Starting phenix.real_space_refine
on Thu Jul  2 07:11:45 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1u_32950/07_2026/7x1u_32950.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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      41      5.16       5
     C    4782      2.51       5
     N    1276      2.21       5
     O    1384      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7483
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 302
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
    Chain: "A"
      Number of atoms: 1918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1918
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 275
          Unresolved non-hydrogen angles: 352
          Unresolved non-hydrogen dihedrals: 246
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'TYR:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 3, 'HIS:plan': 1, 'ASP:plan': 3, 'TRP:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 5}
          Unresolved non-hydrogen planarities: 150
    Chain: "B"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1612
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 215}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 241
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 137
    Chain: "C"
      Number of atoms: 2269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2269
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Unresolved non-hydrogen bonds: 267
          Unresolved non-hydrogen angles: 326
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 9, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 193
    Chain: "D"
      Number of atoms: 1356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1356
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 10, 'TRANS': 197}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 253
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 212
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 157
    Chain: "E"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 25
          Classifications: {'peptide': 3}
          Link IDs: {'PCIS': 1, 'TRANS': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.56, per 1000 atoms: 0.21
  Number of scatterers: 7483
  At special positions: 0
  Unit cell: (85.6, 113.42, 125.19, 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      41     16.00
     O    1384      8.00
     N    1276      7.00
     C    4782      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 179 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 351.9 milliseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  PRO E   3 "
  Number of C-beta restraints generated:  2022

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 16 sheets defined
      29.0% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'F' and resid 12 through 17
      removed outlier: 3.574A  pdb=" N   GLU F  17 " --> pdb=" O   ARG F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 37
    Processing helix  chain 'F' and resid 38 through 41
    Processing helix  chain 'A' and resid 28 through 51
      removed outlier: 3.752A  pdb=" N   VAL A  32 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLY A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A  39 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A  40 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A  49 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 3.525A  pdb=" N   TYR A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A  64 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 59 through 64'
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 4.083A  pdb=" N   VAL A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 3.570A  pdb=" N   SER A  86 " --> pdb=" O   ASN A  82 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 3.628A  pdb=" N   ASN A 110 " --> pdb=" O   TYR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.695A  pdb=" N   ILE A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
      removed outlier: 3.865A  pdb=" N   PHE A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 136 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 131 through 136'
    Processing helix  chain 'A' and resid 138 through 155
      removed outlier: 4.160A  pdb=" N   LYS A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 4.212A  pdb=" N   PHE A 162 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 197
      removed outlier: 3.743A  pdb=" N   MET A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASP A 195 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 219
      removed outlier: 3.596A  pdb=" N   MET A 204 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR A 208 " --> pdb=" O   MET A 204 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A 213 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ILE A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.916A  pdb=" N   VAL A 271 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   TRP A 279 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 289
      removed outlier: 3.893A  pdb=" N   ARG A 283 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
      removed outlier: 4.679A  pdb=" N   ILE A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
      removed outlier: 3.579A  pdb=" N   ASN A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      Proline residue:  A 317  - end of helix
      removed outlier: 3.539A  pdb=" N   TYR A 320 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
      removed outlier: 3.507A  pdb=" N   ARG A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 20
      removed outlier: 3.753A  pdb=" N   ASP B  20 " --> pdb=" O   SER B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.901A  pdb=" N   ILE B  49 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.943A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 130
    Processing helix  chain 'B' and resid 145 through 148
    Processing helix  chain 'B' and resid 149 through 154
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.691A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
      removed outlier: 4.250A  pdb=" N   ALA B 168 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 165 through 168'
    Processing helix  chain 'B' and resid 183 through 202
      removed outlier: 3.770A  pdb=" N   ALA B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 236
      removed outlier: 4.259A  pdb=" N   ASP B 230 " --> pdb=" O   ARG B 226 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ASP B 233 " --> pdb=" O   ASN B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 243
      removed outlier: 3.549A  pdb=" N   TYR B 243 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 26
      removed outlier: 3.857A  pdb=" N   ILE C  18 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP C  20 " --> pdb=" O   ASN C  16 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA C  24 " --> pdb=" O   ASP C  20 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   CYS C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.728A  pdb=" N   SER D  31 " --> pdb=" O   ALA D  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171
      removed outlier: 3.971A  pdb=" N   ASN A 167 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 178 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA A 174 " --> pdb=" O   TYR A 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 76
      removed outlier: 3.957A  pdb=" N   LEU B  38 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 143 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 52
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62
      removed outlier: 3.992A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 105
      removed outlier: 3.581A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 120 through 121
    Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 157
      removed outlier: 3.666A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.903A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER C 201 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.791A  pdb=" N   PHE C 241 " --> pdb=" O   PHE C 253 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.354A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 319 through 320
    Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 34
      removed outlier: 3.950A  pdb=" N   SER D  99 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49
      removed outlier: 6.575A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 148
    Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163
    Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 166

    204 hydrogen bonds defined for protein.
