Starting phenix.real_space_refine
on Sat Aug 23 16:56:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fdu_29014/08_2025/8fdu_29014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fdu_29014/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fdu_29014/08_2025/8fdu_29014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fdu_29014/08_2025/8fdu_29014.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fdu_29014/08_2025/8fdu_29014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fdu_29014/08_2025/8fdu_29014.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.63, per 1000 atoms: 0.20
  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: 0.74
  Conformation dependent library (CDL) restraints added in 446.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.54
  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: 2.36

  Time building geometry restraints manager: 1.09 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:             2.990
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.350
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.540
-------------------------------------------------------------------------------
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 : 12.15
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (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
 ARG   0.010   0.000   ARG A2260 
 TYR   0.018   0.002   TYR A1426 
 PHE   0.018   0.002   PHE B 347 
 TRP   0.021   0.002   TRP A1967 
 HIS   0.007   0.001   HIS B 382 

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

*********************** 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  : 0.405 
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: 0.1203
  time to fit residues: 32.9847
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  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A1258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2004 GLN
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
B 370 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.113221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.088520 restraints weight = 32220.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 3.23
r_work: 0.3267 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13503  Z= 0.166
  Angle     :  0.637   8.234  18313  Z= 0.322
  Chirality :  0.044   0.139   2028
  Planarity :  0.004   0.042   2342
  Dihedral  :  5.461 103.114   1804
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.21), residues: 1625
  helix:  1.58 (0.21), residues: 607
  sheet: -0.43 (0.28), residues: 347
  loop : -0.85 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 411 
 TYR   0.013   0.001   TYR A1426 
 PHE   0.014   0.002   PHE A2216 
 TRP   0.013   0.001   TRP C 324 
 HIS   0.004   0.001   HIS A1745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (13503)
  covalent geometry    : angle       0.63702 (18313)
  hydrogen bonds       : bond        0.04283 (  618)
  hydrogen bonds       : angle       5.01218 ( 1800)

*********************** 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
  166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7747 (mm)
REVERT: A 1257 CYS cc_start: 0.7699 (p) cc_final: 0.7497 (p)
REVERT: A 1677 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8181 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4428 (tttp) cc_final: 0.3896 (pttt)
REVERT: B  268 GLU cc_start: 0.7344 (pm20) cc_final: 0.7050 (pm20)
REVERT: C  145 ARG cc_start: 0.7367 (ttt90) cc_final: 0.6803 (ttt90)
REVERT: C  179 ASP cc_start: 0.7963 (t0) cc_final: 0.7608 (t0)
  outliers start: 14
  outliers final: 6
  residues processed: 159
  average time/residue: 0.1162
  time to fit residues: 26.9455
Evaluate side-chains
  147 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  334 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 157 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 48 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.112347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.087551 restraints weight = 32841.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 3.27
r_work: 0.3242 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1372

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= 0.170
  Angle     :  0.610   7.992  18313  Z= 0.307
  Chirality :  0.044   0.133   2028
  Planarity :  0.004   0.046   2342
  Dihedral  :  5.240  93.602   1804
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.73 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.21), residues: 1625
  helix:  1.75 (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
 ARG   0.006   0.000   ARG A2260 
 TYR   0.013   0.001   TYR A1426 
 PHE   0.012   0.001   PHE B 347 
 TRP   0.012   0.001   TRP C 220 
 HIS   0.004   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (13503)
  covalent geometry    : angle       0.61029 (18313)
  hydrogen bonds       : bond        0.03989 (  618)
  hydrogen bonds       : angle       4.77557 ( 1800)

