Starting phenix.real_space_refine
on Mon May 12 04:13:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vuq_43536/05_2025/8vuq_43536.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5500      2.51       5
     N    1492      2.21       5
     O    1629      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8657
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2789
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 2697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2697
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 15, 'TRANS': 347}
          Unresolved non-hydrogen bonds: 190
          Unresolved non-hydrogen angles: 236
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 125
    Chain: "G"
      Number of atoms: 1617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1617
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "I"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1554
          Classifications: {'peptide': 209}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 6.92, per 1000 atoms: 0.80
  Number of scatterers: 8657
  At special positions: 0
  Unit cell: (107, 113.848, 124.976, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1629      8.00
     N    1492      7.00
     C    5500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B 320 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 149 " - pdb=" SG  CYS G 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  91 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I 134 " - pdb=" SG  CYS I 193 " 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: 2.38
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 19 sheets defined
      24.9% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 53
      removed outlier: 3.570A  pdb=" N   ARG A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   HIS A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 82
      removed outlier: 3.937A  pdb=" N   CYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 99 through 103
      removed outlier: 3.554A  pdb=" N   PHE A 102 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR A 103 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 99 through 103'
    Processing helix  chain 'A' and resid 105 through 113
      removed outlier: 3.506A  pdb=" N   PHE A 113 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 158
      removed outlier: 3.797A  pdb=" N   VAL A 150 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TRP A 151 " --> pdb=" O   GLN A 147 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   PHE A 152 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL A 157 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 185
      removed outlier: 3.518A  pdb=" N   GLN A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LYS A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 188
      No H-bonds generated for 'chain 'A' and resid 186 through 188'
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.659A  pdb=" N   GLU A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLU A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 238
      removed outlier: 3.502A  pdb=" N   ALA A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 255
      removed outlier: 3.757A  pdb=" N   ILE A 254 " --> pdb=" O   GLY A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 297
      removed outlier: 3.832A  pdb=" N   SER A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   HIS A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU A 294 " --> pdb=" O   GLN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 328
    Processing helix  chain 'B' and resid 78 through 92
    Processing helix  chain 'B' and resid 107 through 119
      removed outlier: 4.095A  pdb=" N   GLN B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 3.613A  pdb=" N   SER B 132 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET B 133 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 133'
    Processing helix  chain 'B' and resid 150 through 166
    Processing helix  chain 'B' and resid 179 through 194
      removed outlier: 3.933A  pdb=" N   PHE B 183 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 219
      removed outlier: 4.312A  pdb=" N   GLN B 216 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL B 217 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 246
      removed outlier: 3.675A  pdb=" N   SER B 245 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU B 246 " --> pdb=" O   GLU B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 310
      removed outlier: 3.672A  pdb=" N   ARG B 293 " --> pdb=" O   GLU B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 339
      removed outlier: 3.872A  pdb=" N   VAL B 339 " --> pdb=" O   PRO B 336 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 165 through 167
      No H-bonds generated for 'chain 'G' and resid 165 through 167'
    Processing helix  chain 'G' and resid 196 through 198
      No H-bonds generated for 'chain 'G' and resid 196 through 198'
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 3.768A  pdb=" N   ASN I  32 " --> pdb=" O   ILE I  29 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
      removed outlier: 3.751A  pdb=" N   ALA I 127 " --> pdb=" O   GLU I 123 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 181 through 188
      removed outlier: 3.749A  pdb=" N   HIS I 188 " --> pdb=" O   GLN I 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33
      removed outlier: 3.502A  pdb=" N   LEU A  33 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91
      removed outlier: 6.734A  pdb=" N   ILE A  90 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL A 118 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197