    549 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: 0.99

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1227
        1.31 -     1.43: 2053
        1.43 -     1.56: 4283
        1.56 -     1.69: 7
        1.69 -     1.82: 53
  Bond restraints: 7623
  Sorted by residual:
  bond pdb=" C   PCA E   1 "
       pdb=" N   HIS E   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.499 -0.170 1.40e-02 5.10e+03 1.47e+02
  bond pdb=" C   HIS E   2 "
       pdb=" N   PRO E   3 "
    ideal  model  delta    sigma   weight residual
    1.341  1.507 -0.166 1.60e-02 3.91e+03 1.08e+02
  bond pdb=" CA  PRO E   3 "
       pdb=" CB  PRO E   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.352  0.178 2.00e-02 2.50e+03 7.95e+01
  bond pdb=" CA  PCA E   1 "
       pdb=" CB  PCA E   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.369  0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" N   PCA E   1 "
       pdb=" CA  PCA E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.590 -0.132 1.90e-02 2.77e+03 4.82e+01
  ... (remaining 7618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 10182
        2.74 -     5.48: 218
        5.48 -     8.21: 33
        8.21 -    10.95: 10
       10.95 -    13.69: 2
  Bond angle restraints: 10445
  Sorted by residual:
  angle pdb=" N   VAL A  49 "
        pdb=" CA  VAL A  49 "
        pdb=" C   VAL A  49 "
      ideal   model   delta    sigma   weight residual
     111.90  107.34    4.56 8.10e-01 1.52e+00 3.16e+01
  angle pdb=" N   TYR A 181 "
        pdb=" CA  TYR A 181 "
        pdb=" C   TYR A 181 "
      ideal   model   delta    sigma   weight residual
     108.23  115.97   -7.74 1.38e+00 5.25e-01 3.14e+01
  angle pdb=" N   VAL A 264 "
        pdb=" CA  VAL A 264 "
        pdb=" C   VAL A 264 "
      ideal   model   delta    sigma   weight residual
     112.83  107.32    5.51 9.90e-01 1.02e+00 3.10e+01
  angle pdb=" N   ILE B 227 "
        pdb=" CA  ILE B 227 "
        pdb=" C   ILE B 227 "
      ideal   model   delta    sigma   weight residual
     112.96  107.47    5.49 1.00e+00 1.00e+00 3.02e+01
  angle pdb=" C   ASP C 195 "
        pdb=" N   THR C 196 "
        pdb=" CA  THR C 196 "
      ideal   model   delta    sigma   weight residual
     121.54  132.01  -10.47 1.91e+00 2.74e-01 3.00e+01
  ... (remaining 10440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 3945
       16.39 -    32.78: 386
       32.78 -    49.17: 68
       49.17 -    65.56: 4
       65.56 -    81.95: 2
  Dihedral angle restraints: 4405
    sinusoidal: 1282
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" C   HIS E   2 "
           pdb=" N   HIS E   2 "
           pdb=" CA  HIS E   2 "
           pdb=" CB  HIS E   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.12   14.52     0      2.50e+00 1.60e-01 3.37e+01
  dihedral pdb=" CA  TYR D 223 "
           pdb=" C   TYR D 223 "
           pdb=" N   PRO D 224 "
           pdb=" CA  PRO D 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.86  -26.14     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE D 108 "
           pdb=" C   PHE D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.19  -25.81     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 4402 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.076: 1283
       1.076 -    2.151: 0
       2.151 -    3.226: 0
       3.226 -    4.302: 0
       4.302 -    5.377: 1
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  PRO E   3 "
            pdb=" N   PRO E   3 "
            pdb=" C   PRO E   3 "
            pdb=" CB  PRO E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72   -2.66    5.38 2.00e-01 2.50e+01 7.23e+02
  chirality pdb=" CA  HIS E   2 "
            pdb=" N   HIS E   2 "
            pdb=" C   HIS E   2 "
            pdb=" CB  HIS E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  PCA E   1 "
            pdb=" N   PCA E   1 "
            pdb=" C   PCA E   1 "
            pdb=" CB  PCA E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1331
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 316 "    0.058 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO A 317 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 187 "   -0.057 5.00e-02 4.00e+02   8.70e-02 1.21e+01
