonds       : bond        0.03909 (  414)
  hydrogen bonds       : angle       5.03649 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 252
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7439 (tpt)
REVERT: C  121 MET cc_start: 0.6114 (mmm) cc_final: 0.5690 (mmm)
REVERT: E  110 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7467 (mm-30)
REVERT: G  143 ASP cc_start: 0.8238 (m-30) cc_final: 0.7784 (m-30)
REVERT: D  110 TRP cc_start: 0.7170 (m-10) cc_final: 0.6925 (m-10)
  outliers start: 36
  outliers final: 21
  residues processed: 270
  average time/residue: 1.2435
  time to fit residues: 365.3408
Evaluate side-chains
  271 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 249
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  360 CYS
Chi-restraints excluded: chain D residue  373 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS
D 256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.171900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.149584 restraints weight = 51685.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4129 rms_B_bonded: 2.57
r_work: 0.4012 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  12266  Z= 0.176
  Angle     :  0.588   7.932  16997  Z= 0.298
  Chirality :  0.040   0.166   1969
  Planarity :  0.004   0.054   1800
  Dihedral  : 19.578 175.899   2830
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 30.16 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.23), residues: 1203
  helix:  0.31 (0.28), residues: 344
  sheet: -1.99 (0.32), residues: 219
  loop : -0.97 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 113 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.026   0.002   PHE D 218 
 TRP   0.014   0.001   TRP D 219 
 HIS   0.004   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12266)
  covalent geometry    : angle       0.58760 (16997)
  hydrogen bonds       : bond        0.03761 (  414)
  hydrogen bonds       : angle       4.95721 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 257
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7411 (tpt)
REVERT: C  121 MET cc_start: 0.6103 (mmm) cc_final: 0.5671 (mmm)
REVERT: E  110 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7469 (mm-30)
REVERT: G  143 ASP cc_start: 0.8236 (m-30) cc_final: 0.7791 (m-30)
REVERT: D  110 TRP cc_start: 0.7173 (m-10) cc_final: 0.6931 (m-10)
  outliers start: 30
  outliers final: 23
  residues processed: 271
  average time/residue: 1.2414
  time to fit residues: 366.4428
Evaluate side-chains
  275 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 251
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  333 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS
A 277 ASN
D 256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.171436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.149093 restraints weight = 51502.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 2.56
r_work: 0.4003 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  12266  Z= 0.197
  Angle     :  0.606  10.218  16997  Z= 0.309
  Chirality :  0.041   0.175   1969
  Planarity :  0.005   0.065   1800
  Dihedral  : 19.596 175.613   2830
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 30.16 %
    Favored  : 66.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.23), residues: 1203
  helix:  0.23 (0.28), residues: 344
  sheet: -1.98 (0.32), residues: 219
  loop : -1.03 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 285 
 TYR   0.016   0.002   TYR D  88 
 PHE   0.028   0.002   PHE D 218 
 TRP   0.014   0.002   TRP D 219 
 HIS   0.004   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (12266)
  covalent geometry    : angle       0.60647 (16997)
  hydrogen bonds       : bond        0.03871 (  414)
  hydrogen bonds       : angle       4.99013 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7500 (tpt)
REVERT: C  121 MET cc_start: 0.6077 (mmm) cc_final: 0.5636 (mmm)
REVERT: E  110 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7533 (mm-30)
REVERT: G  143 ASP cc_start: 0.8231 (m-30) cc_final: 0.7789 (m-30)
REVERT: D  110 TRP cc_start: 0.7178 (m-10) cc_final: 0.6933 (m-10)
  outliers start: 33
  outliers final: 25
  residues processed: 266
  average time/residue: 1.0843
  time to fit residues: 314.4818
Evaluate side-chains
  275 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 249
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue   89 ASP
Chi-restraints excluded: chain E residue   92 TYR
Chi-restraints excluded: chain E residue  100 GLU
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  177 LYS
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  373 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS
A 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.169948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.147466 restraints weight = 51962.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.57
r_work: 0.3983 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.124  12266  Z= 0.275
  Angle     :  0.669  10.589  16997  Z= 0.343
  Chirality :  0.043   0.198   1969
  Planarity :  0.005   0.073   1800
  Dihedral  : 19.682 175.111   2830
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 30.25 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.23), residues: 1203