      removed outlier: 3.731A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE A 197 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341
      removed outlier: 3.734A  pdb=" N   ASN A 341 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLY A 344 " --> pdb=" O   ASN A 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72
      removed outlier: 7.047A  pdb=" N   ALA B  37 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU B  98 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200
      removed outlier: 3.878A  pdb=" N   PHE B 170 " --> pdb=" O   ASP B 199 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL B 226 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   TRP B 255 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   VAL B 279 " --> pdb=" O   TRP B 255 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 364 " --> pdb=" O   SER B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 342
      removed outlier: 3.572A  pdb=" N   VAL B 341 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU B 348 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7
      removed outlier: 3.857A  pdb=" N   LEU G  81 " --> pdb=" O   LEU G  20 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER G  78 " --> pdb=" O   ASP G  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60
      removed outlier: 3.551A  pdb=" N   GLY G  59 " --> pdb=" O   GLY G  50 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TRP G  47 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ARG G  38 " --> pdb=" O   TRP G  47 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER G  49 " --> pdb=" O   TRP G  36 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET G  34 " --> pdb=" O   ILE G  51 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ALA G  97 " --> pdb=" O   HIS G  35 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 133
      removed outlier: 4.285A  pdb=" N   GLY G 148 " --> pdb=" O   LEU G 133 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL G 193 " --> pdb=" O   ALA G 145 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU G 147 " --> pdb=" O   VAL G 191 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   TYR G 185 " --> pdb=" O   ASP G 153 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL G 190 " --> pdb=" O   HIS G 173 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 133
      removed outlier: 4.285A  pdb=" N   GLY G 148 " --> pdb=" O   LEU G 133 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL G 193 " --> pdb=" O   ALA G 145 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU G 147 " --> pdb=" O   VAL G 191 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   TYR G 185 " --> pdb=" O   ASP G 153 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER G 186 " --> pdb=" O   VAL G 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 159 through 163
    Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12
      removed outlier: 6.762A  pdb=" N   VAL I  10 " --> pdb=" O   THR I 104 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASP I  88 " --> pdb=" O   GLN I  39 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLN I  39 " --> pdb=" O   ASP I  88 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR I  90 " --> pdb=" O   TYR I  37 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   TRP I  36 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL I  48 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20
      removed outlier: 4.072A  pdb=" N   VAL I  18 " --> pdb=" O   ILE I  78 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE I  78 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER I  66 " --> pdb=" O   SER I  75 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'I' and resid 114 through 118
      removed outlier: 6.057A  pdb=" N   TYR I 172 " --> pdb=" O   ASP I 138 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'I' and resid 114 through 118
      removed outlier: 6.057A  pdb=" N   TYR I 172 " --> pdb=" O   ASP I 138 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA I 173 " --> pdb=" O   SER I 165 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 155
      removed outlier: 4.065A  pdb=" N   TRP I 148 " --> pdb=" O   VAL I 155 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS I 149 " --> pdb=" O   SER I 192 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER I 192 " --> pdb=" O   LYS I 149 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    768 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: 2.44

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2801
        1.34 -     1.46: 2083
        1.46 -     1.58: 3917
        1.58 -     1.70: 2
        1.70 -     1.82: 60
  Bond restraints: 8863
  Sorted by residual:
  bond pdb=" CB  PRO G 156 "
       pdb=" CG  PRO G 156 "
    ideal  model  delta    sigma   weight residual
    1.506  1.587 -0.081 3.90e-02 6.57e+02 4.28e+00
  bond pdb=" N   PRO G 156 "
       pdb=" CA  PRO G 156 "
    ideal  model  delta    sigma   weight residual
    1.468  1.435  0.033 1.70e-02 3.46e+03 3.80e+00
  bond pdb=" CG  PRO G 156 "
       pdb=" CD  PRO G 156 "
    ideal  model  delta    sigma   weight residual
    1.512  1.472  0.040 2.70e-02 1.37e+03 2.18e+00
  bond pdb=" CB  PRO A 304 "
       pdb=" CG  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.492  1.562 -0.070 5.00e-02 4.00e+02 1.93e+00
  bond pdb=" CA  ASN I  53 "
       pdb=" CB  ASN I  53 "
    ideal  model  delta    sigma   weight residual
    1.539  1.598 -0.058 4.88e-02 4.20e+02 1.43e+00
  ... (remaining 8858 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 12010
        2.82 -     5.64: 74
        5.64 -     8.47: 8
        8.47 -    11.29: 1
       11.29 -    14.11: 1
  Bond angle restraints: 12094
  Sorted by residual:
  angle pdb=" CA  PRO G 156 "
        pdb=" N   PRO G 156 "
