Starting phenix.real_space_refine
on Wed Sep 17 12:24:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yh6_39282/09_2025/8yh6_39282.cif"
  }
  resolution = 3.62
  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=   0.005 sd=   1.069
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
     I       1     10.91       5
     S      66      5.16       5
     Cl      1      4.86       5
     C    5570      2.51       5
     N    1464      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8706
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2198
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1705
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 209}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'XS0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.21, per 1000 atoms: 0.25
  Number of scatterers: 8706
  At special positions: 0
  Unit cell: (91.02, 123.21, 127.65, 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)
     I       1     52.95
     Cl      1     17.00
     S      66     16.00
     O    1604      8.00
     N    1464      7.00
     C    5570      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 103 " - pdb=" SG  CYS B 114 " distance=1.70
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R  83 " - pdb=" SG  CYS R 165 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 447.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      37.3% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.637A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.833A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 22
    Processing helix  chain 'G' and resid 33 through 44
      removed outlier: 3.556A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.529A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.928A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'R' and resid 10 through 40
    Processing helix  chain 'R' and resid 41 through 44
    Processing helix  chain 'R' and resid 45 through 64
    Processing helix  chain 'R' and resid 64 through 75
    Processing helix  chain 'R' and resid 79 through 115
    Processing helix  chain 'R' and resid 116 through 122
      removed outlier: 4.435A  pdb=" N   ARG R 120 " --> pdb=" O   VAL R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 144
    Processing helix  chain 'R' and resid 145 through 148
    Processing helix  chain 'R' and resid 150 through 154
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.574A  pdb=" N   VAL R 170 " --> pdb=" O   ARG R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 3.570A  pdb=" N   MET R 176 " --> pdb=" O   ARG R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 185
    Processing helix  chain 'R' and resid 185 through 207
    Processing helix  chain 'R' and resid 225 through 254
      Proline residue:  R 244  - end of helix
    Processing helix  chain 'R' and resid 259 through 282
      removed outlier: 3.824A  pdb=" N   MET R 275 " --> pdb=" O   HIS R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 285 through 295
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 4.118A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 275 through 281
      removed outlier: 3.886A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.615A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.994A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.673A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.301A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.007A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.517A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.912A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276
      removed outlier: 6.515A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 6
    Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.191A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 128 through 130
      removed outlier: 3.636A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.143A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.270A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.159A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1170 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.18 -     1.36: 2831
        1.36 -     1.55: 5959
        1.55 -     1.73: 0
        1.73 -     1.92: 99
        1.92 -     2.10: 1
  Bond restraints: 8890
  Sorted by residual:
  bond pdb=" C   SER A   6 "
       pdb=" O   SER A   6 "
    ideal  model  delta    sigma   weight residual
    1.234  1.305 -0.071 1.35e-02 5.49e+03 2.77e+01
  bond pdb=" C   ASP A 200 "
       pdb=" O   ASP A 200 "
    ideal  model  delta    sigma   weight residual
    1.236  1.299 -0.063 1.22e-02 6.72e+03 2.67e+01
  bond pdb=" C   PHE A 307 "
       pdb=" O   PHE A 307 "
    ideal  model  delta    sigma   weight residual
    1.237  1.181  0.056 1.19e-02 7.06e+03 2.19e+01
  bond pdb=" N   VAL R 170 "
       pdb=" CA  VAL R 170 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 9.10e-03 1.21e+04 1.87e+01