  helix: -0.10 (0.27), residues: 344
  sheet: -2.05 (0.31), residues: 224
  loop : -1.21 (0.23), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 285 
 TYR   0.017   0.002   TYR A 155 
 PHE   0.035   0.002   PHE D 218 
 TRP   0.014   0.002   TRP D 219 
 HIS   0.006   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 (12266)
  covalent geometry    : angle       0.66932 (16997)
  hydrogen bonds       : bond        0.04286 (  414)
  hydrogen bonds       : angle       5.19135 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 256
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (tpt)
REVERT: B  134 LYS cc_start: 0.8145 (mttt) cc_final: 0.7867 (mttt)
REVERT: C  102 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7032 (mt-10)
REVERT: C  121 MET cc_start: 0.6034 (mmm) cc_final: 0.5618 (mmm)
REVERT: E  110 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7578 (mm-30)
REVERT: G  143 ASP cc_start: 0.8250 (m-30) cc_final: 0.7840 (m-30)
REVERT: D  110 TRP cc_start: 0.7183 (m-10) cc_final: 0.6947 (m-10)
  outliers start: 33
  outliers final: 24
  residues processed: 270
  average time/residue: 1.0321
  time to fit residues: 304.2052
Evaluate side-chains
  279 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 254
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   48 LYS
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  333 GLN
Chi-restraints excluded: chain D residue  360 CYS
Chi-restraints excluded: chain D residue  373 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0050
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.173239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.151006 restraints weight = 51650.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 2.56
r_work: 0.4039 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  12266  Z= 0.124
  Angle     :  0.588  10.119  16997  Z= 0.297
  Chirality :  0.039   0.157   1969
  Planarity :  0.004   0.058   1800
  Dihedral  : 19.569 176.277   2830
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 31.75 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.24), residues: 1203
  helix:  0.42 (0.28), residues: 344
  sheet: -1.98 (0.32), residues: 218
  loop : -0.96 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 113 
 TYR   0.020   0.001   TYR D  88 
 PHE   0.018   0.001   PHE A 302 
 TRP   0.015   0.001   TRP D 219 
 HIS   0.005   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12266)
  covalent geometry    : angle       0.58783 (16997)
  hydrogen bonds       : bond        0.03605 (  414)
  hydrogen bonds       : angle       4.84259 ( 1022)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 252
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7524 (tpt)
REVERT: C  121 MET cc_start: 0.6025 (mmm) cc_final: 0.5615 (mmm)
REVERT: E  110 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7538 (mm-30)
REVERT: G   55 LYS cc_start: 0.8291 (tptp) cc_final: 0.7646 (tppp)
REVERT: G  143 ASP cc_start: 0.8261 (m-30) cc_final: 0.7809 (m-30)
REVERT: A  100 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (t)
REVERT: D  110 TRP cc_start: 0.7134 (m-10) cc_final: 0.6887 (m-10)
  outliers start: 22
  outliers final: 17
  residues processed: 263
  average time/residue: 1.1009
  time to fit residues: 315.2123
Evaluate side-chains
  268 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 249
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain E residue   92 TYR
Chi-restraints excluded: chain E residue  120 VAL
Chi-restraints excluded: chain E residue  121 SER
Chi-restraints excluded: chain F residue    8 ASN
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   36 SER
Chi-restraints excluded: chain G residue   69 ILE
Chi-restraints excluded: chain H residue   17 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  262 MET
Chi-restraints excluded: chain A residue  283 TYR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  333 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 110 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
F  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.173474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.151021 restraints weight = 51900.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 2.58
r_work: 0.4039 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12266  Z= 0.133
  Angle     :  0.593  10.967  16997  Z= 0.300
  Chirality :  0.040   0.193   1969
  Planarity :  0.004   0.060   1800
  Dihedral  : 19.522 176.103   2830
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 31.75 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.24), residues: 1203
  helix:  0.62 (0.28), residues: 342
  sheet: -1.95 (0.32), residues: 218
  loop : -0.85 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 113 
 TYR   0.021   0.001   TYR D  88 
 PHE   0.020   0.002   PHE A 302 
 TRP   0.014   0.001   TRP D 219 
 HIS   0.004   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12266)
  covalent geometry    : angle       0.59309 (16997)
  hydrogen bonds       : bond        0.03599 (  414)
  hydrogen bonds       : angle       4.76251 ( 1022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8970.84 seconds
wall clock time: 152 minutes 23.60 seconds (9143.60 seconds total)