        pdb=" N   PRO D 188 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO D 188 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 188 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 223 "   -0.052 5.00e-02 4.00e+02   7.70e-02 9.48e+00
        pdb=" N   PRO D 224 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO D 224 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO D 224 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1328 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.16: 1
        2.16 -     2.85: 2708
        2.85 -     3.53: 9528
        3.53 -     4.22: 17568
        4.22 -     4.90: 29060
  Nonbonded interactions: 58865
  Sorted by model distance:
  nonbonded pdb=" C   PRO E   3 "
            pdb=" N   NH2 E   4 "
     model   vdw
     1.476 3.350
  nonbonded pdb=" NH2 ARG A 306 "
            pdb=" N   NH2 E   4 "
     model   vdw
     2.166 2.560
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" NE  ARG A 306 "
            pdb=" N   NH2 E   4 "
     model   vdw
     2.273 2.560
  nonbonded pdb=" OG  SER C 227 "
            pdb=" OD1 ASP C 228 "
     model   vdw
     2.281 3.040
  ... (remaining 58860 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.630
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.620
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
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      :  0.008   0.178   7625  Z= 0.427
  Angle     :  1.029  13.689  10447  Z= 0.574
  Chirality :  0.161   5.377   1284
  Planarity :  0.007   0.087   1331
  Dihedral  : 13.418  81.955   2380
  Min Nonbonded Distance : 1.476

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.74 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 10.09 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.61 (0.19), residues: 1047
  helix: -4.86 (0.12), residues: 294
  sheet: -3.25 (0.31), residues: 214
  loop : -3.23 (0.22), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 283 
 TYR   0.023   0.002   TYR C  59 
 PHE   0.024   0.003   PHE D  27 
 TRP   0.020   0.003   TRP D  36 
 HIS   0.010   0.002   HIS B  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00826 /  0.41 ( 7623)
  covalent geometry    : angle       1.02882 /  0.57 (10445)
  SS BOND              : bond        0.00088 /  0.05 (    1)
  SS BOND              : angle       1.51844 /  1.01 (    2)
  hydrogen bonds       : bond        0.31558 / 22.06 (  204)
  hydrogen bonds       : angle      11.76200 /  8.16 (  549)
  Misc. bond           : bond        0.10662 /  5.61 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 174
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   49 ARG cc_start: 0.7806 (mpt90) cc_final: 0.7289 (mpp-170)
REVERT: D  110 PHE cc_start: 0.7172 (t80) cc_final: 0.6694 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 177
  average time/residue: 0.0779
  time to fit residues: 18.5757
Evaluate side-chains
  136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain C residue  315 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6902

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  82 ASN
A 105 GLN
A 312 ASN
B  98 GLN
B 237 GLN
C  62 HIS
C  88 ASN
D 174 GLN
D 220 HIS
E   2 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.197478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.164032 restraints weight = 10674.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.4184 rms_B_bonded: 2.99
r_work: 0.4022 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7625  Z= 0.128
  Angle     :  0.683  17.461  10447  Z= 0.346
  Chirality :  0.045   0.206   1284
  Planarity :  0.006   0.069   1331
  Dihedral  :  6.314  28.556   1135
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.69 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.82 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.90 (0.21), residues: 1047
  helix: -3.96 (0.18), residues: 307
  sheet: -2.98 (0.29), residues: 241
  loop : -2.81 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 283 
 TYR   0.014   0.001   TYR D 102 
 PHE   0.021   0.001   PHE A 148 
 TRP   0.031   0.003   TRP D  47 
 HIS   0.006   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 7623)