        pdb=" CD  PRO G 156 "
      ideal   model   delta    sigma   weight residual
     111.50   97.39   14.11 1.40e+00 5.10e-01 1.02e+02
  angle pdb=" C   THR I  83 "
        pdb=" CA  THR I  83 "
        pdb=" CB  THR I  83 "
      ideal   model   delta    sigma   weight residual
     116.54  110.04    6.50 1.15e+00 7.56e-01 3.19e+01
  angle pdb=" N   PRO G 156 "
        pdb=" CD  PRO G 156 "
        pdb=" CG  PRO G 156 "
      ideal   model   delta    sigma   weight residual
     103.80   98.76    5.04 1.20e+00 6.94e-01 1.76e+01
  angle pdb=" CA  THR I  83 "
        pdb=" C   THR I  83 "
        pdb=" N   GLU I  84 "
      ideal   model   delta    sigma   weight residual
     119.52  116.77    2.75 7.90e-01 1.60e+00 1.21e+01
  angle pdb=" CA  PRO A 304 "
        pdb=" N   PRO A 304 "
        pdb=" CD  PRO A 304 "
      ideal   model   delta    sigma   weight residual
     112.00  107.37    4.63 1.40e+00 5.10e-01 1.09e+01
  ... (remaining 12089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4498
       17.96 -    35.91: 566
       35.91 -    53.87: 147
       53.87 -    71.82: 24
       71.82 -    89.78: 12
  Dihedral angle restraints: 5247
    sinusoidal: 1891
      harmonic: 3356
  Sorted by residual:
  dihedral pdb=" CA  ASP A 169 "
           pdb=" C   ASP A 169 "
           pdb=" N   ASP A 170 "
           pdb=" CA  ASP A 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  PRO A 142 "
           pdb=" C   PRO A 142 "
           pdb=" N   PRO A 143 "
           pdb=" CA  PRO A 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ASP I 138 "
           pdb=" CB  ASP I 138 "
           pdb=" CG  ASP I 138 "
           pdb=" OD1 ASP I 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.25   58.25     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 5244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 802
       0.029 -    0.058: 393
       0.058 -    0.087: 105
       0.087 -    0.117: 82
       0.117 -    0.146: 15
  Chirality restraints: 1397
  Sorted by residual:
  chirality pdb=" CB  THR G  91 "
            pdb=" CA  THR G  91 "
            pdb=" OG1 THR G  91 "
            pdb=" CG2 THR G  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  ILE B 227 "
            pdb=" N   ILE B 227 "
            pdb=" C   ILE B 227 "
            pdb=" CB  ILE B 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  VAL G  40 "
            pdb=" N   VAL G  40 "
            pdb=" C   VAL G  40 "
            pdb=" CB  VAL G  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 1394 not shown)

  Planarity restraints: 1541
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G 155 "   -0.089 5.00e-02 4.00e+02   1.24e-01 2.46e+01
        pdb=" N   PRO G 156 "    0.213 5.00e-02 4.00e+02
        pdb=" CA  PRO G 156 "   -0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO G 156 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 303 "   -0.045 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO A 304 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 304 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 304 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 318 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO A 319 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 319 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 319 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1538 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 245
        2.69 -     3.24: 8282
        3.24 -     3.79: 12495
        3.79 -     4.35: 15199
        4.35 -     4.90: 26229
  Nonbonded interactions: 62450
  Sorted by model distance:
  nonbonded pdb=" O   ASN I  53 "
            pdb=" ND2 ASN I  53 "
     model   vdw
     2.133 3.120
  nonbonded pdb=" O   MET I   3 "
            pdb=" OG  SER I  25 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   PHE B 195 "
            pdb=" N   GLY B 197 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" OG  SER A  93 "
            pdb=" OE2 GLU A 277 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLN B 154 "
            pdb=" OG  SER B 259 "
     model   vdw
     2.216 3.040
  ... (remaining 62445 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:             8.460
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.260
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
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      :  0.003   0.081   8869  Z= 0.121
  Angle     :  0.615  14.112  12106  Z= 0.328
  Chirality :  0.042   0.146   1397
  Planarity :  0.005   0.124   1541
  Dihedral  : 17.334  89.781   3071
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 12.06 %
    Favored  : 87.51 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 35.83 %
    Favored  : 63.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.26), residues: 1153
  helix:  0.75 (0.37), residues: 218
  sheet: -1.03 (0.32), residues: 317
  loop : -1.89 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 284 
 HIS   0.005   0.001   HIS B 332 
 PHE   0.009   0.001   PHE B 210 
 TYR   0.021   0.001   TYR B 321 
 ARG   0.004   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27234 (  251)
  hydrogen bonds       : angle       8.89198 (  768)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       0.37306 (   12)
  covalent geometry    : bond        0.00287 ( 8863)
  covalent geometry    : angle       0.61563 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 132
  average time/residue: 0.2132
  time to fit residues: 38.7039
Evaluate side-chains
  127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  338 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0970
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0270
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0570