  bond pdb=" CA  SER A   6 "
       pdb=" CB  SER A   6 "
    ideal  model  delta    sigma   weight residual
    1.528  1.462  0.066 1.61e-02 3.86e+03 1.69e+01
  ... (remaining 8885 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 10006
        1.89 -     3.78: 1844
        3.78 -     5.66: 168
        5.66 -     7.55: 17
        7.55 -     9.44: 6
  Bond angle restraints: 12041
  Sorted by residual:
  angle pdb=" N   ILE R 248 "
        pdb=" CA  ILE R 248 "
        pdb=" C   ILE R 248 "
      ideal   model   delta    sigma   weight residual
     110.42  100.98    9.44 9.60e-01 1.09e+00 9.67e+01
  angle pdb=" N   LYS A 210 "
        pdb=" CA  LYS A 210 "
        pdb=" C   LYS A 210 "
      ideal   model   delta    sigma   weight residual
     112.92  103.60    9.32 1.23e+00 6.61e-01 5.74e+01
  angle pdb=" N   LEU A 268 "
        pdb=" CA  LEU A 268 "
        pdb=" C   LEU A 268 "
      ideal   model   delta    sigma   weight residual
     108.54  100.39    8.15 1.41e+00 5.03e-01 3.34e+01
  angle pdb=" C   ASP R 255 "
        pdb=" N   GLY R 256 "
        pdb=" CA  GLY R 256 "
      ideal   model   delta    sigma   weight residual
     122.27  116.74    5.53 9.90e-01 1.02e+00 3.12e+01
  angle pdb=" CA  ARG B  52 "
        pdb=" C   ARG B  52 "
        pdb=" O   ARG B  52 "
      ideal   model   delta    sigma   weight residual
     121.58  115.15    6.43 1.16e+00 7.43e-01 3.07e+01
  ... (remaining 12036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.67: 5132
       30.67 -    61.35: 139
       61.35 -    92.02: 7
       92.02 -   122.70: 0
      122.70 -   153.37: 4
  Dihedral angle restraints: 5282
    sinusoidal: 2077
      harmonic: 3205
  Sorted by residual:
  dihedral pdb=" CB  CYS B 103 "
           pdb=" SG  CYS B 103 "
           pdb=" SG  CYS B 114 "
           pdb=" CB  CYS B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.91   73.09     1      1.00e+01 1.00e-02 6.81e+01
  dihedral pdb=" CD  ARG B 137 "
           pdb=" NE  ARG B 137 "
           pdb=" CZ  ARG B 137 "
           pdb=" NH1 ARG B 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   51.93  -51.93     1      1.00e+01 1.00e-02 3.68e+01
  dihedral pdb=" CA  TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" N   PRO S 224 "
           pdb=" CA  PRO S 224 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   29.00  -29.00     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 5279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 497
       0.051 -    0.103: 497
       0.103 -    0.154: 272
       0.154 -    0.206: 89
       0.206 -    0.257: 22
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" CB  VAL R 234 "
            pdb=" CA  VAL R 234 "
            pdb=" CG1 VAL R 234 "
            pdb=" CG2 VAL R 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE R  98 "
            pdb=" CA  ILE R  98 "
            pdb=" CG1 ILE R  98 "
            pdb=" CG2 ILE R  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 1374 not shown)

  Planarity restraints: 1501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 XS0 R 801 "    0.173 2.00e-02 2.50e+03   7.77e-02 1.81e+02
        pdb=" C11 XS0 R 801 "   -0.016 2.00e-02 2.50e+03
        pdb=" C13 XS0 R 801 "   -0.081 2.00e-02 2.50e+03
        pdb=" C14 XS0 R 801 "   -0.010 2.00e-02 2.50e+03
        pdb=" C16 XS0 R 801 "   -0.017 2.00e-02 2.50e+03
        pdb=" C18 XS0 R 801 "   -0.080 2.00e-02 2.50e+03
        pdb=" N10 XS0 R 801 "   -0.032 2.00e-02 2.50e+03
        pdb=" N12 XS0 R 801 "   -0.045 2.00e-02 2.50e+03
        pdb=" N15 XS0 R 801 "    0.006 2.00e-02 2.50e+03
        pdb=" N17 XS0 R 801 "   -0.067 2.00e-02 2.50e+03
        pdb=" N20 XS0 R 801 "    0.143 2.00e-02 2.50e+03
        pdb="CL19 XS0 R 801 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 137 "   -0.856 9.50e-02 1.11e+02   3.84e-01 8.93e+01
        pdb=" NE  ARG B 137 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 137 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 137 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 137 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 205 "   -0.726 9.50e-02 1.11e+02   3.25e-01 6.45e+01
        pdb=" NE  ARG A 205 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 205 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 205 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 205 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1498 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1312
        2.76 -     3.31: 8871
        3.31 -     3.86: 14990
        3.86 -     4.41: 18911
        4.41 -     4.96: 31539
  Nonbonded interactions: 75623
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" OD1 ASP B 290 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   MET G  21 "
            pdb=" CG1 ILE G  25 "
     model   vdw
     2.238 3.440
  nonbonded pdb=" O   LEU A 249 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLY B 162 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.279 3.040
