Starting phenix.real_space_refine
on Thu Jun 12 02:31:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fdu_29014/06_2025/8fdu_29014.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      76      5.16       5
     C    8326      2.51       5
     N    2317      2.21       5
     O    2470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13193
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8141
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1001, 8141
          Classifications: {'peptide': 1001}
          Link IDs: {'PTRANS': 50, 'TRANS': 950}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2499
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 11, 'TRANS': 304}
    Chain: "C"
      Number of atoms: 2499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2499
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 11, 'TRANS': 304}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {'ADP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.44, per 1000 atoms: 0.72
  Number of scatterers: 13193
  At special positions: 0
  Unit cell: (96.516, 147.072, 122.943, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      76     16.00
     P       4     15.00
     O    2470      8.00
     N    2317      7.00
     C    8326      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.42
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3100

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 20 sheets defined
      39.9% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1116 through 1132
      removed outlier: 3.525A  pdb=" N   GLU A1132 " --> pdb=" O   THR A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1157
      removed outlier: 3.668A  pdb=" N   ALA A1156 " --> pdb=" O   SER A1152 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A1157 " --> pdb=" O   ALA A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1172 through 1184
      removed outlier: 4.262A  pdb=" N   LEU A1176 " --> pdb=" O   THR A1172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1234
    Processing helix  chain 'A' and resid 1269 through 1274
      removed outlier: 3.618A  pdb=" N   ARG A1274 " --> pdb=" O   HIS A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1285 through 1301
      removed outlier: 3.621A  pdb=" N   PHE A1296 " --> pdb=" O   ILE A1292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1302 through 1304
      No H-bonds generated for 'chain 'A' and resid 1302 through 1304'
    Processing helix  chain 'A' and resid 1307 through 1309
      No H-bonds generated for 'chain 'A' and resid 1307 through 1309'
    Processing helix  chain 'A' and resid 1310 through 1329
      removed outlier: 3.577A  pdb=" N   ALA A1316 " --> pdb=" O   GLU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1355
      removed outlier: 3.809A  pdb=" N   MET A1344 " --> pdb=" O   SER A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1379
    Processing helix  chain 'A' and resid 1384 through 1403
      removed outlier: 3.512A  pdb=" N   ARG A1388 " --> pdb=" O   GLU A1384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1407 through 1412
    Processing helix  chain 'A' and resid 1430 through 1449
      removed outlier: 3.613A  pdb=" N   GLU A1447 " --> pdb=" O   LYS A1443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1457 through 1473
      removed outlier: 3.584A  pdb=" N   GLN A1473 " --> pdb=" O   ARG A1469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1499
    Processing helix  chain 'A' and resid 1513 through 1529
    Processing helix  chain 'A' and resid 1546 through 1560
      removed outlier: 3.667A  pdb=" N   LEU A1550 " --> pdb=" O   ASP A1546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1568 through 1586
    Processing helix  chain 'A' and resid 1591 through 1606
    Processing helix  chain 'A' and resid 1618 through 1627
      removed outlier: 3.858A  pdb=" N   ASP A1622 " --> pdb=" O   GLU A1618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1633
    Processing helix  chain 'A' and resid 1643 through 1655
    Processing helix  chain 'A' and resid 1683 through 1709
      removed outlier: 3.685A  pdb=" N   ASN A1690 " --> pdb=" O   GLU A1686 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   HIS A1700 " --> pdb=" O   HIS A1696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1717 through 1765
      removed outlier: 3.632A  pdb=" N   TYR A1721 " --> pdb=" O   THR A1717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1950 through 1980
      removed outlier: 3.841A  pdb=" N   GLU A1963 " --> pdb=" O   SER A1959 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ARG A1966 " --> pdb=" O   ALA A1962 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LYS A1975 " --> pdb=" O   SER A1971 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   ASN A1976 " --> pdb=" O   GLU A1972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1980 through 1994
      removed outlier: 3.553A  pdb=" N   ASP A1984 " --> pdb=" O   THR A1980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1999 through 2017
    Processing helix  chain 'A' and resid 2026 through 2032
    Processing helix  chain 'A' and resid 2033 through 2043
      removed outlier: 3.564A  pdb=" N   ARG A2039 " --> pdb=" O   ASP A2035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2048 through 2060
    Processing helix  chain 'A' and resid 2072 through 2082
      removed outlier: 3.562A  pdb=" N   GLU A2076 " --> pdb=" O   GLY A2072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2083 through 2086
    Processing helix  chain 'A' and resid 2096 through 2108
    Processing helix  chain 'A' and resid 2115 through 2119
      removed outlier: 3.532A  pdb=" N   SER A2118 " --> pdb=" O   ASP A2115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2120 through 2122
      No H-bonds generated for 'chain 'A' and resid 2120 through 2122'
    Processing helix  chain 'A' and resid 2123 through 2129
    Processing helix  chain 'A' and resid 2167 through 2172
      removed outlier: 4.132A  pdb=" N   SER A2172 " --> pdb=" O   PRO A2168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2182 through 2199
    Processing helix  chain 'A' and resid 2199 through 2234
    Processing helix  chain 'A' and resid 2240 through 2268
      removed outlier: 3.920A  pdb=" N   ILE A2244 " --> pdb=" O   ASP A2240 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A2245 " --> pdb=" O   ASP A2241 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A2268 " --> pdb=" O   GLU A2264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2268 through 2278
      removed outlier: 3.977A  pdb=" N   GLN A2278 " --> pdb=" O   THR A2274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 299
      removed outlier: 3.514A  pdb=" N   TYR B 291 " --> pdb=" O   PRO B 287 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER B 292 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   SER B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLU B 296 " --> pdb=" O   SER B 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 289
      No H-bonds generated for 'chain 'C' and resid 287 through 289'
