Starting phenix.real_space_refine
on Fri Jun  6 08:06:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hti_35010/06_2025/8hti_35010_neut.cif"
  }
  resolution = 2.97
  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=   0.024 sd=   0.080
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      51      5.16       5
     C    4757      2.51       5
     N    1274      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7390
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1311
          Classifications: {'peptide': 157}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 155}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2454
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 49
    Chain: "G"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 364
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "N"
      Number of atoms: 848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 848
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "R"
      Number of atoms: 2403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2403
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 17, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'OCA': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  OCA R 401 " occ=0.00
      ... (8 atoms not shown)
      pdb=" O2  OCA R 401 " occ=0.00
  Time building chain proxies: 5.63, per 1000 atoms: 0.76
  Number of scatterers: 7390
  At special positions: 0
  Unit cell: (82.547, 95.312, 133.607, 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      51     16.00
     O    1308      8.00
     N    1274      7.00
     C    4757      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  99 " - pdb=" SG  CYS R 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 171 " - pdb=" SG  CYS R 191 " 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: 1.77
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      39.5% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.539A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.739A  pdb=" N   CYS A 223 " --> pdb=" O   TRP A 220 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN A 225 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
    Processing helix  chain 'A' and resid 325 through 336
      removed outlier: 3.590A  pdb=" N   ILE A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 377
    Processing helix  chain 'B' and resid 10 through 26
      removed outlier: 3.612A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.587A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 11 through 23
    Processing helix  chain 'G' and resid 30 through 44
      removed outlier: 3.558A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.744A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 26
      removed outlier: 3.882A  pdb=" N   HIS R  26 " --> pdb=" O   GLU R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 54
      removed outlier: 4.285A  pdb=" N   PHE R  33 " --> pdb=" O   ILE R  29 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA R  35 " --> pdb=" O   ILE R  31 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASN R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   SER R  45 " --> pdb=" O   LEU R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 78
      removed outlier: 3.530A  pdb=" N   THR R  77 " --> pdb=" O   LEU R  73 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER R  78 " --> pdb=" O   VAL R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 90
    Processing helix  chain 'R' and resid 96 through 130
    Processing helix  chain 'R' and resid 133 through 138
    Processing helix  chain 'R' and resid 139 through 159
    Processing helix  chain 'R' and resid 159 through 166
      removed outlier: 4.567A  pdb=" N   PHE R 163 " --> pdb=" O   ILE R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 182 through 188
      removed outlier: 3.771A  pdb=" N   VAL R 186 " --> pdb=" O   GLU R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 194 through 228
      removed outlier: 3.607A  pdb=" N   GLY R 210 " --> pdb=" O   LEU R 206 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LEU R 211 " --> pdb=" O   LEU R 207 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 267
      removed outlier: 4.233A  pdb=" N   LYS R 238 " --> pdb=" O   ASP R 234 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU R 240 " --> pdb=" O   ARG R 236 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   SER R 245 " --> pdb=" O   SER R 241 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
      removed outlier: 4.397A  pdb=" N   ARG R 265 " --> pdb=" O   PHE R 261 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY R 267 " --> pdb=" O   THR R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 271 through 280
      removed outlier: 3.670A  pdb=" N   HIS R 275 " --> pdb=" O   PRO R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 295
      removed outlier: 3.596A  pdb=" N   MET R 288 " --> pdb=" O   LEU R 284 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing helix  chain 'R' and resid 298 through 310
      removed outlier: 3.739A  pdb=" N   ARG R 302 " --> pdb=" O   THR R 298 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU R 303 " --> pdb=" O   LYS R 299 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ARG R 304 " --> pdb=" O   GLN R 300 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE R 309 " --> pdb=" O   VAL R 305 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199
