Starting phenix.real_space_refine
on Tue Nov 14 20:46:06 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/11_2023/7uy8_26867.pdb"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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
     Zn      1      6.06       5
     S      42      5.16       5
     C    6123      2.51       5
     N    1592      2.21       5
     O    1794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C TYR   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 9552
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 3187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3187
          Classifications: {'peptide': 392}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1255
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 1, 'TRANS': 154}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 2007
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 5, 'TRANS': 235}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 3102
          Classifications: {'peptide': 372}
          Link IDs: {'PTRANS': 12, 'TRANS': 359}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3324  SG  CYS A1248      21.007  84.408 119.017  1.00104.84           S
  ATOM   3348  SG  CYS A1251      17.659  85.381 117.384  1.00107.89           S
  ATOM   3474  SG  CYS A1273      20.686  86.040 115.527  1.00116.42           S
  ATOM   3489  SG  CYS A1275      20.080  88.042 118.795  1.00130.38           S

  Time building chain proxies: 5.30, per 1000 atoms: 0.55
  Number of scatterers: 9552
  At special positions: 0
  Unit cell: (82.5, 100.1, 159.5, 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)
     Zn      1     29.99
     S      42     16.00
     O    1794      8.00
     N    1592      7.00
     C    6123      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.55
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1251 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1273 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1248 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1275 "
      Number of angles added : 6