    Processing helix  chain 'C' and resid 290 through 299
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1160 through 1166
      removed outlier: 3.769A  pdb=" N   GLU A1161 " --> pdb=" O   TRP A1203 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A1254 " --> pdb=" O   LEU A1206 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A1136 " --> pdb=" O   GLY A1255 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   CYS A1257 " --> pdb=" O   LEU A1136 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU A1138 " --> pdb=" O   CYS A1257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1193 through 1195
      removed outlier: 6.887A  pdb=" N   VAL A1193 " --> pdb=" O   LYS A1247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1418 through 1419
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1504 through 1505
      removed outlier: 6.728A  pdb=" N   TYR A1504 " --> pdb=" O   ILE A1538 " (cutoff:3.500A)
      removed outlier: 8.885A  pdb=" N   ASP A1540 " --> pdb=" O   TYR A1504 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   PHE A1537 " --> pdb=" O   VAL A1610 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   THR A1612 " --> pdb=" O   PHE A1537 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   MET A1539 " --> pdb=" O   THR A1612 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU A1478 " --> pdb=" O   PHE A1611 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   MET A1613 " --> pdb=" O   LEU A1478 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   LEU A1480 " --> pdb=" O   MET A1613 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2088 through 2091
      removed outlier: 6.526A  pdb=" N   LEU A2111 " --> pdb=" O   PHE A2156 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   SER A2158 " --> pdb=" O   LEU A2111 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   VAL A2113 " --> pdb=" O   SER A2158 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   LEU A2066 " --> pdb=" O   VAL A2177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2132 through 2133
      removed outlier: 4.466A  pdb=" N   VAL A2138 " --> pdb=" O   LEU A2149 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105
      removed outlier: 7.647A  pdb=" N   GLU B 101 " --> pdb=" O   GLU B 409 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   GLU B 409 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B 103 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER B 386 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 117
      removed outlier: 6.681A  pdb=" N   ALA B 127 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   VAL B 115 " --> pdb=" O   VAL B 125 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL B 125 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ILE B 133 " --> pdb=" O   THR B 146 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B 146 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL B 135 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 159
      removed outlier: 3.747A  pdb=" N   ASP B 156 " --> pdb=" O   CYS B 169 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B 170 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG B 187 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP B 179 " --> pdb=" O   CYS B 185 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   CYS B 185 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 201
      removed outlier: 6.592A  pdb=" N   ALA B 211 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL B 199 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL B 209 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   ILE B 201 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   HIS B 207 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   SER B 212 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   THR B 216 " --> pdb=" O   SER B 212 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS B 229 " --> pdb=" O   MET B 219 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 243
      removed outlier: 3.688A  pdb=" N   MET B 240 " --> pdb=" O   CYS B 253 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 263 " --> pdb=" O   CYS B 269 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   CYS B 269 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 280 through 285
      removed outlier: 3.532A  pdb=" N   SER B 316 " --> pdb=" O   THR B 320 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   THR B 320 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASP B 325 " --> pdb=" O   CYS B 331 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   CYS B 331 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 342 through 347
    Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 106
      removed outlier: 4.323A  pdb=" N   GLU C 409 " --> pdb=" O   PRO C 100 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL C 407 " --> pdb=" O   LYS C 102 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ALA C 104 " --> pdb=" O   VAL C 405 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   VAL C 405 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 112 through 117
      removed outlier: 6.821A  pdb=" N   VAL C 135 " --> pdb=" O   GLU C 144 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 159
      removed outlier: 6.933A  pdb=" N   CYS C 169 " --> pdb=" O   GLN C 155 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   ILE C 157 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ALA C 167 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   PHE C 159 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LEU C 165 " --> pdb=" O   PHE C 159 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE C 175 " --> pdb=" O   THR C 188 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   THR C 188 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU C 177 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 196 through 201
      removed outlier: 3.532A  pdb=" N   SER C 212 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   THR C 216 " --> pdb=" O   SER C 212 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ILE C 217 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   THR C 230 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   MET C 219 " --> pdb=" O   VAL C 228 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 243
      removed outlier: 3.550A  pdb=" N   MET C 240 " --> pdb=" O   CYS C 253 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL C 263 " --> pdb=" O   CYS C 269 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   CYS C 269 " --> pdb=" O   VAL C 263 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 280 through 285
      removed outlier: 3.515A  pdb=" N   SER C 316 " --> pdb=" O   THR C 320 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   THR C 320 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ASP C 325 " --> pdb=" O   CYS C 331 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   CYS C 331 " --> pdb=" O   ASP C 325 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 342 through 347

    618 hydrogen bonds defined for protein.