  ... (remaining 75618 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.080
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4927
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      :  0.013   0.333   8894  Z= 0.918
  Angle     :  1.506  49.467  12049  Z= 1.058
  Chirality :  0.092   0.257   1377
  Planarity :  0.028   0.384   1501
  Dihedral  : 14.434 153.370   3202
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  6.82 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -2.37 (0.23), residues: 1086
  helix: -0.85 (0.24), residues: 374
  sheet: -1.81 (0.30), residues: 239
  loop : -1.92 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG B  49 
 TYR   0.039   0.005   TYR R  15 
 PHE   0.081   0.006   PHE A 199 
 TRP   0.028   0.004   TRP S  36 
 HIS   0.013   0.003   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.01235 ( 8890)
  covalent geometry    : angle       1.43034 (12041)
  SS BOND              : bond        0.16675 (    4)
  SS BOND              : angle      18.40522 (    8)
  hydrogen bonds       : bond        0.18130 (  414)
  hydrogen bonds       : angle       7.84547 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 289
  time to evaluate  : 0.339 
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: B  308 LEU cc_start: 0.7028 (mt) cc_final: 0.6653 (mt)
REVERT: G   55 PRO cc_start: 0.5700 (Cg_exo) cc_final: 0.5484 (Cg_endo)
  outliers start: 9
  outliers final: 2
  residues processed: 294
  average time/residue: 0.1093
  time to fit residues: 43.1069
Evaluate side-chains
  170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 168
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  119 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B  91 HIS
B 176 GLN
B 293 ASN
G  44 HIS
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 159 ASN
R  79 HIS
A  22 ASN
A  52 GLN
A 213 HIS
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.162587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.140144 restraints weight = 24892.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.143291 restraints weight = 14949.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.145669 restraints weight = 10710.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.147401 restraints weight = 8471.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.148213 restraints weight = 7143.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5831
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8894  Z= 0.166
  Angle     :  0.718  15.090  12049  Z= 0.379
  Chirality :  0.044   0.181   1377
  Planarity :  0.005   0.043   1501
  Dihedral  :  9.367 131.080   1223
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.68 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.30 (0.24), residues: 1086
  helix:  0.49 (0.25), residues: 380
  sheet: -1.29 (0.30), residues: 280
  loop : -1.71 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 134 
 TYR   0.013   0.002   TYR B 105 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.039   0.002   TRP R 128 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8890)
  covalent geometry    : angle       0.71189 (12041)
  SS BOND              : bond        0.01463 (    4)
  SS BOND              : angle       3.76660 (    8)
  hydrogen bonds       : bond        0.04876 (  414)
  hydrogen bonds       : angle       5.58114 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.347 
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: G   55 PRO cc_start: 0.5746 (Cg_exo) cc_final: 0.5521 (Cg_endo)
REVERT: S  182 ASN cc_start: 0.7340 (m-40) cc_final: 0.7118 (m-40)
REVERT: S  218 MET cc_start: 0.4120 (ttp) cc_final: 0.3677 (tmm)
REVERT: R   85 PHE cc_start: 0.7294 (m-80) cc_final: 0.7077 (m-80)
REVERT: R   86 MET cc_start: 0.7351 (mmm) cc_final: 0.7098 (mtt)
REVERT: R   99 MET cc_start: 0.7675 (mmt) cc_final: 0.7365 (mmp)
REVERT: R  184 TRP cc_start: 0.5865 (m100) cc_final: 0.5636 (m100)
REVERT: A  247 MET cc_start: 0.6536 (mmt) cc_final: 0.6223 (mmt)
REVERT: A  256 ASN cc_start: 0.8454 (m110) cc_final: 0.8035 (m110)
REVERT: A  345 LYS cc_start: 0.8456 (mttp) cc_final: 0.8091 (tmtt)
  outliers start: 25
  outliers final: 11
  residues processed: 218
  average time/residue: 0.1010
  time to fit residues: 30.0879
Evaluate side-chains
  172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain A residue  276 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 107 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0770
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
S 130 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 220 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.160101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.137218 restraints weight = 25814.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.140313 restraints weight = 15536.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.142749 restraints weight = 11136.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.144383 restraints weight = 8877.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.145143 restraints weight = 7524.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5942