  covalent geometry    : angle       0.68308 /  0.35 (10445)
  SS BOND              : bond        0.00094 /  0.05 (    1)
  SS BOND              : angle       0.40345 /  0.27 (    2)
  hydrogen bonds       : bond        0.04321 /  2.87 (  204)
  hydrogen bonds       : angle       7.01136 /  5.01 (  549)
  Misc. bond           : bond        0.00042 /  0.02 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  147 ILE cc_start: 0.8491 (mt) cc_final: 0.8286 (mm)
REVERT: A  216 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7678 (ttt180)
REVERT: A  310 TYR cc_start: 0.7761 (m-10) cc_final: 0.6847 (m-10)
REVERT: A  318 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8720 (m)
REVERT: B  232 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7731 (tttm)
REVERT: D  161 TYR cc_start: 0.6560 (m-80) cc_final: 0.6261 (m-80)
  outliers start: 20
  outliers final: 8
  residues processed: 160
  average time/residue: 0.0721
  time to fit residues: 16.2143
Evaluate side-chains
  142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 98 optimal weight:   30.0000
   chunk 91 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 3 optimal weight:    0.4980
   chunk 6 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  82 HIS
B  98 GLN
C 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.192440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.160240 restraints weight = 10633.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 2.80
r_work: 0.3959 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7625  Z= 0.187
  Angle     :  0.715  15.355  10447  Z= 0.357
  Chirality :  0.047   0.238   1284
  Planarity :  0.005   0.062   1331
  Dihedral  :  6.164  28.607   1134
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.83 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.11 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.46 (0.22), residues: 1047
  helix: -3.47 (0.20), residues: 316
  sheet: -2.76 (0.31), residues: 237
  loop : -2.59 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 306 
 TYR   0.021   0.002   TYR A 156 
 PHE   0.019   0.002   PHE A 148 
 TRP   0.029   0.003   TRP D  47 
 HIS   0.005   0.001   HIS B  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.19 ( 7623)
  covalent geometry    : angle       0.71513 /  0.36 (10445)
  SS BOND              : bond        0.00089 /  0.05 (    1)
  SS BOND              : angle       0.28632 /  0.19 (    2)
  hydrogen bonds       : bond        0.04074 /  2.73 (  204)
  hydrogen bonds       : angle       6.56275 /  4.72 (  549)
  Misc. bond           : bond        0.00069 /  0.04 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6569 (mm)
REVERT: A  310 TYR cc_start: 0.7791 (m-10) cc_final: 0.6882 (m-10)
REVERT: A  318 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8714 (m)
REVERT: B   25 GLU cc_start: 0.7864 (pt0) cc_final: 0.7522 (pt0)
REVERT: B  232 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7814 (tttm)
REVERT: C   49 ARG cc_start: 0.8237 (mpt90) cc_final: 0.7602 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6842 (t80)
REVERT: D  110 PHE cc_start: 0.7267 (t80) cc_final: 0.7001 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 162
  average time/residue: 0.0647
  time to fit residues: 15.0327
Evaluate side-chains
  157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 29 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 0 optimal weight:   50.0000
   chunk 8 optimal weight:    2.9990
   chunk 87 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  98 GLN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.194702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.162692 restraints weight = 10841.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 2.92
r_work: 0.4001 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7625  Z= 0.142
  Angle     :  0.653  13.850  10447  Z= 0.328
  Chirality :  0.045   0.242   1284
  Planarity :  0.005   0.057   1331
  Dihedral  :  5.777  29.373   1134
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 21.41 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.04 (0.23), residues: 1047
  helix: -2.96 (0.23), residues: 311
  sheet: -2.68 (0.31), residues: 239