  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      47.5% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'B' and resid 161 through 167
    Processing helix  chain 'B' and resid 189 through 208
      removed outlier: 3.993A  pdb=" N   ILE B 193 " --> pdb=" O   ASN B 189 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU B 202 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 212
    Processing helix  chain 'B' and resid 264 through 268
      removed outlier: 3.897A  pdb=" N   ASN B 267 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP B 268 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 264 through 268'
    Processing helix  chain 'B' and resid 341 through 355
      removed outlier: 4.019A  pdb=" N   ASP B 345 " --> pdb=" O   TYR B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 375
      removed outlier: 3.990A  pdb=" N   LYS B 374 " --> pdb=" O   ASN B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 403
    Processing helix  chain 'B' and resid 461 through 470
      removed outlier: 4.056A  pdb=" N   ILE B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 492
      removed outlier: 3.862A  pdb=" N   GLN B 492 " --> pdb=" O   ALA B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 520
      removed outlier: 4.317A  pdb=" N   ASN B 520 " --> pdb=" O   LEU B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 523
      No H-bonds generated for 'chain 'B' and resid 521 through 523'
    Processing helix  chain 'B' and resid 562 through 566
      removed outlier: 3.759A  pdb=" N   GLY B 565 " --> pdb=" O   ILE B 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1239
    Processing helix  chain 'A' and resid 1279 through 1300
      removed outlier: 3.850A  pdb=" N   GLU A1300 " --> pdb=" O   ARG A1296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1328 through 1342
      removed outlier: 3.723A  pdb=" N   LEU A1332 " --> pdb=" O   SER A1328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1346 through 1351
      removed outlier: 3.738A  pdb=" N   GLU A1351 " --> pdb=" O   LYS A1347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1374
      removed outlier: 3.758A  pdb=" N   ILE A1358 " --> pdb=" O   GLN A1354 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR A1367 " --> pdb=" O   THR A1363 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   LEU A1368 " --> pdb=" O   ILE A1364 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU A1371 " --> pdb=" O   THR A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1382 through 1387
      removed outlier: 4.100A  pdb=" N   PHE A1386 " --> pdb=" O   LEU A1382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1388 through 1390
      No H-bonds generated for 'chain 'A' and resid 1388 through 1390'
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 59 through 80
      removed outlier: 3.749A  pdb=" N   ILE D  63 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL D  64 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLN D  65 " --> pdb=" O   GLN D  61 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ARG D  70 " --> pdb=" O   LEU D  66 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET D  71 " --> pdb=" O   ALA D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
    Processing helix  chain 'D' and resid 115 through 142
      removed outlier: 3.946A  pdb=" N   LYS D 119 " --> pdb=" O   GLU D 115 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN D 120 " --> pdb=" O   TYR D 116 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU D 127 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE D 132 " --> pdb=" O   VAL D 128 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR D 138 " --> pdb=" O   CYS D 134 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE D 140 " --> pdb=" O   MET D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 146
    Processing helix  chain 'D' and resid 147 through 165
    Processing helix  chain 'D' and resid 168 through 179
      removed outlier: 3.562A  pdb=" N   SER D 173 " --> pdb=" O   ALA D 169 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ASP D 174 " --> pdb=" O   ASN D 170 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU D 177 " --> pdb=" O   SER D 173 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS D 178 " --> pdb=" O   ASP D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 190
    Processing helix  chain 'D' and resid 190 through 198
      removed outlier: 3.629A  pdb=" N   THR D 197 " --> pdb=" O   LYS D 193 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 234
      removed outlier: 3.682A  pdb=" N   LEU D 232 " --> pdb=" O   PRO D 229 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER D 233 " --> pdb=" O   SER D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 249
      No H-bonds generated for 'chain 'D' and resid 247 through 249'
    Processing helix  chain 'D' and resid 250 through 276
      removed outlier: 3.547A  pdb=" N   VAL D 255 " --> pdb=" O   THR D 251 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   MET D 267 " --> pdb=" O   LEU D 263 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASN D 276 " --> pdb=" O   LEU D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 292
      removed outlier: 3.563A  pdb=" N   LEU D 286 " --> pdb=" O   ASP D 282 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   PHE D 288 " --> pdb=" O   ASP D 284 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS D 290 " --> pdb=" O   LEU D 286 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ASP D 291 " --> pdb=" O   SER D 287 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU D 292 " --> pdb=" O   PHE D 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 30
      removed outlier: 5.032A  pdb=" N   TYR C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ARG C  28 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   TYR C  30 " --> pdb=" O   TYR C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 42
    Processing helix  chain 'C' and resid 43 through 46
    Processing helix  chain 'C' and resid 73 through 84
    Processing helix  chain 'C' and resid 137 through 156
      removed outlier: 4.298A  pdb=" N   MET C 141 " --> pdb=" O   CYS C 137 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASP C 146 " --> pdb=" O   ARG C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 183
    Processing helix  chain 'C' and resid 184 through 195
      removed outlier: 3.509A  pdb=" N   LEU C 195 " --> pdb=" O   ILE C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 215
      removed outlier: 3.702A  pdb=" N   LYS C 214 " --> pdb=" O   PRO C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 226
      removed outlier: 3.647A  pdb=" N   ASN C 224 " --> pdb=" O   LEU C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 253
      removed outlier: 5.168A  pdb=" N   VAL C 247 " --> pdb=" O   GLU C 243 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLU C 248 " --> pdb=" O   LYS C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 269
      removed outlier: 4.027A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 287
      removed outlier: 3.520A  pdb=" N   SER C 276 " --> pdb=" O   SER C 272 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LYS C 284 " --> pdb=" O   GLU C 280 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   THR C 285 " --> pdb=" O   LYS C 281 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   LEU C 286 " --> pdb=" O   GLU C 282 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS C 287 " --> pdb=" O   TRP C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 302
      removed outlier: 4.456A  pdb=" N   SER C 302 " --> pdb=" O   GLU C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 321
      removed outlier: 3.727A  pdb=" N   LEU C 315 " --> pdb=" O   LEU C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 354 through 358
    Processing helix  chain 'C' and resid 374 through 399
      removed outlier: 3.630A  pdb=" N   PHE C 391 " --> pdb=" O   ILE C 387 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 172
      removed outlier: 3.567A  pdb=" N   VAL B 171 " --> pdb=" O   ASP B 449 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 536 " --> pdb=" O   ARG B 454 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ILE B 537 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 260 through 262
      removed outlier: 3.691A  pdb=" N   PHE B 261 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE B 253 " --> pdb=" O   PHE B 261 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG B 252 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 407 through 411
      removed outlier: 7.324A  pdb=" N   LEU B 325 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   ILE B 360 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   MET B 327 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   LEU B 362 " --> pdb=" O   MET B 327 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ALA B 329 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE B 574 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA B 572 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   ALA B 330 " --> pdb=" O   ASN B 570 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ASN B 570 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ARG B 587 " --> pdb=" O   PHE B 577 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1245 through 1248
      removed outlier: 3.502A  pdb=" N   GLN A1253 " --> pdb=" O   VAL A1246 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   CYS A1251 " --> pdb=" O   CYS A1248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1303 through 1304
    Processing sheet with id=AA6, first strand: chain 'D' and resid 223 through 224
      removed outlier: 3.665A  pdb=" N   VAL D 238 " --> pdb=" O   ILE D 245 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 65 through 67
      removed outlier: 4.523A  pdb=" N   ALA C  93 " --> pdb=" O   GLU C  55 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   SER C  57 " --> pdb=" O   ILE C  91 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE C  91 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   THR C  59 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ILE C  89 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 67
      removed outlier: 4.523A  pdb=" N   ALA C  93 " --> pdb=" O   GLU C  55 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   SER C  57 " --> pdb=" O   ILE C  91 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ILE C  91 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   THR C  59 " --> pdb=" O   ILE C  89 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ILE C  89 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 115
      removed outlier: 4.509A  pdb=" N   GLY C 170 " --> pdb=" O   SER C 166 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL C 164 " --> pdb=" O   HIS C 172 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 342 through 343
      removed outlier: 4.322A  pdb=" N   HIS C 343 " --> pdb=" O   ASN C 348 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ASN C 348 " --> pdb=" O   HIS C 343 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    369 hydrogen bonds defined for protein.
    1050 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: 2.42