    1800 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: 5.54

  Time building geometry restraints manager: 4.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3571
        1.33 -     1.45: 2459
        1.45 -     1.57: 7347
        1.57 -     1.69: 6
        1.69 -     1.81: 120
  Bond restraints: 13503
  Sorted by residual:
  bond pdb=" C4  ADP A3201 "
       pdb=" C5  ADP A3201 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" C4  ADP A3202 "
       pdb=" C5  ADP A3202 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" N   ARG B  98 "
       pdb=" CA  ARG B  98 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.035 7.00e-03 2.04e+04 2.57e+01
  bond pdb=" N   VAL B 120 "
       pdb=" CA  VAL B 120 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 9.00e-03 1.23e+04 1.83e+01
  bond pdb=" CA  PRO A1141 "
       pdb=" C   PRO A1141 "
    ideal  model  delta    sigma   weight residual
    1.514  1.537 -0.022 5.50e-03 3.31e+04 1.67e+01
  ... (remaining 13498 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 17960
        2.58 -     5.16: 310
        5.16 -     7.75: 30
        7.75 -    10.33: 8
       10.33 -    12.91: 5
  Bond angle restraints: 18313
  Sorted by residual:
  angle pdb=" N   VAL A1674 "
        pdb=" CA  VAL A1674 "
        pdb=" C   VAL A1674 "
      ideal   model   delta    sigma   weight residual
     111.62  106.52    5.10 7.90e-01 1.60e+00 4.17e+01
  angle pdb=" N   PRO C  99 "
        pdb=" CA  PRO C  99 "
        pdb=" C   PRO C  99 "
      ideal   model   delta    sigma   weight residual
     110.70  118.42   -7.72 1.22e+00 6.72e-01 4.00e+01
  angle pdb=" N   PRO B  99 "
        pdb=" CA  PRO B  99 "
        pdb=" C   PRO B  99 "
      ideal   model   delta    sigma   weight residual
     110.70  117.54   -6.84 1.22e+00 6.72e-01 3.14e+01
  angle pdb=" PA  ADP A3202 "
        pdb=" O3A ADP A3202 "
        pdb=" PB  ADP A3202 "
      ideal   model   delta    sigma   weight residual
     120.50  133.41  -12.91 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" CA  PRO C  99 "
        pdb=" C   PRO C  99 "
        pdb=" N   PRO C 100 "
      ideal   model   delta    sigma   weight residual
     117.93  123.06   -5.13 1.20e+00 6.94e-01 1.83e+01
  ... (remaining 18308 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 7631
       22.27 -    44.54: 428
       44.54 -    66.81: 42
       66.81 -    89.09: 8
       89.09 -   111.36: 4
  Dihedral angle restraints: 8113
    sinusoidal: 3340
      harmonic: 4773
  Sorted by residual:
  dihedral pdb=" C5' ADP A3201 "
           pdb=" O5' ADP A3201 "
           pdb=" PA  ADP A3201 "
           pdb=" O2A ADP A3201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -171.35  111.36     1      2.00e+01 2.50e-03 3.27e+01
  dihedral pdb=" CA  HIS B 192 "
           pdb=" C   HIS B 192 "
           pdb=" N   ASP B 193 "
           pdb=" CA  ASP B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.32  -18.68     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  PRO B  99 "
           pdb=" C   PRO B  99 "
           pdb=" N   PRO B 100 "
           pdb=" CA  PRO B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.01  -17.99     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 8110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1436
       0.046 -    0.091: 413
       0.091 -    0.137: 143
       0.137 -    0.182: 31
       0.182 -    0.228: 5
  Chirality restraints: 2028
  Sorted by residual:
  chirality pdb=" CA  LEU C 177 "
            pdb=" N   LEU C 177 "
            pdb=" C   LEU C 177 "
            pdb=" CB  LEU C 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C3' ADP A3202 "
            pdb=" C2' ADP A3202 "
            pdb=" C4' ADP A3202 "
            pdb=" O3' ADP A3202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.73    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  VAL A1674 "
            pdb=" N   VAL A1674 "
            pdb=" C   VAL A1674 "
            pdb=" CB  VAL A1674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 2025 not shown)

  Planarity restraints: 2342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1318 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.30e+00
        pdb=" C   MET A1318 "    0.031 2.00e-02 2.50e+03
        pdb=" O   MET A1318 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A1319 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A1671 "    0.030 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO A1672 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1672 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1672 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1320 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   GLU A1320 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A1320 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A1321 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2339 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1586
        2.75 -     3.29: 13470
        3.29 -     3.82: 22663
        3.82 -     4.36: 27127
        4.36 -     4.90: 45737
  Nonbonded interactions: 110583
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A1101 "
            pdb=" NH2 ARG A1302 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   ASN A1420 "
            pdb=" NZ  LYS C 319 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OH  TYR A1322 "
            pdb=" OE1 GLN A1326 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OE2 GLU A1561 "
            pdb=" OH  TYR A1596 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" NZ  LYS B 102 "
            pdb=" OH  TYR B 395 "
     model   vdw
     2.247 3.120
  ... (remaining 110578 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.240
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     36.990
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108  13503  Z= 0.343