  loop : -2.36 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.022   0.001   TYR A 156 
 PHE   0.024   0.002   PHE B 228 
 TRP   0.034   0.002   TRP D  47 
 HIS   0.005   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 7623)
  covalent geometry    : angle       0.65268 /  0.33 (10445)
  SS BOND              : bond        0.00051 /  0.03 (    1)
  SS BOND              : angle       0.20589 /  0.14 (    2)
  hydrogen bonds       : bond        0.03405 /  2.28 (  204)
  hydrogen bonds       : angle       6.22389 /  4.49 (  549)
  Misc. bond           : bond        0.00038 /  0.02 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6465 (mm)
REVERT: A  310 TYR cc_start: 0.7720 (m-10) cc_final: 0.6913 (m-10)
REVERT: A  318 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8643 (m)
REVERT: B   25 GLU cc_start: 0.7892 (pt0) cc_final: 0.7523 (pt0)
REVERT: B  142 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7130 (t80)
REVERT: B  232 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7747 (tttm)
REVERT: C   49 ARG cc_start: 0.8161 (mpt90) cc_final: 0.7511 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6876 (t80)
REVERT: D  110 PHE cc_start: 0.7364 (t80) cc_final: 0.6950 (t80)
  outliers start: 32
  outliers final: 22
  residues processed: 161
  average time/residue: 0.0637
  time to fit residues: 14.6954
Evaluate side-chains
  159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   98 GLN
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0570
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  88 ASN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.197768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.165047 restraints weight = 10761.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 2.95
r_work: 0.4036 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7625  Z= 0.110
  Angle     :  0.622  13.079  10447  Z= 0.311
  Chirality :  0.044   0.228   1284
  Planarity :  0.005   0.056   1331
  Dihedral  :  5.380  29.891   1134
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.06 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.48 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.24), residues: 1047
  helix: -2.50 (0.25), residues: 312
  sheet: -2.42 (0.33), residues: 222
  loop : -2.28 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 137 
 TYR   0.022   0.001   TYR A 156 
 PHE   0.018   0.001   PHE B 228 
 TRP   0.034   0.002   TRP D  47 
 HIS   0.004   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 7623)
  covalent geometry    : angle       0.62187 /  0.31 (10445)
  SS BOND              : bond        0.00078 /  0.04 (    1)
  SS BOND              : angle       0.33937 /  0.23 (    2)
  hydrogen bonds       : bond        0.03018 /  2.01 (  204)
  hydrogen bonds       : angle       5.89050 /  4.25 (  549)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6367 (mm)
REVERT: A  310 TYR cc_start: 0.7729 (m-10) cc_final: 0.7010 (m-10)
REVERT: A  318 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8519 (m)
REVERT: B   25 GLU cc_start: 0.7840 (pt0) cc_final: 0.7481 (pt0)
REVERT: B  142 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6978 (t80)
REVERT: C   49 ARG cc_start: 0.8084 (mpt90) cc_final: 0.7458 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6920 (t80)
REVERT: C  323 ASP cc_start: 0.7156 (p0) cc_final: 0.6367 (p0)
REVERT: D  110 PHE cc_start: 0.7142 (t80) cc_final: 0.6854 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 160
  average time/residue: 0.0686
  time to fit residues: 15.4433
Evaluate side-chains
  155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 4 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 53 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0470
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.3482

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.194803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.161070 restraints weight = 10767.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 3.13
r_work: 0.3978 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7625  Z= 0.146
  Angle     :  0.649  13.467  10447  Z= 0.323
  Chirality :  0.045   0.221   1284
  Planarity :  0.005   0.052   1331