      removed outlier: 3.588A  pdb=" N   PHE A 208 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 9.884A  pdb=" N   ALA A 229 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   ILE A 231 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL A 233 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE A 230 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   PHE A 276 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   PHE A 232 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.858A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 7.080A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.742A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.783A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.205A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.786A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.543A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.573A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 93 through 95
      removed outlier: 8.244A  pdb=" N   ILE R 176 " --> pdb=" O   SER R  13 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU R  15 " --> pdb=" O   ILE R 176 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1008 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: 2.07

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2367
        1.34 -     1.46: 1821
        1.46 -     1.58: 3291
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 7551
  Sorted by residual:
  bond pdb=" N   ASP B 312 "
       pdb=" CA  ASP B 312 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.35e-02 5.49e+03 6.24e+00
  bond pdb=" N   HIS R 183 "
       pdb=" CA  HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.24e-02 6.50e+03 5.42e+00
  bond pdb=" CE1 HIS R 183 "
       pdb=" NE2 HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.86e+00
  bond pdb=" C   HIS R 183 "
       pdb=" O   HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.012 1.19e-02 7.06e+03 9.35e-01
  bond pdb=" CA  ILE R 159 "
       pdb=" C   ILE R 159 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.05e-02 9.07e+03 8.68e-01
  ... (remaining 7546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 9911
        1.45 -     2.90: 294
        2.90 -     4.35: 32
        4.35 -     5.81: 10
        5.81 -     7.26: 5
  Bond angle restraints: 10252
  Sorted by residual:
  angle pdb=" N   ILE R 159 "
        pdb=" CA  ILE R 159 "
        pdb=" C   ILE R 159 "
      ideal   model   delta    sigma   weight residual
     108.88  114.86   -5.98 2.16e+00 2.14e-01 7.66e+00
  angle pdb=" C   HIS R  10 "
        pdb=" N   PRO R  11 "
        pdb=" CA  PRO R  11 "
      ideal   model   delta    sigma   weight residual
     120.03  122.72   -2.69 9.90e-01 1.02e+00 7.38e+00
  angle pdb=" N   ASP B 312 "
        pdb=" CA  ASP B 312 "
        pdb=" C   ASP B 312 "
      ideal   model   delta    sigma   weight residual
     113.38  110.28    3.10 1.23e+00 6.61e-01 6.34e+00
  angle pdb=" N   GLY B 306 "
        pdb=" CA  GLY B 306 "
        pdb=" C   GLY B 306 "
      ideal   model   delta    sigma   weight residual
     110.38  114.03   -3.65 1.48e+00 4.57e-01 6.09e+00
  angle pdb=" CA  HIS R 183 "
        pdb=" C   HIS R 183 "
        pdb=" O   HIS R 183 "
      ideal   model   delta    sigma   weight residual
     120.55  117.99    2.56 1.07e+00 8.73e-01 5.73e+00
  ... (remaining 10247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 3913
       17.74 -    35.49: 418
       35.49 -    53.23: 96
       53.23 -    70.98: 18
       70.98 -    88.72: 7
  Dihedral angle restraints: 4452
    sinusoidal: 1657
      harmonic: 2795
  Sorted by residual:
  dihedral pdb=" CB  CYS R 171 "
           pdb=" SG  CYS R 171 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -134.25   48.25     1      1.00e+01 1.00e-02 3.21e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.96  -22.04     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASP R 123 "
           pdb=" CB  ASP R 123 "
           pdb=" CG  ASP R 123 "
           pdb=" OD1 ASP R 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.16   59.16     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 4449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 774
       0.036 -    0.073: 309
       0.073 -    0.109: 76
       0.109 -    0.146: 28
       0.146 -    0.182: 1
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CB  ILE R 159 "
            pdb=" CA  ILE R 159 "
            pdb=" CG1 ILE R 159 "
            pdb=" CG2 ILE R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CA  PHE R 109 "
            pdb=" N   PHE R 109 "
            pdb=" C   PHE R 109 "
            pdb=" CB  PHE R 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.68e-01
  ... (remaining 1185 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 159 "    0.042 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO R 160 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO R 160 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 160 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 286 "    0.042 5.00e-02 4.00e+02   6.26e-02 6.27e+00
        pdb=" N   PRO R 287 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 287 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 287 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.12e+00
        pdb=" N   PRO B 236 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1874
        2.80 -     3.33: 6272
        3.33 -     3.85: 11515
        3.85 -     4.38: 13093
        4.38 -     4.90: 24242
  Nonbonded interactions: 56996
  Sorted by model distance:
  nonbonded pdb=" O   ASN N  77 "
            pdb=" OD1 ASN N  77 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER R 114 "