  Angle     :  0.830  12.911  18313  Z= 0.498
  Chirality :  0.050   0.228   2028
  Planarity :  0.004   0.052   2342
  Dihedral  : 13.461 111.356   5013
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.06 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.82 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.21), residues: 1625
  helix:  1.05 (0.21), residues: 604
  sheet: -0.66 (0.27), residues: 365
  loop : -1.02 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1967 
 HIS   0.007   0.001   HIS B 382 
 PHE   0.018   0.002   PHE B 347 
 TYR   0.018   0.002   TYR A1426 
 ARG   0.010   0.000   ARG A2260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14043 (  618)
  hydrogen bonds       : angle       6.75648 ( 1800)
  covalent geometry    : bond        0.00537 (13503)
  covalent geometry    : angle       0.82966 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 1.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1257 CYS cc_start: 0.7274 (p) cc_final: 0.7036 (p)
REVERT: B  206 ASP cc_start: 0.8571 (m-30) cc_final: 0.8367 (m-30)
REVERT: C  179 ASP cc_start: 0.7667 (t0) cc_final: 0.7393 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2835
  time to fit residues: 77.8903
Evaluate side-chains
  143 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 136 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0970
   chunk 68 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 126 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 147 optimal weight:    4.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A1297 ASN
A2004 GLN
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.113272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.088559 restraints weight = 32290.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 3.23
r_work: 0.3268 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13503  Z= 0.168
  Angle     :  0.638   8.259  18313  Z= 0.322
  Chirality :  0.044   0.139   2028
  Planarity :  0.004   0.043   2342
  Dihedral  :  5.463 102.990   1804
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.00 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.21), residues: 1625
  helix:  1.58 (0.21), residues: 607
  sheet: -0.43 (0.27), residues: 347
  loop : -0.85 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 324 
 HIS   0.004   0.001   HIS A1745 
 PHE   0.015   0.002   PHE A2216 
 TYR   0.017   0.002   TYR B 291 
 ARG   0.013   0.001   ARG B 411 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  618)
  hydrogen bonds       : angle       4.98838 ( 1800)
  covalent geometry    : bond        0.00375 (13503)
  covalent geometry    : angle       0.63754 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7754 (mm)
REVERT: A 1677 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8198 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4429 (tttp) cc_final: 0.3897 (pttt)
REVERT: B  268 GLU cc_start: 0.7338 (pm20) cc_final: 0.7040 (pm20)
REVERT: C  145 ARG cc_start: 0.7381 (ttt90) cc_final: 0.6810 (ttt90)
REVERT: C  179 ASP cc_start: 0.7965 (t0) cc_final: 0.7590 (t0)
REVERT: C  325 ASP cc_start: 0.8104 (t0) cc_final: 0.7902 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 162
  average time/residue: 0.2685
  time to fit residues: 63.4374
Evaluate side-chains
  148 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 142 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 161 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 146 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 150 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.112209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.086991 restraints weight = 33001.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.32
r_work: 0.3238 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13503  Z= 0.179
  Angle     :  0.616   7.717  18313  Z= 0.311
  Chirality :  0.044   0.134   2028
  Planarity :  0.004   0.046   2342
  Dihedral  :  5.259  93.270   1804
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.87 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.21), residues: 1625
  helix:  1.73 (0.21), residues: 607
  sheet: -0.38 (0.28), residues: 359
  loop : -0.78 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 220 
 HIS   0.004   0.001   HIS A1745 
 PHE   0.013   0.002   PHE B 183 
 TYR   0.013   0.001   TYR A1426 
 ARG   0.005   0.000   ARG A2260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  618)
  hydrogen bonds       : angle       4.78174 ( 1800)
  covalent geometry    : bond        0.00408 (13503)
  covalent geometry    : angle       0.61617 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7933 (mm)
REVERT: A 1346 ARG cc_start: 0.8748 (ptp-170) cc_final: 0.8483 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8266 (mmtp)
REVERT: A 1733 HIS cc_start: 0.7774 (t-90) cc_final: 0.7461 (m-70)
REVERT: A 1742 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4484 (tttp) cc_final: 0.3925 (pttt)
REVERT: A 1978 MET cc_start: 0.8989 (tpp) cc_final: 0.8689 (tpp)
REVERT: B  268 GLU cc_start: 0.7358 (pm20) cc_final: 0.7028 (pm20)
REVERT: C  145 ARG cc_start: 0.7567 (ttt90) cc_final: 0.6916 (ttt90)
REVERT: C  179 ASP cc_start: 0.7999 (t0) cc_final: 0.7596 (t0)
REVERT: C  325 ASP cc_start: 0.8130 (t0) cc_final: 0.7893 (t0)
REVERT: C  367 ASP cc_start: 0.7433 (t0) cc_final: 0.7100 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 165
  average time/residue: 0.2514
  time to fit residues: 61.2788
Evaluate side-chains
  156 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1613 MET
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1954 THR
Chi-restraints excluded: chain A residue 2223 LEU
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 160 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 137 optimal weight:    0.3980