  Dihedral  :  5.406  30.502   1134
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.78 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.55 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.52 (0.24), residues: 1047
  helix: -2.29 (0.26), residues: 313
  sheet: -2.43 (0.33), residues: 224
  loop : -2.23 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  52 
 TYR   0.025   0.001   TYR A 156 
 PHE   0.025   0.002   PHE B 228 
 TRP   0.036   0.002   TRP D  47 
 HIS   0.005   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 ( 7623)
  covalent geometry    : angle       0.64888 /  0.32 (10445)
  SS BOND              : bond        0.00059 /  0.03 (    1)
  SS BOND              : angle       0.25234 /  0.17 (    2)
  hydrogen bonds       : bond        0.03203 /  2.14 (  204)
  hydrogen bonds       : angle       5.84423 /  4.22 (  549)
  Misc. bond           : bond        0.00028 /  0.01 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6325 (mm)
REVERT: A  310 TYR cc_start: 0.7776 (m-10) cc_final: 0.6967 (m-10)
REVERT: B   25 GLU cc_start: 0.7894 (pt0) cc_final: 0.7542 (pt0)
REVERT: B  142 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7108 (t80)
REVERT: B  229 ASN cc_start: 0.7782 (p0) cc_final: 0.7502 (p0)
REVERT: C   49 ARG cc_start: 0.7924 (mpt90) cc_final: 0.7334 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6927 (t80)
REVERT: C  323 ASP cc_start: 0.7265 (p0) cc_final: 0.6430 (p0)
REVERT: D  110 PHE cc_start: 0.7176 (t80) cc_final: 0.6902 (t80)
  outliers start: 31
  outliers final: 23
  residues processed: 156
  average time/residue: 0.0659
  time to fit residues: 14.6381
Evaluate side-chains
  161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.194798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.162563 restraints weight = 10722.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 2.87
r_work: 0.4001 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7625  Z= 0.145
  Angle     :  0.650  13.284  10447  Z= 0.322
  Chirality :  0.045   0.232   1284
  Planarity :  0.004   0.050   1331
  Dihedral  :  5.374  30.923   1134
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.30 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 23.70 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.24), residues: 1047
  helix: -2.09 (0.26), residues: 313
  sheet: -2.35 (0.34), residues: 219
  loop : -2.14 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  52 
 TYR   0.026   0.001   TYR A 156 
 PHE   0.022   0.002   PHE A 148 
 TRP   0.041   0.003   TRP D  47 
 HIS   0.005   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 7623)
  covalent geometry    : angle       0.64959 /  0.32 (10445)
  SS BOND              : bond        0.00043 /  0.02 (    1)
  SS BOND              : angle       0.20312 /  0.14 (    2)
  hydrogen bonds       : bond        0.03128 /  2.10 (  204)
  hydrogen bonds       : angle       5.77074 /  4.17 (  549)
  Misc. bond           : bond        0.00017 /  0.01 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6332 (mm)
REVERT: A  310 TYR cc_start: 0.7724 (m-10) cc_final: 0.6840 (m-10)
REVERT: B   25 GLU cc_start: 0.7887 (pt0) cc_final: 0.7563 (pt0)
REVERT: B  142 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7360 (t80)
REVERT: B  229 ASN cc_start: 0.7772 (p0) cc_final: 0.7500 (p0)
REVERT: C   49 ARG cc_start: 0.7910 (mpt90) cc_final: 0.7355 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: C  339 TRP cc_start: 0.7096 (m100) cc_final: 0.6842 (m100)
REVERT: D  110 PHE cc_start: 0.7144 (t80) cc_final: 0.6838 (t80)
  outliers start: 34
  outliers final: 30
  residues processed: 162
  average time/residue: 0.0595
  time to fit residues: 14.0579
Evaluate side-chains
  166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   93 TYR
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 102 optimal weight:    0.0270
   chunk 4 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    2.2044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.190761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.158324 restraints weight = 10936.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 2.88
r_work: 0.3945 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7625  Z= 0.205