*********************** 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
  175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7897 (mm)
REVERT: A 1257 CYS cc_start: 0.7862 (p) cc_final: 0.7630 (p)
REVERT: A 1346 ARG cc_start: 0.8752 (ptp-170) cc_final: 0.8487 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8241 (mmtp)
REVERT: A 1733 HIS cc_start: 0.7760 (t-90) cc_final: 0.7457 (m-70)
REVERT: A 1742 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8205 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4468 (tttp) cc_final: 0.3921 (pttt)
REVERT: A 1978 MET cc_start: 0.8987 (tpp) cc_final: 0.8694 (tpp)
REVERT: B  268 GLU cc_start: 0.7342 (pm20) cc_final: 0.7021 (pm20)
REVERT: C  145 ARG cc_start: 0.7525 (ttt90) cc_final: 0.6890 (ttt90)
REVERT: C  179 ASP cc_start: 0.8014 (t0) cc_final: 0.7635 (t0)
REVERT: C  367 ASP cc_start: 0.7421 (t0) cc_final: 0.7069 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 168
  average time/residue: 0.1155
  time to fit residues: 28.7826
Evaluate side-chains
  157 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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 1361 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 87 optimal weight:    0.3980
   chunk 111 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 140 optimal weight:    6.9990
   chunk 108 optimal weight:    1.9990
   chunk 148 optimal weight:    5.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.112142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.087454 restraints weight = 32430.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.23
r_work: 0.3254 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13503  Z= 0.146
  Angle     :  0.589   7.714  18313  Z= 0.296
  Chirality :  0.043   0.258   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.118  85.215   1804
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.96 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.21), residues: 1625
  helix:  1.84 (0.21), residues: 607
  sheet: -0.32 (0.28), residues: 349
  loop : -0.69 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1605 
 TYR   0.014   0.001   TYR A1293 
 PHE   0.010   0.001   PHE B 347 
 TRP   0.011   0.001   TRP C 220 
 HIS   0.003   0.001   HIS A1745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13503)
  covalent geometry    : angle       0.58875 (18313)
  hydrogen bonds       : bond        0.03779 (  618)
  hydrogen bonds       : angle       4.59642 ( 1800)

*********************** 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
  176 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: A 1160 MET cc_start: 0.8443 (mmt) cc_final: 0.8224 (tpp)
REVERT: A 1213 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7867 (mm)
REVERT: A 1257 CYS cc_start: 0.7895 (p) cc_final: 0.7658 (p)
REVERT: A 1346 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8469 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8348 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4498 (tttp) cc_final: 0.3887 (pttt)
REVERT: A 1978 MET cc_start: 0.9003 (tpp) cc_final: 0.8690 (tpp)
REVERT: A 2000 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7353 (tt0)
REVERT: A 2076 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7438 (pm20)
REVERT: B  268 GLU cc_start: 0.7232 (pm20) cc_final: 0.6948 (pm20)
REVERT: C  145 ARG cc_start: 0.7584 (ttt90) cc_final: 0.6913 (ttt90)
REVERT: C  179 ASP cc_start: 0.8019 (t0) cc_final: 0.7615 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 166
  average time/residue: 0.0956
  time to fit residues: 23.6460
Evaluate side-chains
  159 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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 1544 VAL
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  146 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  370 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 52 optimal weight:    0.5980
   chunk 95 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 149 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 86 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 150 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   overall best weight:    2.2784

-------------------------------------------------------------------------------
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**
** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1559 ASN
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1976 ASN
B 370 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.110776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.086183 restraints weight = 33618.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 3.18
r_work: 0.3241 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13503  Z= 0.220
  Angle     :  0.644   8.623  18313  Z= 0.324
  Chirality :  0.045   0.144   2028
  Planarity :  0.004   0.047   2342
  Dihedral  :  5.265  86.276   1804
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.01 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.21), residues: 1625
  helix:  1.66 (0.21), residues: 607
  sheet: -0.40 (0.27), residues: 359
  loop : -0.78 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 242 
 TYR   0.013   0.002   TYR A1293 
 PHE   0.012   0.002   PHE A2156 
 TRP   0.029   0.002   TRP B 178 
 HIS   0.005   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (13503)
  covalent geometry    : angle       0.64374 (18313)
  hydrogen bonds       : bond        0.04056 (  618)
  hydrogen bonds       : angle       4.66922 ( 1800)