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.4154

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

Flipped N/Q/H residues before XYZ refinement:
I  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.153100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.114994 restraints weight = 15656.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111625 restraints weight = 16576.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113165 restraints weight = 17248.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8869  Z= 0.117
  Angle     :  0.587   7.991  12106  Z= 0.306
  Chirality :  0.043   0.136   1397
  Planarity :  0.004   0.079   1541
  Dihedral  :  4.098  22.399   1244
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 11.10 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 29.33 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.26), residues: 1153
  helix:  0.87 (0.35), residues: 246
  sheet: -0.88 (0.32), residues: 321
  loop : -2.05 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 284 
 HIS   0.004   0.001   HIS B 332 
 PHE   0.012   0.001   PHE B 210 
 TYR   0.012   0.001   TYR B 321 
 ARG   0.003   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04869 (  251)
  hydrogen bonds       : angle       5.88839 (  768)
  SS BOND              : bond        0.00348 (    6)
  SS BOND              : angle       0.77239 (   12)
  covalent geometry    : bond        0.00258 ( 8863)
  covalent geometry    : angle       0.58636 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8132 (ptm160)
REVERT: A  162 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6919 (m90)
REVERT: A  295 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8925 (tp)
REVERT: A  392 TYR cc_start: 0.6715 (m-10) cc_final: 0.6146 (m-10)
REVERT: G   49 SER cc_start: 0.8861 (p) cc_final: 0.8419 (m)
REVERT: G  180 GLN cc_start: 0.5780 (pm20) cc_final: 0.3659 (tm-30)
REVERT: I   53 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7859 (p0)
  outliers start: 48
  outliers final: 23
  residues processed: 172
  average time/residue: 0.1972
  time to fit residues: 47.6032
Evaluate side-chains
  146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  162 HIS
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  162 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
I   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112803 restraints weight = 15936.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110848 restraints weight = 16435.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.112119 restraints weight = 15098.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8869  Z= 0.118
  Angle     :  0.570   7.444  12106  Z= 0.294
  Chirality :  0.043   0.143   1397
  Planarity :  0.004   0.067   1541
  Dihedral  :  4.064  23.165   1241
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 11.27 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 28.67 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.26), residues: 1153
  helix:  0.76 (0.34), residues: 256
  sheet: -0.92 (0.32), residues: 311
  loop : -2.04 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 160 
 HIS   0.002   0.000   HIS G 173 
 PHE   0.016   0.001   PHE A 152 
 TYR   0.012   0.001   TYR B 321 
 ARG   0.003   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  251)
  hydrogen bonds       : angle       5.43760 (  768)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.65729 (   12)
  covalent geometry    : bond        0.00271 ( 8863)
  covalent geometry    : angle       0.57010 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 132
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8068 (ptm160)
REVERT: B  206 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7806 (pp)
REVERT: B  348 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (pp)
REVERT: B  378 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7687 (t60)
REVERT: G   49 SER cc_start: 0.9048 (p) cc_final: 0.8531 (m)
  outliers start: 54
  outliers final: 32
  residues processed: 168
  average time/residue: 0.1921
  time to fit residues: 45.5055
Evaluate side-chains
  158 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  162 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0030
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.0994

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
I  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.150669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111806 restraints weight = 15806.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.108651 restraints weight = 16944.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.109987 restraints weight = 18178.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8869  Z= 0.147
  Angle     :  0.588   7.717  12106  Z= 0.301
  Chirality :  0.044   0.352   1397
  Planarity :  0.004   0.061   1541
  Dihedral  :  4.201  22.480   1241
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 12.84 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 28.45 %
    Favored  : 64.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.26), residues: 1153
  helix:  0.74 (0.34), residues: 251
  sheet: -0.95 (0.31), residues: 323
  loop : -2.03 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP I 148 
 HIS   0.007   0.001   HIS A 293 
 PHE   0.016   0.001   PHE A 152 
 TYR   0.023   0.001   TYR B 180 
 ARG   0.004   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  251)
  hydrogen bonds       : angle       5.23477 (  768)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       0.82154 (   12)
  covalent geometry    : bond        0.00346 ( 8863)
  covalent geometry    : angle       0.58734 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 132
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8150 (ptm160)