  Angle     :  0.708  13.780  10447  Z= 0.353
  Chirality :  0.047   0.227   1284
  Planarity :  0.005   0.053   1331
  Dihedral  :  5.691  30.550   1134
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.21 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 23.09 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.24), residues: 1047
  helix: -2.14 (0.26), residues: 312
  sheet: -2.31 (0.34), residues: 218
  loop : -2.14 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  52 
 TYR   0.028   0.002   TYR A 156 
 PHE   0.026   0.002   PHE B  84 
 TRP   0.044   0.003   TRP D  47 
 HIS   0.007   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.21 ( 7623)
  covalent geometry    : angle       0.70807 /  0.35 (10445)
  SS BOND              : bond        0.00020 /  0.01 (    1)
  SS BOND              : angle       0.48004 /  0.32 (    2)
  hydrogen bonds       : bond        0.03516 /  2.38 (  204)
  hydrogen bonds       : angle       5.97023 /  4.32 (  549)
  Misc. bond           : bond        0.00022 /  0.01 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6399 (mm)
REVERT: A  310 TYR cc_start: 0.7703 (m-10) cc_final: 0.6787 (m-10)
REVERT: B   25 GLU cc_start: 0.7989 (pt0) cc_final: 0.7650 (pt0)
REVERT: B  229 ASN cc_start: 0.7817 (p0) cc_final: 0.7545 (p0)
REVERT: C   49 ARG cc_start: 0.7996 (mpt90) cc_final: 0.7387 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6817 (t80)
REVERT: D  110 PHE cc_start: 0.7244 (t80) cc_final: 0.7030 (t80)
  outliers start: 40
  outliers final: 33
  residues processed: 156
  average time/residue: 0.0701
  time to fit residues: 15.9175
Evaluate side-chains
  164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    0.0970
   chunk 83 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  98 GLN
C 110 ASN
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.194184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.161021 restraints weight = 10836.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4159 rms_B_bonded: 2.96
r_work: 0.3979 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7625  Z= 0.140
  Angle     :  0.660  12.961  10447  Z= 0.329
  Chirality :  0.045   0.218   1284
  Planarity :  0.005   0.052   1331
  Dihedral  :  5.466  31.156   1134
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 24.62 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.25), residues: 1047
  helix: -1.92 (0.27), residues: 311
  sheet: -2.17 (0.35), residues: 208
  loop : -2.10 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  52 
 TYR   0.032   0.002   TYR C 111 
 PHE   0.023   0.002   PHE B  84 
 TRP   0.047   0.003   TRP D  47 
 HIS   0.005   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 7623)
  covalent geometry    : angle       0.65965 /  0.33 (10445)
  SS BOND              : bond        0.00069 /  0.04 (    1)
  SS BOND              : angle       0.12106 /  0.08 (    2)
  hydrogen bonds       : bond        0.03112 /  2.10 (  204)
  hydrogen bonds       : angle       5.75662 /  4.17 (  549)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6353 (mm)
REVERT: A  310 TYR cc_start: 0.7722 (m-10) cc_final: 0.6896 (m-10)
REVERT: B   25 GLU cc_start: 0.7949 (pt0) cc_final: 0.7613 (pt0)
REVERT: B  229 ASN cc_start: 0.7804 (p0) cc_final: 0.7534 (p0)
REVERT: C   49 ARG cc_start: 0.7942 (mpt90) cc_final: 0.7411 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6927 (t80)
REVERT: D  110 PHE cc_start: 0.7225 (t80) cc_final: 0.6904 (t80)
  outliers start: 32
  outliers final: 27
  residues processed: 157
  average time/residue: 0.0688
  time to fit residues: 15.5632
Evaluate side-chains
  160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.195723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.162334 restraints weight = 10742.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 3.06
r_work: 0.3991 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7625  Z= 0.128
  Angle     :  0.642  12.794  10447  Z= 0.320
  Chirality :  0.045   0.216   1284
  Planarity :  0.004   0.053   1331
  Dihedral  :  5.294  31.792   1134
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.40 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 24.92 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.25), residues: 1047