            pdb=" OD2 ASP R 212 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NE2 GLN G  18 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   ILE R 276 "
            pdb=" ND2 ASN R 280 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   SER R   8 "
            pdb=" OG  SER R   8 "
     model   vdw
     2.342 3.040
  ... (remaining 56991 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.120
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.250
  Find NCS groups from input model:        0.080
  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:12.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7554  Z= 0.167
  Angle     :  0.603   7.257  10258  Z= 0.341
  Chirality :  0.043   0.182   1188
  Planarity :  0.005   0.064   1288
  Dihedral  : 15.486  88.721   2633
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.04 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.28), residues: 940
  helix:  1.81 (0.30), residues: 345
  sheet:  0.26 (0.37), residues: 201
  loop : -1.35 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 339 
 HIS   0.006   0.001   HIS R 178 
 PHE   0.021   0.001   PHE A 259 
 TYR   0.016   0.002   TYR N 117 
 ARG   0.003   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14097 (  348)
  hydrogen bonds       : angle       5.79338 ( 1008)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.96062 (    6)
  covalent geometry    : bond        0.00360 ( 7551)
  covalent geometry    : angle       0.60289 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.866 
Fit side-chains
REVERT: B  294 CYS cc_start: 0.8392 (p) cc_final: 0.8171 (m)
REVERT: G   19 LEU cc_start: 0.8130 (mt) cc_final: 0.7906 (mm)
REVERT: R    9 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 1.2923
  time to fit residues: 145.6424
Evaluate side-chains
  91 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
A 376 GLN
R 107 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.111990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.094999 restraints weight = 12235.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.96
r_work: 0.3207 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.0888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7554  Z= 0.136
  Angle     :  0.546   7.061  10258  Z= 0.286
  Chirality :  0.043   0.142   1188
  Planarity :  0.005   0.061   1288
  Dihedral  :  4.150  28.943   1042
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.00 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.28), residues: 940
  helix:  2.14 (0.30), residues: 342
  sheet:  0.33 (0.38), residues: 200
  loop : -1.18 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 220 
 HIS   0.005   0.001   HIS R 178 
 PHE   0.016   0.001   PHE R 109 
 TYR   0.011   0.001   TYR N 117 
 ARG   0.009   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05252 (  348)
  hydrogen bonds       : angle       4.45194 ( 1008)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       1.50097 (    6)
  covalent geometry    : bond        0.00317 ( 7551)
  covalent geometry    : angle       0.54476 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8394 (tp-100)
REVERT: B   96 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7114 (ttt-90)
REVERT: B  101 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8431 (ptm)
REVERT: B  294 CYS cc_start: 0.8525 (p) cc_final: 0.8103 (p)
REVERT: R   93 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7500 (tm-30)
REVERT: R  304 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.5951 (mpp80)
  outliers start: 22
  outliers final: 6
  residues processed: 111
  average time/residue: 1.2508
  time to fit residues: 146.9215
Evaluate side-chains
  103 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   93 GLU
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0870
   chunk 19 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0370
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.113966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.096974 restraints weight = 12396.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.99
r_work: 0.3243 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   7554  Z= 0.099
  Angle     :  0.487   6.919  10258  Z= 0.254
  Chirality :  0.041   0.135   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  3.877  28.246   1042
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.40 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 940
  helix:  2.49 (0.30), residues: 341
  sheet:  0.33 (0.37), residues: 211
  loop : -1.19 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.014   0.001   PHE R 109 
 TYR   0.009   0.001   TYR R 134 
 ARG   0.003   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  348)
  hydrogen bonds       : angle       4.11879 ( 1008)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       1.19107 (    6)
  covalent geometry    : bond        0.00212 ( 7551)
  covalent geometry    : angle       0.48593 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8431 (tp-100)
REVERT: B   52 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7678 (ptp90)
REVERT: B   96 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7089 (ttt-90)
REVERT: B  101 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8442 (ptm)
REVERT: B  294 CYS cc_start: 0.8485 (p) cc_final: 0.8062 (p)
REVERT: R  304 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5860 (mpp80)
REVERT: R  307 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7493 (ttmm)
  outliers start: 25
  outliers final: 7
  residues processed: 114
  average time/residue: 1.0918