   chunk 53 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.113959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.088823 restraints weight = 32346.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.30
r_work: 0.3281 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13503  Z= 0.109
  Angle     :  0.565   8.204  18313  Z= 0.282
  Chirality :  0.042   0.145   2028
  Planarity :  0.004   0.043   2342
  Dihedral  :  4.994  78.897   1804
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.37 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.21), residues: 1625
  helix:  2.01 (0.21), residues: 601
  sheet: -0.25 (0.28), residues: 349
  loop : -0.66 (0.23), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 324 
 HIS   0.002   0.001   HIS B 380 
 PHE   0.011   0.001   PHE B 347 
 TYR   0.014   0.001   TYR A1293 
 ARG   0.003   0.000   ARG A2173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03519 (  618)
  hydrogen bonds       : angle       4.47088 ( 1800)
  covalent geometry    : bond        0.00240 (13503)
  covalent geometry    : angle       0.56465 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 1.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1160 MET cc_start: 0.8409 (mmt) cc_final: 0.8204 (tpp)
REVERT: A 1169 SER cc_start: 0.9279 (p) cc_final: 0.8983 (p)
REVERT: A 1213 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7899 (mm)
REVERT: A 1346 ARG cc_start: 0.8771 (ptp-170) cc_final: 0.8492 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8325 (mmtp)
REVERT: A 1733 HIS cc_start: 0.7746 (t-90) cc_final: 0.7413 (t70)
REVERT: A 1742 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4425 (tttp) cc_final: 0.3846 (pttt)
REVERT: A 1978 MET cc_start: 0.8994 (tpp) cc_final: 0.8683 (tpp)
REVERT: A 2000 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7288 (tt0)
REVERT: A 2076 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7371 (pm20)
REVERT: B  268 GLU cc_start: 0.7255 (pm20) cc_final: 0.7048 (pm20)
REVERT: C  145 ARG cc_start: 0.7540 (ttt90) cc_final: 0.6886 (ttt90)
REVERT: C  179 ASP cc_start: 0.7967 (t0) cc_final: 0.7595 (t0)
REVERT: C  325 ASP cc_start: 0.8092 (t0) cc_final: 0.7847 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2552
  time to fit residues: 65.2778
Evaluate side-chains
  156 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1613 MET
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1744 MET
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 159 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1326 GLN
A1509 HIS
A1559 ASN
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1649 GLN
A1976 ASN
** A2232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.107826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.083349 restraints weight = 34023.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.15
r_work: 0.3191 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.075  13503  Z= 0.377
  Angle     :  0.776   8.877  18313  Z= 0.398
  Chirality :  0.050   0.150   2028
  Planarity :  0.006   0.052   2342
  Dihedral  :  5.747  99.180   1804
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.63 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.20), residues: 1625
  helix:  1.12 (0.20), residues: 612
  sheet: -0.54 (0.27), residues: 351
  loop : -0.99 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP B 178 
 HIS   0.009   0.002   HIS A1745 
 PHE   0.019   0.002   PHE A2156 
 TYR   0.015   0.002   TYR A1648 
 ARG   0.005   0.001   ARG A1469 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04900 (  618)
  hydrogen bonds       : angle       5.09911 ( 1800)
  covalent geometry    : bond        0.00861 (13503)
  covalent geometry    : angle       0.77592 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
REVERT: A 1150 LEU cc_start: 0.8963 (tt) cc_final: 0.8739 (tt)
REVERT: A 1213 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8177 (mm)
REVERT: A 1338 ILE cc_start: 0.8812 (pt) cc_final: 0.8609 (pt)
REVERT: A 1346 ARG cc_start: 0.8666 (ptp-170) cc_final: 0.8450 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8475 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4738 (tttp) cc_final: 0.3992 (pttt)
REVERT: A 2000 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7555 (tt0)
REVERT: A 2076 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7546 (pm20)
REVERT: A 2114 GLN cc_start: 0.8081 (mt0) cc_final: 0.7737 (mt0)
REVERT: A 2130 GLU cc_start: 0.8339 (tt0) cc_final: 0.7876 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8777 (pp20) cc_final: 0.8525 (pp20)
REVERT: B  150 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6358 (t-90)
REVERT: B  268 GLU cc_start: 0.7411 (pm20) cc_final: 0.6963 (pm20)
REVERT: B  323 MET cc_start: 0.4565 (OUTLIER) cc_final: 0.4315 (ptm)
REVERT: B  346 LEU cc_start: 0.8431 (pt) cc_final: 0.8040 (mt)
REVERT: B  382 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7683 (t-90)
REVERT: C  145 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7165 (ttt90)
REVERT: C  179 ASP cc_start: 0.8089 (t0) cc_final: 0.7571 (t0)
REVERT: C  325 ASP cc_start: 0.8064 (t0) cc_final: 0.7862 (t0)
REVERT: C  388 ASP cc_start: 0.8655 (t0) cc_final: 0.8260 (t0)
  outliers start: 34
  outliers final: 20
  residues processed: 176
  average time/residue: 0.2523
  time to fit residues: 66.3644
Evaluate side-chains
  168 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 1.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1444 VAL
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1550 LEU
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1954 THR
Chi-restraints excluded: chain A residue 2028 THR
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  164 LYS
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  212 SER
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 157 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 124 optimal weight:    8.9990