REVERT: B  206 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7848 (pp)
REVERT: B  207 ASP cc_start: 0.8362 (p0) cc_final: 0.8039 (p0)
REVERT: B  348 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8778 (pp)
REVERT: B  378 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7807 (t60)
REVERT: G   49 SER cc_start: 0.8997 (p) cc_final: 0.8535 (m)
REVERT: I   53 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7991 (p0)
  outliers start: 62
  outliers final: 45
  residues processed: 180
  average time/residue: 0.1923
  time to fit residues: 48.5917
Evaluate side-chains
  175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 125
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue   28 THR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    0.0470
   chunk 6 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 112 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
I  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.151868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.113035 restraints weight = 15727.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110994 restraints weight = 15940.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111891 restraints weight = 16076.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8869  Z= 0.121
  Angle     :  0.580   7.205  12106  Z= 0.295
  Chirality :  0.043   0.287   1397
  Planarity :  0.004   0.056   1541
  Dihedral  :  4.162  22.333   1241
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 11.45 %
    Favored  : 88.12 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 28.67 %
    Favored  : 64.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.26), residues: 1153
  helix:  0.76 (0.34), residues: 253
  sheet: -1.02 (0.31), residues: 322
  loop : -2.00 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I 148 
 HIS   0.007   0.001   HIS A 293 
 PHE   0.013   0.001   PHE A 152 
 TYR   0.013   0.001   TYR B 321 
 ARG   0.004   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  251)
  hydrogen bonds       : angle       4.98760 (  768)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       0.75808 (   12)
  covalent geometry    : bond        0.00288 ( 8863)
  covalent geometry    : angle       0.57956 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 133
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8186 (ptm160)
REVERT: B  206 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (pp)
REVERT: B  207 ASP cc_start: 0.8385 (p0) cc_final: 0.8038 (p0)
REVERT: B  348 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8771 (pp)
REVERT: B  378 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.7791 (t60)
REVERT: I   53 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7879 (p0)
  outliers start: 62
  outliers final: 46
  residues processed: 181
  average time/residue: 0.1883
  time to fit residues: 48.2859
Evaluate side-chains
  179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 128
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  134 CYS
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    0.1980
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0070
   chunk 83 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
I  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111738 restraints weight = 15687.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110393 restraints weight = 15637.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.111492 restraints weight = 15115.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8869  Z= 0.124
  Angle     :  0.589   7.324  12106  Z= 0.298
  Chirality :  0.043   0.258   1397
  Planarity :  0.004   0.052   1541
  Dihedral  :  4.161  21.972   1241
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 12.14 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 28.78 %
    Favored  : 64.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.26), residues: 1153
  helix:  0.89 (0.34), residues: 247
  sheet: -1.05 (0.31), residues: 311
  loop : -1.95 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I 148 
 HIS   0.006   0.001   HIS A 293 
 PHE   0.028   0.001   PHE B 186 
 TYR   0.018   0.001   TYR B 180 
 ARG   0.005   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  251)
  hydrogen bonds       : angle       4.82441 (  768)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       0.75497 (   12)
  covalent geometry    : bond        0.00294 ( 8863)
  covalent geometry    : angle       0.58872 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 134
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8194 (ptm160)
REVERT: B  206 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7800 (pp)
REVERT: B  207 ASP cc_start: 0.8451 (p0) cc_final: 0.8136 (p0)
REVERT: B  348 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8783 (pp)
REVERT: B  378 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.7813 (t60)
REVERT: I   53 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7965 (p0)
  outliers start: 61
  outliers final: 48
  residues processed: 182
  average time/residue: 0.2028
  time to fit residues: 51.0757
Evaluate side-chains
  178 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 125
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  150 SER
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue   28 THR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   52 ASP
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 111 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0020
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
B 111 GLN
I  53 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.152468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.112998 restraints weight = 15797.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111576 restraints weight = 14379.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.112600 restraints weight = 14863.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8869  Z= 0.113