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8894  Z= 0.147
  Angle     :  0.741  20.286  12049  Z= 0.377
  Chirality :  0.043   0.185   1377
  Planarity :  0.005   0.050   1501
  Dihedral  :  7.507  92.107   1220
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.62 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.76 (0.25), residues: 1086
  helix:  0.93 (0.26), residues: 375
  sheet: -1.04 (0.30), residues: 289
  loop : -1.34 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 242 
 TYR   0.015   0.002   TYR A 287 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.026   0.002   TRP R 128 
 HIS   0.010   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8890)
  covalent geometry    : angle       0.72109 (12041)
  SS BOND              : bond        0.01572 (    4)
  SS BOND              : angle       6.66255 (    8)
  hydrogen bonds       : bond        0.04625 (  414)
  hydrogen bonds       : angle       5.37553 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.356 
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: B   57 LYS cc_start: 0.7648 (mtmm) cc_final: 0.7414 (ttmt)
REVERT: B  101 MET cc_start: 0.7270 (tpp) cc_final: 0.7059 (tpp)
REVERT: B  268 ASN cc_start: 0.7291 (t0) cc_final: 0.7033 (t0)
REVERT: G   55 PRO cc_start: 0.6219 (Cg_exo) cc_final: 0.5973 (Cg_endo)
REVERT: S  103 TYR cc_start: 0.6429 (t80) cc_final: 0.6013 (t80)
REVERT: S  218 MET cc_start: 0.4063 (ttp) cc_final: 0.3719 (tmm)
REVERT: R   86 MET cc_start: 0.7412 (mmm) cc_final: 0.7074 (mtt)
REVERT: R   99 MET cc_start: 0.7484 (mmt) cc_final: 0.7186 (mmp)
REVERT: R  183 LEU cc_start: 0.8049 (tp) cc_final: 0.7656 (tp)
REVERT: R  275 MET cc_start: 0.8030 (tmm) cc_final: 0.7829 (tmm)
REVERT: A  198 MET cc_start: 0.7730 (mtp) cc_final: 0.7520 (mtp)
REVERT: A  243 MET cc_start: 0.6918 (mpp) cc_final: 0.6590 (mpp)
REVERT: A  247 MET cc_start: 0.6773 (mmm) cc_final: 0.6541 (mmt)
REVERT: A  256 ASN cc_start: 0.8612 (m110) cc_final: 0.8235 (m110)
REVERT: A  345 LYS cc_start: 0.8475 (mttp) cc_final: 0.8102 (tmtt)
  outliers start: 26
  outliers final: 19
  residues processed: 192
  average time/residue: 0.0976
  time to fit residues: 26.0103
Evaluate side-chains
  179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue  273 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 108 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
S 159 ASN
R  95 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 256 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.151374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.127795 restraints weight = 28393.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.130422 restraints weight = 17606.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.132396 restraints weight = 12994.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.133947 restraints weight = 10558.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.134811 restraints weight = 9161.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.7202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8894  Z= 0.230
  Angle     :  0.821  17.969  12049  Z= 0.427
  Chirality :  0.047   0.173   1377
  Planarity :  0.005   0.062   1501
  Dihedral  :  6.254  57.009   1220
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 18.36 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.00 (0.25), residues: 1086
  helix:  0.38 (0.25), residues: 366
  sheet: -0.99 (0.31), residues: 281
  loop : -1.20 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S  98 
 TYR   0.032   0.003   TYR B 105 
 PHE   0.025   0.003   PHE R 200 
 TRP   0.036   0.003   TRP B  82 
 HIS   0.011   0.002   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 8890)
  covalent geometry    : angle       0.80474 (12041)
  SS BOND              : bond        0.00711 (    4)
  SS BOND              : angle       6.41484 (    8)
  hydrogen bonds       : bond        0.05675 (  414)
  hydrogen bonds       : angle       5.74496 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7961 (ttmt)
REVERT: B  296 VAL cc_start: 0.8271 (t) cc_final: 0.8004 (p)
REVERT: B  331 SER cc_start: 0.7931 (m) cc_final: 0.7726 (m)
REVERT: G   55 PRO cc_start: 0.4990 (Cg_exo) cc_final: 0.4750 (Cg_endo)
REVERT: S   34 MET cc_start: 0.4956 (mtp) cc_final: 0.4721 (mtt)
REVERT: S  148 ARG cc_start: 0.6764 (mtm-85) cc_final: 0.6513 (mtm-85)
REVERT: S  218 MET cc_start: 0.4834 (ttp) cc_final: 0.4629 (tmm)
REVERT: R   99 MET cc_start: 0.7787 (mmt) cc_final: 0.7411 (mmp)
REVERT: R  183 LEU cc_start: 0.8222 (tp) cc_final: 0.7706 (tp)
REVERT: A  243 MET cc_start: 0.7037 (mpp) cc_final: 0.6834 (pmm)
REVERT: A  252 SER cc_start: 0.8332 (p) cc_final: 0.7997 (p)
REVERT: A  256 ASN cc_start: 0.8455 (m-40) cc_final: 0.7866 (m110)
REVERT: A  337 ASP cc_start: 0.8518 (m-30) cc_final: 0.8032 (m-30)
  outliers start: 42
  outliers final: 28