  time to fit residues: 132.2360
Evaluate side-chains
  109 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  179 THR
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.112573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.095829 restraints weight = 12246.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.93
r_work: 0.3224 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7554  Z= 0.120
  Angle     :  0.516   7.100  10258  Z= 0.267
  Chirality :  0.042   0.133   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  3.971  27.671   1042
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.10 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.28), residues: 940
  helix:  2.44 (0.30), residues: 343
  sheet:  0.55 (0.37), residues: 209
  loop : -1.27 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.021   0.001   PHE R  89 
 TYR   0.011   0.001   TYR R 134 
 ARG   0.004   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  348)
  hydrogen bonds       : angle       4.07242 ( 1008)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       1.18981 (    6)
  covalent geometry    : bond        0.00280 ( 7551)
  covalent geometry    : angle       0.51528 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8436 (tp-100)
REVERT: A  371 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7999 (mtp-110)
REVERT: B   52 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7647 (ptp90)
REVERT: B   96 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7057 (ttt-90)
REVERT: B  101 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8449 (ptm)
REVERT: B  294 CYS cc_start: 0.8471 (p) cc_final: 0.8031 (p)
REVERT: R   26 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7660 (m170)
REVERT: R  304 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5714 (mpp80)
REVERT: R  307 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7441 (ttmm)
  outliers start: 25
  outliers final: 8
  residues processed: 115
  average time/residue: 1.1816
  time to fit residues: 143.7126
Evaluate side-chains
  109 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.094313 restraints weight = 12318.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.96
r_work: 0.3199 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7554  Z= 0.144
  Angle     :  0.545   7.359  10258  Z= 0.285
  Chirality :  0.043   0.144   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  4.165  30.165   1042
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.84 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.28), residues: 940
  helix:  2.31 (0.29), residues: 347
  sheet:  0.63 (0.37), residues: 200
  loop : -1.23 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 220 
 HIS   0.005   0.001   HIS R 275 
 PHE   0.016   0.001   PHE R 109 
 TYR   0.012   0.001   TYR A 344 
 ARG   0.004   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04980 (  348)
  hydrogen bonds       : angle       4.09153 ( 1008)
  SS BOND              : bond        0.00172 (    3)
  SS BOND              : angle       1.19655 (    6)
  covalent geometry    : bond        0.00346 ( 7551)
  covalent geometry    : angle       0.54460 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 1.008 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8454 (tp-100)
REVERT: A  371 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8000 (mtm110)
REVERT: B   52 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7663 (ptp90)
REVERT: B   96 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7085 (ttt-90)
REVERT: B  101 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8496 (ptm)
REVERT: B  128 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7085 (m)
REVERT: B  156 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8624 (mt0)
REVERT: B  294 CYS cc_start: 0.8525 (p) cc_final: 0.8068 (p)
REVERT: R   26 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7681 (m170)
REVERT: R  304 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.5810 (mpp80)
REVERT: R  307 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7421 (ttmm)
  outliers start: 27
  outliers final: 13
  residues processed: 113
  average time/residue: 1.1915
  time to fit residues: 142.7498
Evaluate side-chains
  116 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 6 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 55 optimal weight:    0.3980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.112339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.095603 restraints weight = 12273.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.95
r_work: 0.3221 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7554  Z= 0.108
  Angle     :  0.498   6.931  10258  Z= 0.262
  Chirality :  0.042   0.134   1188
  Planarity :  0.004   0.056   1288
  Dihedral  :  4.044  29.597   1042
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.49 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.28), residues: 940
  helix:  2.49 (0.29), residues: 347
  sheet:  0.38 (0.36), residues: 212
  loop : -1.22 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.023   0.001   PHE R  89 
 TYR   0.010   0.001   TYR R 134 
 ARG   0.005   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  348)
  hydrogen bonds       : angle       3.99823 ( 1008)
  SS BOND              : bond        0.00206 (    3)
  SS BOND              : angle       1.08968 (    6)
  covalent geometry    : bond        0.00242 ( 7551)
  covalent geometry    : angle       0.49791 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8429 (tp-100)
REVERT: A   34 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8501 (ttpp)