  Time building geometry restraints manager: 3.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3063
        1.34 -     1.46: 2016
        1.46 -     1.58: 4570
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 9719
  Sorted by residual:
  bond pdb=" N   THR C 346 "
       pdb=" CA  THR C 346 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.23e-02 6.61e+03 4.06e+00
  bond pdb=" C   ILE B 423 "
       pdb=" N   PRO B 424 "
    ideal  model  delta    sigma   weight residual
    1.339  1.399 -0.059 3.40e-02 8.65e+02 3.06e+00
  bond pdb=" CA  LEU B 173 "
       pdb=" C   LEU B 173 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 1.39e-02 5.18e+03 1.83e+00
  bond pdb=" N   LYS A1272 "
       pdb=" CA  LYS A1272 "
    ideal  model  delta    sigma   weight residual
    1.454  1.472 -0.018 1.31e-02 5.83e+03 1.82e+00
  bond pdb=" CA  ILE A1270 "
       pdb=" CB  ILE A1270 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.23e-02 6.61e+03 1.33e+00
  ... (remaining 9714 not shown)

  Histogram of bond angle deviations from ideal:
       99.49 -   106.39: 192
      106.39 -   113.30: 5291
      113.30 -   120.21: 3524
      120.21 -   127.12: 4007
      127.12 -   134.03: 65
  Bond angle restraints: 13079
  Sorted by residual:
  angle pdb=" N   LYS A1272 "
        pdb=" CA  LYS A1272 "
        pdb=" C   LYS A1272 "
      ideal   model   delta    sigma   weight residual
     110.48  118.52   -8.04 1.48e+00 4.57e-01 2.95e+01
  angle pdb=" N   LYS C 345 "
        pdb=" CA  LYS C 345 "
        pdb=" C   LYS C 345 "
      ideal   model   delta    sigma   weight residual
     109.59  102.21    7.38 1.47e+00 4.63e-01 2.52e+01
  angle pdb=" N   LEU A1271 "
        pdb=" CA  LEU A1271 "
        pdb=" C   LEU A1271 "
      ideal   model   delta    sigma   weight residual
     113.17  118.27   -5.10 1.26e+00 6.30e-01 1.64e+01
  angle pdb=" N   ILE A1270 "
        pdb=" CA  ILE A1270 "
        pdb=" C   ILE A1270 "
      ideal   model   delta    sigma   weight residual
     108.11  113.62   -5.51 1.40e+00 5.10e-01 1.55e+01
  angle pdb=" N   ILE B 368 "
        pdb=" CA  ILE B 368 "
        pdb=" C   ILE B 368 "
      ideal   model   delta    sigma   weight residual
     112.80  108.86    3.94 1.15e+00 7.56e-01 1.17e+01
  ... (remaining 13074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 5352
       16.85 -    33.70: 482
       33.70 -    50.55: 117
       50.55 -    67.39: 23
       67.39 -    84.24: 17
  Dihedral angle restraints: 5991
    sinusoidal: 2531
      harmonic: 3460
  Sorted by residual:
  dihedral pdb=" CA  SER B 460 "
           pdb=" C   SER B 460 "
           pdb=" N   ASP B 461 "
           pdb=" CA  ASP B 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.82   25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" N   THR C 346 "
           pdb=" C   THR C 346 "
           pdb=" CA  THR C 346 "
           pdb=" CB  THR C 346 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  134.67  -11.27     0      2.50e+00 1.60e-01 2.03e+01
  dihedral pdb=" C   THR C 346 "
           pdb=" N   THR C 346 "
           pdb=" CA  THR C 346 "
           pdb=" CB  THR C 346 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.96   10.96     0      2.50e+00 1.60e-01 1.92e+01
  ... (remaining 5988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1351
       0.082 -    0.165: 117
       0.165 -    0.247: 4
       0.247 -    0.329: 0
       0.329 -    0.412: 1
  Chirality restraints: 1473
  Sorted by residual:
  chirality pdb=" CA  THR C 346 "
            pdb=" N   THR C 346 "
            pdb=" C   THR C 346 "
            pdb=" CB  THR C 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.11    0.41 2.00e-01 2.50e+01 4.24e+00
  chirality pdb=" CA  LYS C 345 "
            pdb=" N   LYS C 345 "
            pdb=" C   LYS C 345 "
            pdb=" CB  LYS C 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  LYS A1272 "
            pdb=" N   LYS A1272 "
            pdb=" C   LYS A1272 "
            pdb=" CB  LYS A1272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1470 not shown)