  residues processed: 196
  average time/residue: 0.0964
  time to fit residues: 26.4238
Evaluate side-chains
  179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  100 ILE
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  331 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.152134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.129084 restraints weight = 27269.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.131964 restraints weight = 16337.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.134139 restraints weight = 11853.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.135814 restraints weight = 9520.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.136713 restraints weight = 8118.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6379
moved from start:          0.7986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8894  Z= 0.210
  Angle     :  0.762  13.485  12049  Z= 0.395
  Chirality :  0.046   0.162   1377
  Planarity :  0.005   0.044   1501
  Dihedral  :  5.536  50.918   1220
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.30 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.92 (0.25), residues: 1086
  helix:  0.39 (0.26), residues: 370
  sheet: -0.95 (0.32), residues: 273
  loop : -1.12 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG S 168 
 TYR   0.020   0.002   TYR B 105 
 PHE   0.027   0.002   PHE R 288 
 TRP   0.018   0.002   TRP B 211 
 HIS   0.005   0.002   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 8890)
  covalent geometry    : angle       0.74832 (12041)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       5.52517 (    8)
  hydrogen bonds       : bond        0.05377 (  414)
  hydrogen bonds       : angle       5.67880 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7670 (ttmt)
REVERT: B  135 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7517 (p)
REVERT: B  234 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6465 (m-80)
REVERT: B  260 GLU cc_start: 0.6326 (pt0) cc_final: 0.6008 (pm20)
REVERT: B  296 VAL cc_start: 0.8324 (t) cc_final: 0.8101 (p)
REVERT: B  331 SER cc_start: 0.7813 (m) cc_final: 0.7591 (m)
REVERT: G   55 PRO cc_start: 0.5396 (Cg_exo) cc_final: 0.5141 (Cg_endo)
REVERT: S  103 TYR cc_start: 0.6722 (t80) cc_final: 0.6348 (t80)
REVERT: S  148 ARG cc_start: 0.6436 (mtm-85) cc_final: 0.6015 (mtm-85)
REVERT: S  190 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6304 (mtp180)
REVERT: R   99 MET cc_start: 0.7792 (mmt) cc_final: 0.7512 (mmp)
REVERT: R  183 LEU cc_start: 0.8175 (tp) cc_final: 0.7634 (tp)
REVERT: A   34 VAL cc_start: 0.7761 (t) cc_final: 0.7550 (t)
REVERT: A  256 ASN cc_start: 0.8487 (m-40) cc_final: 0.7972 (m110)
REVERT: A  297 GLU cc_start: 0.8614 (pm20) cc_final: 0.8383 (pm20)
  outliers start: 35
  outliers final: 24
  residues processed: 181
  average time/residue: 0.0954
  time to fit residues: 24.1664
Evaluate side-chains
  170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  190 ARG
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   51 ILE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   83 CYS
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue  273 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.151367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.124614 restraints weight = 20604.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.124502 restraints weight = 14498.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.125704 restraints weight = 10750.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.127040 restraints weight = 9504.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.127390 restraints weight = 8652.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6452
moved from start:          0.8423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8894  Z= 0.174
  Angle     :  0.730  13.142  12049  Z= 0.376
  Chirality :  0.045   0.159   1377
  Planarity :  0.004   0.037   1501
  Dihedral  :  5.326  49.844   1220
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 20.99 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.81 (0.25), residues: 1086
  helix:  0.40 (0.25), residues: 376
  sheet: -0.88 (0.32), residues: 271
  loop : -1.01 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  32 
 TYR   0.018   0.002   TYR B 105 
 PHE   0.022   0.002   PHE R 288 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8890)
  covalent geometry    : angle       0.71636 (12041)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       5.44260 (    8)
  hydrogen bonds       : bond        0.04972 (  414)
  hydrogen bonds       : angle       5.53206 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 154
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7815 (ttmt)
REVERT: B  111 TYR cc_start: 0.6491 (m-80) cc_final: 0.6168 (m-80)
REVERT: B  234 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6481 (m-80)
REVERT: B  260 GLU cc_start: 0.6708 (pt0) cc_final: 0.6229 (pm20)