   chunk 142 optimal weight:    0.9990
   chunk 160 optimal weight:    0.8980
   chunk 151 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.111135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.086615 restraints weight = 33460.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 3.19
r_work: 0.3257 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13503  Z= 0.134
  Angle     :  0.607  10.102  18313  Z= 0.306
  Chirality :  0.044   0.146   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.276  83.765   1804
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.24 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.21), residues: 1625
  helix:  1.61 (0.21), residues: 608
  sheet: -0.19 (0.29), residues: 325
  loop : -0.86 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP B 178 
 HIS   0.002   0.001   HIS B 118 
 PHE   0.013   0.001   PHE A1457 
 TYR   0.017   0.001   TYR B 291 
 ARG   0.004   0.000   ARG A1414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03866 (  618)
  hydrogen bonds       : angle       4.58385 ( 1800)
  covalent geometry    : bond        0.00302 (13503)
  covalent geometry    : angle       0.60677 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8067 (mm)
REVERT: A 1266 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7830 (mtmt)
REVERT: A 1346 ARG cc_start: 0.8658 (ptp-170) cc_final: 0.8424 (ttp-110)
REVERT: A 1575 MET cc_start: 0.8301 (mtt) cc_final: 0.8032 (mtp)
REVERT: A 1677 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8660 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4554 (tttp) cc_final: 0.3837 (pttt)
REVERT: A 2000 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7400 (tt0)
REVERT: A 2031 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8859 (mm)
REVERT: A 2076 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7495 (pm20)
REVERT: A 2078 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8812 (mm)
REVERT: A 2114 GLN cc_start: 0.7927 (mt0) cc_final: 0.7680 (mt0)
REVERT: A 2254 GLU cc_start: 0.8742 (pp20) cc_final: 0.8469 (pp20)
REVERT: B  268 GLU cc_start: 0.7366 (pm20) cc_final: 0.7142 (pm20)
REVERT: B  323 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.4076 (ptm)
REVERT: B  382 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7659 (t-90)
REVERT: C  145 ARG cc_start: 0.7912 (ttt90) cc_final: 0.7154 (ttt90)
REVERT: C  179 ASP cc_start: 0.8125 (t0) cc_final: 0.7684 (t0)
  outliers start: 32
  outliers final: 19
  residues processed: 180
  average time/residue: 0.2654
  time to fit residues: 71.3923
Evaluate side-chains
  172 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 1.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1545 LEU
Chi-restraints excluded: chain A residue 1612 THR
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2031 LEU
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2222 GLN
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 148 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 131 optimal weight:    0.3980
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0020
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1649 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.112159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.087663 restraints weight = 33166.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 3.18
r_work: 0.3272 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13503  Z= 0.126
  Angle     :  0.611  10.567  18313  Z= 0.305
  Chirality :  0.043   0.140   2028
  Planarity :  0.004   0.043   2342
  Dihedral  :  5.160  79.915   1804
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.72 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.21), residues: 1625
  helix:  1.73 (0.21), residues: 608
  sheet: -0.09 (0.29), residues: 325
  loop : -0.77 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A1336 
 PHE   0.012   0.001   PHE A1457 
 TYR   0.015   0.001   TYR A1293 
 ARG   0.005   0.000   ARG A1493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  618)
  hydrogen bonds       : angle       4.46432 ( 1800)
  covalent geometry    : bond        0.00284 (13503)
  covalent geometry    : angle       0.61098 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 1.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 SER cc_start: 0.9432 (p) cc_final: 0.9141 (p)
REVERT: A 1213 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8122 (mm)
REVERT: A 1346 ARG cc_start: 0.8656 (ptp-170) cc_final: 0.8413 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8090 (mp)
REVERT: A 1575 MET cc_start: 0.8316 (mtt) cc_final: 0.8018 (mtp)
REVERT: A 1677 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8662 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4590 (tttp) cc_final: 0.3849 (pttt)
REVERT: A 2031 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8862 (mm)
REVERT: A 2076 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7497 (pm20)
REVERT: A 2078 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8824 (mm)
REVERT: A 2114 GLN cc_start: 0.7922 (mt0) cc_final: 0.7689 (mt0)
REVERT: A 2130 GLU cc_start: 0.8681 (tt0) cc_final: 0.8100 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8742 (pp20) cc_final: 0.8457 (pp20)
REVERT: B  323 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.4094 (ptm)
REVERT: B  382 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7716 (t-90)
REVERT: C  145 ARG cc_start: 0.7912 (ttt90) cc_final: 0.7176 (ttt90)
REVERT: C  179 ASP cc_start: 0.8093 (t0) cc_final: 0.7647 (t0)
  outliers start: 36
  outliers final: 23
  residues processed: 176
  average time/residue: 0.3436
  time to fit residues: 91.5020
Evaluate side-chains
  174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 1.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1481 ILE