REVERT: A  371 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7977 (mtm110)
REVERT: B   52 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7671 (ptp90)
REVERT: B   96 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7064 (ttt-90)
REVERT: B  101 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8450 (ptm)
REVERT: B  128 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7117 (m)
REVERT: B  251 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7939 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8501 (p) cc_final: 0.8015 (p)
REVERT: G   19 LEU cc_start: 0.7828 (mt) cc_final: 0.7608 (mm)
REVERT: R   26 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7725 (m170)
REVERT: R  304 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.5751 (mpp80)
REVERT: R  307 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7393 (ttmm)
  outliers start: 23
  outliers final: 9
  residues processed: 109
  average time/residue: 1.3116
  time to fit residues: 151.1696
Evaluate side-chains
  110 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 56 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.094391 restraints weight = 12370.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.96
r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7554  Z= 0.135
  Angle     :  0.534   7.182  10258  Z= 0.278
  Chirality :  0.043   0.141   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  4.156  32.063   1042
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.84 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 940
  helix:  2.40 (0.29), residues: 347
  sheet:  0.52 (0.37), residues: 201
  loop : -1.25 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.016   0.001   PHE R 109 
 TYR   0.012   0.001   TYR A 344 
 ARG   0.004   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04812 (  348)
  hydrogen bonds       : angle       4.04151 ( 1008)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       1.13319 (    6)
  covalent geometry    : bond        0.00323 ( 7551)
  covalent geometry    : angle       0.53312 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8451 (tp-100)
REVERT: A   34 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8483 (ttpp)
REVERT: A  371 ARG cc_start: 0.8343 (mtt90) cc_final: 0.7949 (mtm110)
REVERT: B   52 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7673 (ptp90)
REVERT: B   96 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7078 (ttt-90)
REVERT: B  101 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8448 (ptm)
REVERT: B  251 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7967 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8500 (p) cc_final: 0.8230 (m)
REVERT: B  336 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8816 (mp)
REVERT: R   26 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7723 (m170)
REVERT: R  304 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.5846 (mpp80)
REVERT: R  307 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7403 (ttmm)
  outliers start: 30
  outliers final: 14
  residues processed: 111
  average time/residue: 1.1200
  time to fit residues: 131.9520
Evaluate side-chains
  116 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.092468 restraints weight = 12436.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.96
r_work: 0.3167 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7554  Z= 0.189
  Angle     :  0.594   7.525  10258  Z= 0.311
  Chirality :  0.045   0.153   1188
  Planarity :  0.005   0.057   1288
  Dihedral  :  4.544  40.981   1042
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.36 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.27), residues: 940
  helix:  2.11 (0.29), residues: 345
  sheet:  0.56 (0.36), residues: 204
  loop : -1.34 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  63 
 HIS   0.007   0.001   HIS R 275 
 PHE   0.020   0.002   PHE R 109 
 TYR   0.012   0.002   TYR R 134 
 ARG   0.004   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05733 (  348)
  hydrogen bonds       : angle       4.21151 ( 1008)
  SS BOND              : bond        0.00168 (    3)
  SS BOND              : angle       1.24005 (    6)
  covalent geometry    : bond        0.00466 ( 7551)
  covalent geometry    : angle       0.59372 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8412 (tp-100)
REVERT: A   34 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8500 (ttpp)
REVERT: A  371 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7954 (mtm110)
REVERT: B   52 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7671 (ptp90)
REVERT: B   96 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7097 (ttt-90)
REVERT: B  101 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8565 (ptm)
REVERT: B  251 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8002 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8527 (p) cc_final: 0.8255 (m)
REVERT: B  336 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8808 (mp)
REVERT: R   26 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7803 (m170)
REVERT: R  304 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.5788 (mpp80)
REVERT: R  307 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7301 (ttmm)
  outliers start: 24
  outliers final: 14
  residues processed: 112
  average time/residue: 1.0892
  time to fit residues: 129.7750
Evaluate side-chains
  117 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.110742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.093906 restraints weight = 12480.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.96