REVERT: B  296 VAL cc_start: 0.8311 (t) cc_final: 0.8108 (p)
REVERT: B  331 SER cc_start: 0.7774 (m) cc_final: 0.7521 (m)
REVERT: G   55 PRO cc_start: 0.4957 (Cg_exo) cc_final: 0.4662 (Cg_endo)
REVERT: S  103 TYR cc_start: 0.6608 (t80) cc_final: 0.6104 (t80)
REVERT: S  148 ARG cc_start: 0.6513 (mtm-85) cc_final: 0.6243 (mtm-85)
REVERT: S  168 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7894 (mtm110)
REVERT: R   99 MET cc_start: 0.7649 (mmt) cc_final: 0.7375 (mmp)
REVERT: R  183 LEU cc_start: 0.8216 (tp) cc_final: 0.7670 (tp)
REVERT: R  275 MET cc_start: 0.8181 (tmm) cc_final: 0.7625 (tmm)
REVERT: A   53 MET cc_start: 0.2902 (OUTLIER) cc_final: 0.2668 (mtp)
REVERT: A  256 ASN cc_start: 0.8605 (m-40) cc_final: 0.8025 (m110)
REVERT: A  297 GLU cc_start: 0.8902 (pm20) cc_final: 0.8654 (pm20)
  outliers start: 43
  outliers final: 32
  residues processed: 180
  average time/residue: 0.1005
  time to fit residues: 25.0784
Evaluate side-chains
  179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   51 ILE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  331 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.151110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.125734 restraints weight = 21598.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.125010 restraints weight = 14150.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.126309 restraints weight = 10679.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.127397 restraints weight = 9148.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.127401 restraints weight = 8258.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.8722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8894  Z= 0.143
  Angle     :  0.704  12.251  12049  Z= 0.361
  Chirality :  0.044   0.172   1377
  Planarity :  0.004   0.039   1501
  Dihedral  :  5.108  46.760   1220
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.51 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.55 (0.26), residues: 1086
  helix:  0.67 (0.26), residues: 374
  sheet: -0.74 (0.32), residues: 279
  loop : -0.89 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.012   0.001   TYR B 105 
 PHE   0.015   0.002   PHE R 288 
 TRP   0.010   0.002   TRP B 211 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8890)
  covalent geometry    : angle       0.69064 (12041)
  SS BOND              : bond        0.00390 (    4)
  SS BOND              : angle       5.38838 (    8)
  hydrogen bonds       : bond        0.04604 (  414)
  hydrogen bonds       : angle       5.38435 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7710 (ttmt)
REVERT: B  111 TYR cc_start: 0.6409 (m-80) cc_final: 0.6130 (m-80)
REVERT: B  234 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6352 (m-80)
REVERT: B  260 GLU cc_start: 0.6713 (pt0) cc_final: 0.6219 (pm20)
REVERT: B  296 VAL cc_start: 0.8292 (t) cc_final: 0.8092 (p)
REVERT: B  331 SER cc_start: 0.7644 (m) cc_final: 0.7440 (m)
REVERT: S  103 TYR cc_start: 0.6561 (t80) cc_final: 0.6054 (t80)
REVERT: S  148 ARG cc_start: 0.6605 (mtm-85) cc_final: 0.6327 (mtm-85)
REVERT: S  168 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8006 (mtm110)
REVERT: R   99 MET cc_start: 0.7550 (mmt) cc_final: 0.7291 (mmp)
REVERT: R  183 LEU cc_start: 0.8109 (tp) cc_final: 0.7614 (tp)
REVERT: A   53 MET cc_start: 0.2779 (mpp) cc_final: 0.2491 (mtp)
REVERT: A  247 MET cc_start: 0.7469 (mmt) cc_final: 0.6325 (mmm)
REVERT: A  256 ASN cc_start: 0.8590 (m-40) cc_final: 0.8086 (m110)
REVERT: A  297 GLU cc_start: 0.8882 (pm20) cc_final: 0.8634 (pm20)
  outliers start: 33
  outliers final: 29
  residues processed: 171
  average time/residue: 0.0966
  time to fit residues: 23.1205
Evaluate side-chains
  174 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  194 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
S 219 GLN
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.144514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.118213 restraints weight = 21214.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.118181 restraints weight = 14732.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.119471 restraints weight = 11370.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.120423 restraints weight = 9678.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.120875 restraints weight = 8943.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.9249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8894  Z= 0.250
  Angle     :  0.824  13.344  12049  Z= 0.424
  Chirality :  0.048   0.215   1377
  Planarity :  0.005   0.041   1501
  Dihedral  :  5.719  46.687   1220
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 21.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 21.20 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -1.00 (0.25), residues: 1086
  helix:  0.23 (0.26), residues: 373
  sheet: -1.03 (0.32), residues: 273
  loop : -1.04 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.026   0.002   TYR B 105 
 PHE   0.024   0.002   PHE R 200 