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1545 LEU
Chi-restraints excluded: chain A residue 1612 THR
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2028 THR
Chi-restraints excluded: chain A residue 2031 LEU
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2222 GLN
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 161 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1577 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.110316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085791 restraints weight = 33504.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.18
r_work: 0.3240 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13503  Z= 0.199
  Angle     :  0.654  10.367  18313  Z= 0.329
  Chirality :  0.045   0.141   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.268  82.872   1804
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.40 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.21), residues: 1625
  helix:  1.61 (0.21), residues: 608
  sheet: -0.19 (0.29), residues: 325
  loop : -0.84 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 178 
 HIS   0.004   0.001   HIS A1745 
 PHE   0.011   0.002   PHE A2156 
 TYR   0.016   0.002   TYR B 291 
 ARG   0.003   0.000   ARG A1493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  618)
  hydrogen bonds       : angle       4.58798 ( 1800)
  covalent geometry    : bond        0.00456 (13503)
  covalent geometry    : angle       0.65375 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8017 (mm)
REVERT: A 1346 ARG cc_start: 0.8675 (ptp-170) cc_final: 0.8441 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8119 (mp)
REVERT: A 1575 MET cc_start: 0.8290 (mtt) cc_final: 0.8051 (mtp)
REVERT: A 1677 LYS cc_start: 0.8891 (mmtp) cc_final: 0.8674 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4632 (tttp) cc_final: 0.3880 (pttt)
REVERT: A 2000 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7419 (tt0)
REVERT: A 2031 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: A 2076 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7515 (pm20)
REVERT: A 2130 GLU cc_start: 0.8648 (tt0) cc_final: 0.8041 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8743 (pp20) cc_final: 0.8456 (pp20)
REVERT: B  323 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.4007 (ptm)
REVERT: B  382 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7677 (t-90)
REVERT: C  145 ARG cc_start: 0.8023 (ttt90) cc_final: 0.7210 (ttt90)
REVERT: C  179 ASP cc_start: 0.8144 (t0) cc_final: 0.7657 (t0)
REVERT: C  323 MET cc_start: 0.7595 (ttm) cc_final: 0.7348 (ttm)
  outliers start: 36
  outliers final: 28
  residues processed: 172
  average time/residue: 0.3239
  time to fit residues: 81.4585
Evaluate side-chains
  170 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 136
  time to evaluate  : 1.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1276 VAL
Chi-restraints excluded: chain A residue 1278 VAL
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1481 ILE
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1545 LEU
Chi-restraints excluded: chain A residue 1612 THR
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2028 THR
Chi-restraints excluded: chain A residue 2031 LEU
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2222 GLN
Chi-restraints excluded: chain A residue 2257 GLU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 144 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 104 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 151 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.111584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.087098 restraints weight = 32977.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.19
r_work: 0.3263 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13503  Z= 0.141
  Angle     :  0.629  11.318  18313  Z= 0.315
  Chirality :  0.043   0.139   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.172  79.004   1804
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.61 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.21), residues: 1625
  helix:  1.68 (0.21), residues: 610
  sheet: -0.17 (0.29), residues: 325
  loop : -0.82 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 178 
 HIS   0.003   0.001   HIS C 207 
 PHE   0.011   0.001   PHE A1457 
 TYR   0.016   0.001   TYR B 291 
 ARG   0.004   0.000   ARG A1356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  618)
  hydrogen bonds       : angle       4.44909 ( 1800)
  covalent geometry    : bond        0.00324 (13503)
  covalent geometry    : angle       0.62944 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 2.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7782 (mm)
REVERT: A 1346 ARG cc_start: 0.8667 (ptp-170) cc_final: 0.8429 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: A 1677 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8723 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4673 (tttp) cc_final: 0.3870 (pttt)
REVERT: A 2000 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7370 (tt0)
REVERT: A 2031 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8867 (mm)
REVERT: A 2076 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7501 (pm20)
REVERT: A 2130 GLU cc_start: 0.8636 (tt0) cc_final: 0.7906 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8744 (pp20) cc_final: 0.8460 (pp20)
REVERT: B  202 MET cc_start: 0.5399 (mtm) cc_final: 0.5158 (mtm)
REVERT: B  382 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7685 (t-90)
REVERT: C  145 ARG cc_start: 0.7960 (ttt90) cc_final: 0.7256 (ttt90)
REVERT: C  179 ASP cc_start: 0.8121 (t0) cc_final: 0.7664 (t0)
REVERT: C  323 MET cc_start: 0.7562 (ttm) cc_final: 0.7310 (ttm)
  outliers start: 36
  outliers final: 25
  residues processed: 171
  average time/residue: 0.4783
  time to fit residues: 122.7240
Evaluate side-chains