*********************** 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
  174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7984 (mm)
REVERT: A 1257 CYS cc_start: 0.8121 (p) cc_final: 0.7907 (p)
REVERT: A 1266 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7860 (mtmt)
REVERT: A 1346 ARG cc_start: 0.8677 (ptp-170) cc_final: 0.8433 (ttp-110)
REVERT: A 1677 LYS cc_start: 0.8652 (mmtp) cc_final: 0.8348 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4544 (tttp) cc_final: 0.3896 (pttt)
REVERT: A 2000 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7465 (tt0)
REVERT: A 2076 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7490 (pm20)
REVERT: A 2254 GLU cc_start: 0.8701 (pp20) cc_final: 0.8447 (pp20)
REVERT: B  268 GLU cc_start: 0.7300 (pm20) cc_final: 0.6883 (pm20)
REVERT: B  323 MET cc_start: 0.4283 (OUTLIER) cc_final: 0.4022 (ptm)
REVERT: B  346 LEU cc_start: 0.8442 (pt) cc_final: 0.8106 (mt)
REVERT: B  382 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7552 (t-90)
REVERT: C  145 ARG cc_start: 0.7752 (ttt90) cc_final: 0.6991 (ttt90)
REVERT: C  179 ASP cc_start: 0.8039 (t0) cc_final: 0.7557 (t0)
REVERT: C  367 ASP cc_start: 0.7421 (t70) cc_final: 0.7140 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 166
  average time/residue: 0.0962
  time to fit residues: 23.9673
Evaluate side-chains
  161 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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 1544 VAL
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1744 MET
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  323 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 113 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9980
   chunk 161 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 117 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 207 HIS
B 370 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.111766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.087347 restraints weight = 33296.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.19
r_work: 0.3263 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1925

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= 0.150
  Angle     :  0.602   8.644  18313  Z= 0.302
  Chirality :  0.044   0.146   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.145  80.787   1804
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.01 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.21), residues: 1625
  helix:  1.79 (0.21), residues: 607
  sheet: -0.15 (0.29), residues: 337
  loop : -0.79 (0.23), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.015   0.001   TYR A1293 
 PHE   0.012   0.001   PHE B 347 
 TRP   0.041   0.001   TRP B 178 
 HIS   0.006   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (13503)
  covalent geometry    : angle       0.60188 (18313)
  hydrogen bonds       : bond        0.03746 (  618)
  hydrogen bonds       : angle       4.49374 ( 1800)

*********************** 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
  188 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8133 (mm)
REVERT: A 1346 ARG cc_start: 0.8642 (ptp-170) cc_final: 0.8389 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8028 (mp)
REVERT: A 1677 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8638 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4656 (tttp) cc_final: 0.3959 (pttt)
REVERT: A 2031 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8890 (mm)
REVERT: A 2076 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7445 (pm20)
REVERT: A 2254 GLU cc_start: 0.8704 (pp20) cc_final: 0.8430 (pp20)
REVERT: B  240 MET cc_start: 0.5218 (tpp) cc_final: 0.4853 (tpp)
REVERT: B  268 GLU cc_start: 0.7255 (pm20) cc_final: 0.6872 (pm20)
REVERT: B  323 MET cc_start: 0.4234 (OUTLIER) cc_final: 0.3984 (ptm)
REVERT: B  382 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7575 (t-90)
REVERT: C  145 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7080 (ttt90)
REVERT: C  179 ASP cc_start: 0.8052 (t0) cc_final: 0.7607 (t0)
  outliers start: 33
  outliers final: 21
  residues processed: 177
  average time/residue: 0.0980
  time to fit residues: 26.1731
Evaluate side-chains
  171 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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 1481 ILE
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain A residue 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1744 MET
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 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  196 VAL
Chi-restraints excluded: chain B residue  199 VAL
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 40 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 46 optimal weight:    0.4980
   chunk 33 optimal weight:    0.5980
   chunk 153 optimal weight:    3.9990
   chunk 137 optimal weight:    0.1980
   chunk 122 optimal weight:    9.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088403 restraints weight = 32936.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.19
r_work: 0.3288 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2021