  Angle     :  0.593   7.711  12106  Z= 0.298
  Chirality :  0.043   0.248   1397
  Planarity :  0.004   0.051   1541
  Dihedral  :  4.149  21.612   1241
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  : 11.36 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 29.88 %
    Favored  : 64.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.26), residues: 1153
  helix:  0.98 (0.34), residues: 245
  sheet: -1.02 (0.31), residues: 312
  loop : -1.98 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I 148 
 HIS   0.007   0.001   HIS A 293 
 PHE   0.011   0.001   PHE A 152 
 TYR   0.013   0.001   TYR B 321 
 ARG   0.005   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03407 (  251)
  hydrogen bonds       : angle       4.71915 (  768)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       0.78321 (   12)
  covalent geometry    : bond        0.00268 ( 8863)
  covalent geometry    : angle       0.59317 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 132
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8222 (ptm160)
REVERT: B  206 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7706 (pp)
REVERT: B  207 ASP cc_start: 0.8423 (p0) cc_final: 0.8105 (p0)
REVERT: B  348 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: B  378 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7671 (t60)
REVERT: G  154 TYR cc_start: 0.5747 (p90) cc_final: 0.5326 (p90)
REVERT: I   53 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (p0)
  outliers start: 53
  outliers final: 42
  residues processed: 170
  average time/residue: 0.1888
  time to fit residues: 45.2597
Evaluate side-chains
  174 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 127
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   52 ASP
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.0470
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
B 119 HIS
I  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.152591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.112956 restraints weight = 15911.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111347 restraints weight = 14527.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112453 restraints weight = 14904.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8869  Z= 0.117
  Angle     :  0.590   7.841  12106  Z= 0.297
  Chirality :  0.043   0.239   1397
  Planarity :  0.004   0.049   1541
  Dihedral  :  4.138  21.731   1241
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 11.54 %
    Favored  : 87.94 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 29.88 %
    Favored  : 63.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.26), residues: 1153
  helix:  1.01 (0.35), residues: 245
  sheet: -1.02 (0.31), residues: 315
  loop : -1.96 (0.25), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 284 
 HIS   0.003   0.000   HIS G 173 
 PHE   0.010   0.001   PHE A 152 
 TYR   0.019   0.001   TYR B 180 
 ARG   0.006   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03389 (  251)
  hydrogen bonds       : angle       4.65888 (  768)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       1.01604 (   12)
  covalent geometry    : bond        0.00279 ( 8863)
  covalent geometry    : angle       0.58895 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 130
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8234 (ptm160)
REVERT: B  206 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7722 (pp)
REVERT: B  207 ASP cc_start: 0.8413 (p0) cc_final: 0.8118 (p0)
REVERT: B  348 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8753 (pp)
REVERT: B  378 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7697 (t60)
REVERT: G  154 TYR cc_start: 0.5825 (p90) cc_final: 0.5358 (p90)
REVERT: I   53 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (p0)
  outliers start: 59
  outliers final: 47
  residues processed: 175
  average time/residue: 0.1895
  time to fit residues: 46.6081
Evaluate side-chains
  179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 127
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  164 ASN
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0370
   chunk 68 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 HIS
I  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.152804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.113996 restraints weight = 15795.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112770 restraints weight = 15343.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.113747 restraints weight = 15066.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   8869  Z= 0.118
  Angle     :  0.604   8.252  12106  Z= 0.304
  Chirality :  0.043   0.234   1397
  Planarity :  0.004   0.048   1541
  Dihedral  :  4.160  22.954   1241
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 11.27 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 30.54 %
    Favored  : 63.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.25), residues: 1153
  helix:  1.02 (0.34), residues: 245
  sheet: -1.07 (0.30), residues: 325
  loop : -1.97 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 284 
 HIS   0.003   0.000   HIS G 173 
 PHE   0.012   0.001   PHE B 115 
 TYR   0.015   0.001   TYR G  80 
 ARG   0.007   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  251)
  hydrogen bonds       : angle       4.59176 (  768)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       1.11494 (   12)
  covalent geometry    : bond        0.00289 ( 8863)
  covalent geometry    : angle       0.60364 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 131
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8166 (ptm160)