 TRP   0.014   0.002   TRP S 164 
 HIS   0.008   0.002   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 8890)
  covalent geometry    : angle       0.81093 (12041)
  SS BOND              : bond        0.00317 (    4)
  SS BOND              : angle       5.82999 (    8)
  hydrogen bonds       : bond        0.05643 (  414)
  hydrogen bonds       : angle       5.81018 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 142
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6276 (mm-30)
REVERT: B  234 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6644 (m-80)
REVERT: B  260 GLU cc_start: 0.6447 (pt0) cc_final: 0.6044 (pm20)
REVERT: B  331 SER cc_start: 0.7985 (m) cc_final: 0.7614 (m)
REVERT: S   34 MET cc_start: 0.4740 (mtm) cc_final: 0.4475 (mtt)
REVERT: S  103 TYR cc_start: 0.6583 (t80) cc_final: 0.6101 (t80)
REVERT: S  148 ARG cc_start: 0.6684 (mtm-85) cc_final: 0.6449 (mtm-85)
REVERT: S  168 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8202 (mtm110)
REVERT: S  234 GLU cc_start: 0.8958 (tp30) cc_final: 0.8170 (pm20)
REVERT: R   99 MET cc_start: 0.7738 (mmt) cc_final: 0.7313 (mmp)
REVERT: R  171 MET cc_start: 0.8079 (tpp) cc_final: 0.7838 (tpp)
REVERT: R  183 LEU cc_start: 0.8100 (tp) cc_final: 0.7533 (tp)
REVERT: R  275 MET cc_start: 0.8275 (tmm) cc_final: 0.7543 (tmm)
REVERT: A   51 LYS cc_start: 0.9229 (pttp) cc_final: 0.8910 (pptt)
REVERT: A  256 ASN cc_start: 0.8586 (m-40) cc_final: 0.7981 (m110)
  outliers start: 49
  outliers final: 40
  residues processed: 175
  average time/residue: 0.0980
  time to fit residues: 23.8647
Evaluate side-chains
  178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 136
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  219 GLN
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   51 ILE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  122 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  331 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0270
   chunk 34 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0670
   chunk 76 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0870
   overall best weight:    0.3556

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

Flipped N/Q/H residues before XYZ refinement:
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.154162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.131677 restraints weight = 27242.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.134394 restraints weight = 16686.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.136563 restraints weight = 12085.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.137346 restraints weight = 9729.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.138891 restraints weight = 8675.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6258
moved from start:          0.9268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8894  Z= 0.133
  Angle     :  0.738  11.853  12049  Z= 0.375
  Chirality :  0.045   0.190   1377
  Planarity :  0.004   0.033   1501
  Dihedral  :  5.089  45.662   1220
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.03 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.51 (0.26), residues: 1086
  helix:  0.92 (0.27), residues: 371
  sheet: -0.79 (0.32), residues: 267
  loop : -1.03 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.010   0.001   TYR S 102 
 PHE   0.019   0.002   PHE S 165 
 TRP   0.016   0.002   TRP A 211 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8890)
  covalent geometry    : angle       0.72647 (12041)
  SS BOND              : bond        0.00268 (    4)
  SS BOND              : angle       5.09425 (    8)
  hydrogen bonds       : bond        0.04341 (  414)
  hydrogen bonds       : angle       5.31151 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6576 (mm-30)
REVERT: B  234 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6183 (m-80)
REVERT: B  300 LEU cc_start: 0.8281 (mp) cc_final: 0.7871 (tp)
REVERT: S   34 MET cc_start: 0.4489 (mtm) cc_final: 0.4253 (mtt)
REVERT: S  103 TYR cc_start: 0.6448 (t80) cc_final: 0.5984 (t80)
REVERT: S  148 ARG cc_start: 0.6407 (mtm-85) cc_final: 0.6141 (mtm-85)
REVERT: S  168 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8128 (mtm110)
REVERT: R   99 MET cc_start: 0.7541 (mmt) cc_final: 0.7296 (mmm)
REVERT: R  171 MET cc_start: 0.7664 (tpp) cc_final: 0.7215 (tpp)
REVERT: R  173 MET cc_start: 0.5431 (mmt) cc_final: 0.4664 (mmp)
REVERT: R  183 LEU cc_start: 0.8028 (tp) cc_final: 0.7511 (tp)
REVERT: R  275 MET cc_start: 0.7640 (tmm) cc_final: 0.7004 (tpp)
REVERT: A  247 MET cc_start: 0.7504 (mmt) cc_final: 0.6222 (mmm)
REVERT: A  256 ASN cc_start: 0.8433 (m-40) cc_final: 0.7962 (m110)
  outliers start: 22
  outliers final: 19
  residues processed: 178
  average time/residue: 0.0957
  time to fit residues: 23.8477
Evaluate side-chains
  164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue    4 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 0 optimal weight:   50.0000