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= 0.116
  Angle     :  0.592   9.371  18313  Z= 0.296
  Chirality :  0.043   0.157   2028
  Planarity :  0.004   0.043   2342
  Dihedral  :  5.048  76.777   1804
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.17 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.21), residues: 1625
  helix:  1.95 (0.21), residues: 601
  sheet: -0.07 (0.29), residues: 337
  loop : -0.72 (0.23), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 114 
 TYR   0.015   0.001   TYR A1293 
 PHE   0.012   0.001   PHE A1457 
 TRP   0.030   0.001   TRP B 178 
 HIS   0.004   0.001   HIS A1477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13503)
  covalent geometry    : angle       0.59173 (18313)
  hydrogen bonds       : bond        0.03555 (  618)
  hydrogen bonds       : angle       4.39964 ( 1800)

*********************** 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
  184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 SER cc_start: 0.9348 (p) cc_final: 0.9070 (p)
REVERT: A 1213 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7962 (mm)
REVERT: A 1346 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8385 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: A 1575 MET cc_start: 0.8266 (mtt) cc_final: 0.8023 (mtp)
REVERT: A 1677 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8602 (mmtp)
REVERT: A 1733 HIS cc_start: 0.7950 (t-90) cc_final: 0.7701 (t70)
REVERT: A 1742 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: A 1762 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5966 (mt-10)
REVERT: A 1949 LYS cc_start: 0.4677 (tttp) cc_final: 0.3956 (pttt)
REVERT: A 2000 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7406 (tt0)
REVERT: A 2031 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8821 (mm)
REVERT: A 2076 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7406 (pm20)
REVERT: A 2254 GLU cc_start: 0.8691 (pp20) cc_final: 0.8400 (pp20)
REVERT: A 2257 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7440 (tt0)
REVERT: B  240 MET cc_start: 0.5426 (tpp) cc_final: 0.5214 (tpp)
REVERT: B  268 GLU cc_start: 0.7287 (pm20) cc_final: 0.6974 (pm20)
REVERT: B  323 MET cc_start: 0.4140 (OUTLIER) cc_final: 0.3888 (ptm)
REVERT: B  382 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7546 (t-90)
REVERT: C  145 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7171 (ttt90)
REVERT: C  179 ASP cc_start: 0.8072 (t0) cc_final: 0.7632 (t0)
  outliers start: 31
  outliers final: 18
  residues processed: 175
  average time/residue: 0.1007
  time to fit residues: 25.9607
Evaluate side-chains
  173 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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 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 1635 VAL
Chi-restraints excluded: chain A residue 1699 LEU
Chi-restraints excluded: chain A residue 1744 MET
Chi-restraints excluded: chain A residue 1762 GLU
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 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  196 VAL
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  382 HIS
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 1 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 148 optimal weight:    6.9990
   chunk 134 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.111236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.086797 restraints weight = 33148.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.17
r_work: 0.3256 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13503  Z= 0.176
  Angle     :  0.635  11.891  18313  Z= 0.318
  Chirality :  0.044   0.200   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.158  79.821   1804
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.79 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.21), residues: 1625
  helix:  1.78 (0.21), residues: 601
  sheet: -0.07 (0.29), residues: 325
  loop : -0.80 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  98 
 TYR   0.015   0.001   TYR B 291 
 PHE   0.014   0.001   PHE B 347 
 TRP   0.023   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A1745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (13503)
  covalent geometry    : angle       0.63475 (18313)
  hydrogen bonds       : bond        0.03833 (  618)
  hydrogen bonds       : angle       4.51231 ( 1800)