  167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 2.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1266 LYS
Chi-restraints excluded: chain A residue 1276 VAL
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1481 ILE
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1545 LEU
Chi-restraints excluded: chain A residue 1612 THR
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2028 THR
Chi-restraints excluded: chain A residue 2031 LEU
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2222 GLN
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 101 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0270
   chunk 59 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    1.1642

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1577 GLN ** 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 = 0.3857 r_free = 0.3857 target = 0.112230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.087706 restraints weight = 33302.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 3.21
r_work: 0.3267 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13503  Z= 0.144
  Angle     :  0.633  10.927  18313  Z= 0.314
  Chirality :  0.043   0.150   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.127  77.748   1804
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.40 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.21), residues: 1625
  helix:  1.71 (0.21), residues: 610
  sheet: -0.17 (0.29), residues: 325
  loop : -0.79 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 178 
 HIS   0.003   0.001   HIS C 207 
 PHE   0.014   0.001   PHE A1549 
 TYR   0.016   0.001   TYR B 291 
 ARG   0.005   0.000   ARG A1356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  618)
  hydrogen bonds       : angle       4.41963 ( 1800)
  covalent geometry    : bond        0.00331 (13503)
  covalent geometry    : angle       0.63279 (18313)

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

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

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3250 Ramachandran restraints generated.
    1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 3.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8014 (mm)
REVERT: A 1346 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.8424 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8128 (mp)
REVERT: A 1677 LYS cc_start: 0.8945 (mmtp) cc_final: 0.8729 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4962 (tttp) cc_final: 0.4050 (pttt)
REVERT: A 2000 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7415 (tt0)
REVERT: A 2031 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8882 (mm)
REVERT: A 2076 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7497 (pm20)
REVERT: A 2130 GLU cc_start: 0.8660 (tt0) cc_final: 0.7948 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8702 (pp20) cc_final: 0.8407 (pp20)
REVERT: B  150 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6170 (t-90)
REVERT: B  202 MET cc_start: 0.5419 (mtm) cc_final: 0.5136 (mtm)
REVERT: B  219 MET cc_start: 0.6038 (tpt) cc_final: 0.5607 (tpt)
REVERT: B  382 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7519 (t-90)
REVERT: C  145 ARG cc_start: 0.7974 (ttt90) cc_final: 0.7269 (ttt90)
REVERT: C  179 ASP cc_start: 0.8142 (t0) cc_final: 0.7666 (t0)
REVERT: C  323 MET cc_start: 0.7585 (ttm) cc_final: 0.7328 (ttm)
  outliers start: 37
  outliers final: 26
  residues processed: 170
  average time/residue: 0.5460
  time to fit residues: 144.9321
Evaluate side-chains
  166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 3.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1206 LEU
Chi-restraints excluded: chain A residue 1213 LEU
Chi-restraints excluded: chain A residue 1266 LYS
Chi-restraints excluded: chain A residue 1276 VAL
Chi-restraints excluded: chain A residue 1278 VAL
Chi-restraints excluded: chain A residue 1481 ILE
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1612 THR
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 2028 THR
Chi-restraints excluded: chain A residue 2031 LEU
Chi-restraints excluded: chain A residue 2076 GLU
Chi-restraints excluded: chain A residue 2078 ILE
Chi-restraints excluded: chain A residue 2222 GLN
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  382 HIS
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  366 TRP
Chi-restraints excluded: chain C residue  385 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 105 optimal weight:    0.7980
   chunk 150 optimal weight:    3.9990
   chunk 151 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   chunk 98 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1258 ASN
A1291 GLN
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 382 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.088692 restraints weight = 33475.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 3.19
r_work: 0.3291 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13503  Z= 0.121
  Angle     :  0.626  11.506  18313  Z= 0.307
  Chirality :  0.043   0.137   2028
  Planarity :  0.004   0.043   2342
  Dihedral  :  5.050  74.072   1804
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.88 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.21), residues: 1625
  helix:  1.81 (0.21), residues: 610
  sheet: -0.10 (0.29), residues: 325
  loop : -0.72 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A1336 
 PHE   0.013   0.001   PHE A1457 
 TYR   0.015   0.001   TYR A1293 
 ARG   0.005   0.000   ARG A1356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  618)
  hydrogen bonds       : angle       4.34445 ( 1800)
  covalent geometry    : bond        0.00276 (13503)
  covalent geometry    : angle       0.62561 (18313)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8348.68 seconds
wall clock time: 150 minutes 22.50 seconds (9022.50 seconds total)