   chunk 65 optimal weight:    0.8980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.150590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.122005 restraints weight = 20557.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.120863 restraints weight = 14773.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.121874 restraints weight = 11848.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.122394 restraints weight = 10137.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.123398 restraints weight = 9438.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.9468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8894  Z= 0.155
  Angle     :  0.792  15.222  12049  Z= 0.399
  Chirality :  0.045   0.203   1377
  Planarity :  0.004   0.038   1501
  Dihedral  :  5.135  46.962   1220
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.87 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.55 (0.26), residues: 1086
  helix:  0.82 (0.27), residues: 373
  sheet: -0.79 (0.32), residues: 274
  loop : -1.01 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.053   0.002   TYR S  59 
 PHE   0.040   0.002   PHE R 181 
 TRP   0.014   0.002   TRP S  47 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8890)
  covalent geometry    : angle       0.78077 (12041)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       5.22657 (    8)
  hydrogen bonds       : bond        0.04714 (  414)
  hydrogen bonds       : angle       5.38921 ( 1170)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  234 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6353 (m-80)
REVERT: B  284 LEU cc_start: 0.7868 (tt) cc_final: 0.7383 (mm)
REVERT: S  148 ARG cc_start: 0.6495 (mtm-85) cc_final: 0.6273 (mtm-85)
REVERT: S  168 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8139 (mtm110)
REVERT: R   64 LEU cc_start: 0.8332 (tt) cc_final: 0.8088 (tp)
REVERT: R   99 MET cc_start: 0.7580 (mmt) cc_final: 0.7309 (mmm)
REVERT: R  171 MET cc_start: 0.7799 (tpp) cc_final: 0.7594 (tpp)
REVERT: R  183 LEU cc_start: 0.8041 (tp) cc_final: 0.7613 (tp)
REVERT: R  275 MET cc_start: 0.8174 (tmm) cc_final: 0.7468 (tpp)
REVERT: A   53 MET cc_start: 0.4416 (mpp) cc_final: 0.4197 (mtp)
REVERT: A  247 MET cc_start: 0.7474 (mmt) cc_final: 0.6229 (mmm)
REVERT: A  256 ASN cc_start: 0.8512 (m-40) cc_final: 0.7970 (m110)
  outliers start: 26
  outliers final: 25
  residues processed: 166
  average time/residue: 0.0958
  time to fit residues: 22.2611
Evaluate side-chains
  175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  265 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain R residue   22 ILE
Chi-restraints excluded: chain R residue   36 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  104 ILE
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  177 VAL
Chi-restraints excluded: chain R residue  226 LYS
Chi-restraints excluded: chain R residue  237 LEU
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  246 SER
Chi-restraints excluded: chain R residue  287 LYS
Chi-restraints excluded: chain A residue    4 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 2 optimal weight:   40.0000
   chunk 90 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0670
   overall best weight:    0.8118

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

Flipped N/Q/H residues before XYZ refinement:
S 174 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.151514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.125989 restraints weight = 21396.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.125540 restraints weight = 14920.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.126822 restraints weight = 11009.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.127656 restraints weight = 9360.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.128269 restraints weight = 8482.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.9632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8894  Z= 0.134
  Angle     :  0.759  14.055  12049  Z= 0.382
  Chirality :  0.044   0.203   1377
  Planarity :  0.004   0.047   1501
  Dihedral  :  4.928  45.240   1220
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 24.45 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 aren not related in a simple way.
  whole: -0.40 (0.26), residues: 1086
  helix:  0.99 (0.27), residues: 375
  sheet: -0.67 (0.32), residues: 268
  loop : -1.00 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 313 
 TYR   0.044   0.001   TYR S  59 
 PHE   0.021   0.002   PHE R 167 
 TRP   0.013   0.002   TRP R 184 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8890)
  covalent geometry    : angle       0.74767 (12041)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       5.04053 (    8)
  hydrogen bonds       : bond        0.04427 (  414)
  hydrogen bonds       : angle       5.28337 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1997.70 seconds
wall clock time: 35 minutes 19.61 seconds (2119.61 seconds total)