*********************** 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
  179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 SER cc_start: 0.9436 (p) cc_final: 0.9156 (p)
REVERT: A 1213 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7864 (mm)
REVERT: A 1346 ARG cc_start: 0.8645 (ptp-170) cc_final: 0.8398 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8126 (mp)
REVERT: A 1575 MET cc_start: 0.8210 (mtt) cc_final: 0.7961 (mtp)
REVERT: A 1677 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8672 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4604 (tttp) cc_final: 0.3845 (pttt)
REVERT: A 2000 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7470 (tt0)
REVERT: A 2031 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8920 (mm)
REVERT: A 2076 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7489 (pm20)
REVERT: A 2130 GLU cc_start: 0.8221 (tt0) cc_final: 0.7791 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8658 (pp20) cc_final: 0.8350 (pp20)
REVERT: A 2257 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7471 (tt0)
REVERT: B  150 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.5838 (t-90)
REVERT: B  268 GLU cc_start: 0.7376 (pm20) cc_final: 0.7026 (pm20)
REVERT: B  323 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3924 (ptm)
REVERT: B  382 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7605 (t-90)
REVERT: C  145 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7194 (ttt90)
REVERT: C  179 ASP cc_start: 0.8107 (t0) cc_final: 0.7666 (t0)
  outliers start: 34
  outliers final: 23
  residues processed: 172
  average time/residue: 0.0945
  time to fit residues: 24.4029
Evaluate side-chains
  167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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 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 1744 MET
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 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  196 VAL
Chi-restraints excluded: chain B residue  323 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 26 optimal weight:    0.7980
   chunk 139 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 109 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0060
   chunk 97 optimal weight:    8.9990
   chunk 81 optimal weight:    7.9990
   chunk 93 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 143 optimal weight:    4.9990
   chunk 147 optimal weight:    3.9990
   overall best weight:    2.1400

-------------------------------------------------------------------------------
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**
** A2222 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 = 0.110111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085659 restraints weight = 33576.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 3.16
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: 0.7938
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13503  Z= 0.209
  Angle     :  0.661  11.303  18313  Z= 0.332
  Chirality :  0.045   0.190   2028
  Planarity :  0.004   0.045   2342
  Dihedral  :  5.285  82.745   1804
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.65 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.21), residues: 1625
  helix:  1.59 (0.21), residues: 608
  sheet: -0.16 (0.29), residues: 325
  loop : -0.83 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1356 
 TYR   0.023   0.002   TYR B 291 
 PHE   0.012   0.002   PHE C 389 
 TRP   0.021   0.002   TRP B 178 
 HIS   0.004   0.001   HIS A1745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (13503)
  covalent geometry    : angle       0.66138 (18313)
  hydrogen bonds       : bond        0.04039 (  618)
  hydrogen bonds       : angle       4.58906 ( 1800)

*********************** 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
  175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1213 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: A 1346 ARG cc_start: 0.8647 (ptp-170) cc_final: 0.8416 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8128 (mp)
REVERT: A 1575 MET cc_start: 0.8201 (mtt) cc_final: 0.7908 (mtp)
REVERT: A 1677 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8656 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4921 (tttp) cc_final: 0.4066 (pttt)
REVERT: A 2000 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7484 (tt0)
REVERT: A 2031 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8958 (mm)
REVERT: A 2076 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7514 (pm20)
REVERT: A 2130 GLU cc_start: 0.8353 (tt0) cc_final: 0.7814 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8719 (pp20) cc_final: 0.8416 (pp20)
REVERT: B  150 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.5962 (t-90)
REVERT: B  268 GLU cc_start: 0.7553 (pm20) cc_final: 0.7253 (pm20)
REVERT: B  323 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.3986 (ptm)
REVERT: B  382 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7523 (t-90)
REVERT: C  145 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7107 (ttt90)
REVERT: C  179 ASP cc_start: 0.8140 (t0) cc_final: 0.7698 (t0)
REVERT: C  323 MET cc_start: 0.7629 (ttm) cc_final: 0.7383 (ttm)
  outliers start: 35
  outliers final: 26
  residues processed: 167
  average time/residue: 0.0937
  time to fit residues: 23.4144
Evaluate side-chains
  169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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 1266 LYS
Chi-restraints excluded: chain A residue 1276 VAL
Chi-restraints excluded: chain A residue 1279 VAL
Chi-restraints excluded: chain A residue 1444 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 1744 MET
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 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 115 optimal weight:   10.0000
   chunk 128 optimal weight:   20.0000
   chunk 110 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 159 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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**
** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 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 = 0.3856 r_free = 0.3856 target = 0.111711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.087288 restraints weight = 33193.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.19
r_work: 0.3274 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13503  Z= 0.134
  Angle     :  0.621  11.209  18313  Z= 0.309
  Chirality :  0.043   0.181   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  5.110  77.314   1804
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.21), residues: 1625
  helix:  1.74 (0.21), residues: 608
  sheet: -0.09 (0.29), residues: 325
  loop : -0.79 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1356 
 TYR   0.020   0.001   TYR B 291 
 PHE   0.012   0.001   PHE A1549 
 TRP   0.017   0.001   TRP B 178 
 HIS   0.002   0.001   HIS A1733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13503)
  covalent geometry    : angle       0.62083 (18313)
  hydrogen bonds       : bond        0.03686 (  618)
  hydrogen bonds       : angle       4.42716 ( 1800)