  helix: -1.67 (0.28), residues: 313
  sheet: -2.20 (0.33), residues: 214
  loop : -2.05 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  52 
 TYR   0.028   0.001   TYR A 156 
 PHE   0.026   0.002   PHE B  84 
 TRP   0.048   0.003   TRP D  47 
 HIS   0.005   0.001   HIS C 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 7623)
  covalent geometry    : angle       0.64201 /  0.32 (10445)
  SS BOND              : bond        0.00071 /  0.04 (    1)
  SS BOND              : angle       0.19990 /  0.13 (    2)
  hydrogen bonds       : bond        0.02973 /  1.98 (  204)
  hydrogen bonds       : angle       5.60651 /  4.06 (  549)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  166 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6345 (mm)
REVERT: A  310 TYR cc_start: 0.7701 (m-10) cc_final: 0.6906 (m-10)
REVERT: B   21 LYS cc_start: 0.6905 (tptm) cc_final: 0.5532 (pttt)
REVERT: B   25 GLU cc_start: 0.7915 (pt0) cc_final: 0.7589 (pt0)
REVERT: B  229 ASN cc_start: 0.7796 (p0) cc_final: 0.7542 (p0)
REVERT: C   49 ARG cc_start: 0.7877 (mpt90) cc_final: 0.7326 (mpp-170)
REVERT: C  234 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6897 (t80)
  outliers start: 30
  outliers final: 27
  residues processed: 155
  average time/residue: 0.0704
  time to fit residues: 15.7114
Evaluate side-chains
  161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain D residue   80 PHE
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
                        ^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
                  ^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
           ^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites
    pair_proxies = self.pair_proxies(
                   ^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 65.3408 > 50:
  distance: 42 - 44:  12.551
  distance: 44 - 45:  28.013
  distance: 45 - 46:  41.073
  distance: 45 - 48:  57.392
  distance: 46 - 47:  30.471
  distance: 46 - 49:  41.707
  distance: 49 - 50:  12.690
  distance: 50 - 51:  36.651
  distance: 50 - 53:  41.183
  distance: 51 - 52:  19.636
  distance: 51 - 57:  13.100
  distance: 52 - 76:  44.310
  distance: 53 - 54:  31.252
  distance: 54 - 55:  37.945
  distance: 54 - 56:  26.227
  distance: 57 - 58:  27.417
  distance: 57 - 63:  12.176
  distance: 58 - 59:  26.112
  distance: 58 - 61:  25.396
  distance: 59 - 60:   5.814
  distance: 59 - 64:  18.446
  distance: 60 - 83:  31.895
  distance: 61 - 62:  44.012
  distance: 62 - 63:  28.312
  distance: 64 - 65:  18.229
  distance: 65 - 66:  40.431
  distance: 65 - 68:  22.582
  distance: 66 - 67:  24.322
  distance: 66 - 69:  23.343
  distance: 69 - 70:  30.354
  distance: 70 - 71:  35.352
  distance: 70 - 73:   9.274
  distance: 71 - 72:  14.130
  distance: 71 - 76:   3.429
  distance: 72 - 93:  28.289
  distance: 73 - 74:  41.369
  distance: 73 - 75:  18.786
  distance: 76 - 77:  16.979
  distance: 77 - 78:  22.566
  distance: 77 - 80:   3.307
  distance: 78 - 79:  12.933
  distance: 78 - 83:  17.889
  distance: 79 - 102:  24.482
  distance: 80 - 81:  32.899
  distance: 80 - 82:  37.766
  distance: 83 - 84:  18.538
  distance: 84 - 85:  15.355
  distance: 84 - 87:  20.276
  distance: 85 - 86:  24.593
  distance: 85 - 88:  24.566
  distance: 86 - 114:  31.025
  distance: 88 - 89:  18.487
  distance: 89 - 90:  15.319
  distance: 89 - 92:  32.879
  distance: 90 - 91:  25.013
  distance: 90 - 93:  19.183
  distance: 91 - 121:  21.077
  distance: 93 - 94:   4.937
  distance: 94 - 95:   8.589
  distance: 94 - 97:  17.993
  distance: 95 - 96:  21.871
  distance: 97 - 98:  27.814
  distance: 98 - 99:  33.330
  distance: 99 - 100:  24.832
  distance: 100 - 101:  24.985
  distance: 102 - 103:   5.590
  distance: 103 - 104:  11.766
  distance: 103 - 106:   9.206
  distance: 104 - 105:  11.961
  distance: 104 - 114:  26.321
  distance: 105 - 135:  34.418
  distance: 106 - 107:   8.498
  distance: 107 - 108:  25.697
  distance: 107 - 109:  10.234
  distance: 108 - 110:   9.710
  distance: 109 - 111:  13.336
  distance: 110 - 112:  12.758
  distance: 111 - 112:  11.880
  distance: 112 - 113:  16.870