REVERT: B  206 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7740 (pp)
REVERT: B  207 ASP cc_start: 0.8335 (p0) cc_final: 0.8029 (p0)
REVERT: B  348 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8735 (pp)
REVERT: B  378 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7706 (t60)
REVERT: I   53 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7891 (p0)
  outliers start: 58
  outliers final: 51
  residues processed: 175
  average time/residue: 0.1851
  time to fit residues: 45.7993
Evaluate side-chains
  183 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 127
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  346 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  382 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue   28 THR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   53 ASN
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  136 ILE
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 19 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0070
   chunk 48 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.2798

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
B 119 HIS
B 340 ASN
I  53 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.153984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.115031 restraints weight = 15716.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.112577 restraints weight = 15473.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113918 restraints weight = 15690.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8869  Z= 0.108
  Angle     :  0.594   8.519  12106  Z= 0.298
  Chirality :  0.043   0.234   1397
  Planarity :  0.004   0.048   1541
  Dihedral  :  4.117  22.324   1241
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 10.58 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 31.20 %
    Favored  : 62.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.26), residues: 1153
  helix:  1.08 (0.35), residues: 245
  sheet: -0.98 (0.31), residues: 310
  loop : -1.93 (0.25), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 284 
 HIS   0.004   0.001   HIS B 119 
 PHE   0.009   0.001   PHE B 115 
 TYR   0.020   0.001   TYR B 180 
 ARG   0.007   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03159 (  251)
  hydrogen bonds       : angle       4.50568 (  768)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       1.01515 (   12)
  covalent geometry    : bond        0.00252 ( 8863)
  covalent geometry    : angle       0.59342 (12094)

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 137
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8242 (ptm160)
REVERT: B  206 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7732 (pp)
REVERT: B  207 ASP cc_start: 0.8354 (p0) cc_final: 0.8076 (p0)
REVERT: B  348 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8769 (pp)
REVERT: B  378 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7639 (t60)
REVERT: G  154 TYR cc_start: 0.5790 (p90) cc_final: 0.5370 (p90)
REVERT: G  180 GLN cc_start: 0.5731 (pm20) cc_final: 0.3447 (tm-30)
  outliers start: 53
  outliers final: 41
  residues processed: 176
  average time/residue: 0.2084
  time to fit residues: 51.5021
Evaluate side-chains
  173 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 128
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  139 ARG
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  160 TRP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   42 HIS
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  251 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  378 TRP
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  393 TYR
Chi-restraints excluded: chain G residue  118 VAL
Chi-restraints excluded: chain G residue  178 VAL
Chi-restraints excluded: chain G residue  187 LEU
Chi-restraints excluded: chain I residue   34 VAL
Chi-restraints excluded: chain I residue   35 GLN
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   63 PHE
Chi-restraints excluded: chain I residue   66 SER
Chi-restraints excluded: chain I residue  202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 92 optimal weight:   30.0000
   chunk 94 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0370
   chunk 83 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.9862

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.151486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112012 restraints weight = 15931.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.109998 restraints weight = 14659.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110930 restraints weight = 15378.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8869  Z= 0.144
  Angle     :  0.625   8.399  12106  Z= 0.316
  Chirality :  0.044   0.223   1397
  Planarity :  0.004   0.046   1541
  Dihedral  :  4.232  22.245   1241
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 12.06 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 31.09 %
    Favored  : 62.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.25), residues: 1153
  helix:  0.96 (0.34), residues: 246
  sheet: -1.04 (0.30), residues: 323
  loop : -1.98 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 284 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.017   0.001   PHE B 115 
 TYR   0.027   0.001   TYR G 105 
 ARG   0.007   0.000   ARG G  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  251)
  hydrogen bonds       : angle       4.63799 (  768)
  SS BOND              : bond        0.00442 (    6)
  SS BOND              : angle       0.98302 (   12)
  covalent geometry    : bond        0.00350 ( 8863)
  covalent geometry    : angle       0.62443 (12094)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2989.99 seconds
wall clock time: 53 minutes 16.95 seconds (3196.95 seconds total)