r_work: 0.3192 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7554  Z= 0.136
  Angle     :  0.540   7.230  10258  Z= 0.285
  Chirality :  0.043   0.141   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  4.408  44.272   1042
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.02 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 940
  helix:  2.31 (0.29), residues: 345
  sheet:  0.54 (0.36), residues: 211
  loop : -1.33 (0.28), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.016   0.001   PHE R 109 
 TYR   0.014   0.001   TYR A 344 
 ARG   0.005   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04955 (  348)
  hydrogen bonds       : angle       4.12503 ( 1008)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       1.11037 (    6)
  covalent geometry    : bond        0.00320 ( 7551)
  covalent geometry    : angle       0.53948 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8455 (tp-100)
REVERT: A  371 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7959 (mtm110)
REVERT: B   52 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7710 (ptp90)
REVERT: B   96 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7085 (ttt-90)
REVERT: B  101 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8457 (ptm)
REVERT: B  251 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7941 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8499 (p) cc_final: 0.8189 (m)
REVERT: B  336 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8793 (mp)
REVERT: R   26 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7712 (m170)
REVERT: R  304 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5821 (mpp80)
REVERT: R  307 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7400 (ttmm)
  outliers start: 23
  outliers final: 11
  residues processed: 108
  average time/residue: 1.1901
  time to fit residues: 136.5962
Evaluate side-chains
  112 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 82 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.111516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094559 restraints weight = 12510.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.02
r_work: 0.3201 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7554  Z= 0.120
  Angle     :  0.521   7.100  10258  Z= 0.274
  Chirality :  0.042   0.134   1188
  Planarity :  0.004   0.058   1288
  Dihedral  :  4.325  47.322   1042
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.28 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.28), residues: 940
  helix:  2.43 (0.29), residues: 345
  sheet:  0.40 (0.36), residues: 210
  loop : -1.26 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.015   0.001   PHE R 109 
 TYR   0.009   0.001   TYR R 134 
 ARG   0.006   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  348)
  hydrogen bonds       : angle       4.04168 ( 1008)
  SS BOND              : bond        0.00196 (    3)
  SS BOND              : angle       1.06837 (    6)
  covalent geometry    : bond        0.00276 ( 7551)
  covalent geometry    : angle       0.52024 (10252)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8461 (tp-100)
REVERT: A  371 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7986 (mtm110)
REVERT: B   52 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7690 (ptp90)
REVERT: B   96 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7114 (ttt-90)
REVERT: B  101 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8468 (ptm)
REVERT: B  251 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8008 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8503 (p) cc_final: 0.8203 (m)
REVERT: B  336 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8789 (mp)
REVERT: R   26 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7694 (m170)
REVERT: R  304 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.5761 (mpp80)
REVERT: R  307 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7466 (ttmm)
  outliers start: 19
  outliers final: 13
  residues processed: 110
  average time/residue: 1.1823
  time to fit residues: 137.8851
Evaluate side-chains
  115 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 68 optimal weight:    0.2980
   chunk 91 optimal weight:    0.8980
   chunk 54 optimal weight:    0.3980
   chunk 81 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.111917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095273 restraints weight = 12383.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.94
r_work: 0.3215 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7554  Z= 0.113
  Angle     :  0.513   6.876  10258  Z= 0.271
  Chirality :  0.042   0.133   1188
  Planarity :  0.004   0.057   1288
  Dihedral  :  4.295  48.408   1042
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.07 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.28), residues: 940
  helix:  2.47 (0.29), residues: 345
  sheet:  0.42 (0.36), residues: 210
  loop : -1.24 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 220 
 HIS   0.003   0.001   HIS R 275 
 PHE   0.024   0.001   PHE R  89 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.006   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04461 (  348)
  hydrogen bonds       : angle       4.01857 ( 1008)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       1.03445 (    6)
  covalent geometry    : bond        0.00254 ( 7551)
  covalent geometry    : angle       0.51286 (10252)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5886.53 seconds
wall clock time: 101 minutes 7.56 seconds (6067.56 seconds total)