********************** 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
  170 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1160 MET cc_start: 0.8464 (mmt) cc_final: 0.7871 (mmt)
REVERT: A 1213 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8073 (mm)
REVERT: A 1346 ARG cc_start: 0.8647 (ptp-170) cc_final: 0.8408 (ttp-110)
REVERT: A 1481 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: A 1575 MET cc_start: 0.8164 (mtt) cc_final: 0.7954 (mtp)
REVERT: A 1677 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8706 (mmtp)
REVERT: A 1742 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: A 1949 LYS cc_start: 0.4966 (tttp) cc_final: 0.4075 (pttt)
REVERT: A 2000 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7415 (tt0)
REVERT: A 2031 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8890 (mm)
REVERT: A 2076 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7501 (pm20)
REVERT: A 2130 GLU cc_start: 0.8226 (tt0) cc_final: 0.7666 (tm-30)
REVERT: A 2254 GLU cc_start: 0.8708 (pp20) cc_final: 0.8401 (pp20)
REVERT: A 2257 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7594 (tt0)
REVERT: A 2269 MET cc_start: 0.7161 (mmm) cc_final: 0.6959 (mmm)
REVERT: B  150 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.5881 (t-90)
REVERT: B  219 MET cc_start: 0.5894 (tpt) cc_final: 0.5421 (tpt)
REVERT: B  382 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7570 (t-90)
REVERT: C  145 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7251 (ttt90)
REVERT: C  179 ASP cc_start: 0.8119 (t0) cc_final: 0.7672 (t0)
REVERT: C  323 MET cc_start: 0.7586 (ttm) cc_final: 0.7339 (ttm)
  outliers start: 30
  outliers final: 21
  residues processed: 163
  average time/residue: 0.0884
  time to fit residues: 21.8388
Evaluate side-chains
  166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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 1266 LYS
Chi-restraints excluded: chain A residue 1276 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 1744 MET
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 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  196 VAL
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 4 optimal weight:    0.0570
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 128 optimal weight:    9.9990
   chunk 117 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0670
   chunk 3 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6036

-------------------------------------------------------------------------------
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**
A1291 GLN
** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 HIS
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.113367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.089112 restraints weight = 32928.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.17
r_work: 0.3304 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13503  Z= 0.112
  Angle     :  0.606  11.060  18313  Z= 0.300
  Chirality :  0.043   0.173   2028
  Planarity :  0.004   0.044   2342
  Dihedral  :  4.980  73.374   1804
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.34 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.21), residues: 1625
  helix:  1.92 (0.21), residues: 604
  sheet:  0.01 (0.29), residues: 325
  loop : -0.76 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1356 
 TYR   0.019   0.001   TYR B 291 
 PHE   0.013   0.001   PHE A1457 
 TRP   0.021   0.001   TRP B 178 
 HIS   0.004   0.001   HIS A1477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13503)
  covalent geometry    : angle       0.60568 (18313)
  hydrogen bonds       : bond        0.03453 (  618)
  hydrogen bonds       : angle       4.33542 ( 1800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2782.30 seconds
wall clock time: 48 minutes 39.98 seconds (2919.98 seconds total)