  Planarity restraints: 1659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C 343 "   -0.025 2.00e-02 2.50e+03   5.05e-02 2.55e+01
        pdb=" C   HIS C 343 "    0.087 2.00e-02 2.50e+03
        pdb=" O   HIS C 343 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   PRO C 344 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 351 "    0.069 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO C 352 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO C 352 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO C 352 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A1268 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.14e+00
        pdb=" C   ALA A1268 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ALA A1268 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   SER A1269 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1656 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 930
        2.75 -     3.28: 10141
        3.28 -     3.82: 14469
        3.82 -     4.36: 16706
        4.36 -     4.90: 28141
  Nonbonded interactions: 70387
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 177 "
            pdb=" OD1 ASN B 518 "
     model   vdw
     2.207 2.440
  nonbonded pdb=" O   GLY C 347 "
            pdb=" OD1 ASN C 368 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   VAL C  37 "
            pdb=" OG  SER C  41 "
     model   vdw
     2.221 2.440
  nonbonded pdb=" OG1 THR C  52 "
            pdb=" OD1 ASN C  72 "
     model   vdw
     2.244 2.440
  nonbonded pdb=" OH  TYR B 341 "
            pdb=" O   PHE B 365 "
     model   vdw
     2.245 2.440
  ... (remaining 70382 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  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:          3.960
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     28.510
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6355
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9719  Z= 0.180
  Angle     :  0.634   8.479  13079  Z= 0.342
  Chirality :  0.046   0.412   1473
  Planarity :  0.004   0.105   1659
  Dihedral  : 14.554  84.242   3725
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.25), residues: 1135
  helix:  0.63 (0.26), residues: 418
  sheet: -0.54 (0.46), residues: 131
  loop : -1.20 (0.26), residues: 586

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2621
  time to fit residues: 43.4968
Evaluate side-chains
  57 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.180 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5787
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 90 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A1253 GLN
A1315 GLN
A1352 ASN
D  94 ASN
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9719  Z= 0.185
  Angle     :  0.589   9.546  13079  Z= 0.312
  Chirality :  0.043   0.165   1473
  Planarity :  0.004   0.071   1659
  Dihedral  :  4.740  23.471   1235
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  5.23 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1135
  helix:  0.67 (0.25), residues: 441
  sheet: -0.77 (0.45), residues: 134
  loop : -1.17 (0.27), residues: 560

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2148
  time to fit residues: 22.0229
Evaluate side-chains
  49 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.267 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6185
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 113 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 196 HIS
B 303 HIS
B 391 GLN
B 407 GLN
B 425 GLN
B 444 ASN
** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 ASN
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6827
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9719  Z= 0.262
  Angle     :  0.625   5.875  13079  Z= 0.337
  Chirality :  0.044   0.163   1473
  Planarity :  0.004   0.057   1659
  Dihedral  :  4.999  21.365   1235
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.17 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.79 %
    Favored  : 94.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1135
  helix:  0.64 (0.25), residues: 439
  sheet: -1.15 (0.41), residues: 136
  loop : -1.22 (0.27), residues: 560

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2363
  time to fit residues: 20.6728
Evaluate side-chains
  43 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.085 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4601
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 104 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 425 GLN
B 491 ASN
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9719  Z= 0.206
  Angle     :  0.579   5.740  13079  Z= 0.311
  Chirality :  0.043   0.146   1473
  Planarity :  0.004   0.055   1659
  Dihedral  :  4.948  24.259   1235
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.90 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.25), residues: 1135
  helix:  0.71 (0.24), residues: 447
  sheet: -1.17 (0.42), residues: 136
  loop : -1.26 (0.27), residues: 552

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2148
  time to fit residues: 18.0413
Evaluate side-chains
  42 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.257 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6452
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 94 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 56 optimal weight:    8.9990
   chunk 99 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 GLN
B 469 ASN
** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9719  Z= 0.268
  Angle     :  0.645   5.871  13079  Z= 0.348
  Chirality :  0.044   0.192   1473
  Planarity :  0.004   0.044   1659
  Dihedral  :  5.263  21.438   1235
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 24.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.26 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1135
  helix:  0.52 (0.24), residues: 453
  sheet: -1.15 (0.43), residues: 132
  loop : -1.34 (0.27), residues: 550

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2030
  time to fit residues: 16.2579
Evaluate side-chains
  39 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.171 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5668
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 111 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0970
   chunk 9 optimal weight:    0.0270
   chunk 36 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    0.4294

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

Flipped N/Q/H residues before XYZ refinement:
B 391 GLN
B 425 GLN
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.071   9719  Z= 0.155
  Angle     :  0.573   6.684  13079  Z= 0.294
  Chirality :  0.044   0.186   1473
  Planarity :  0.003   0.046   1659
  Dihedral  :  4.702  22.038   1235
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.85 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.25), residues: 1135
  helix:  0.90 (0.25), residues: 450
  sheet: -1.03 (0.42), residues: 133
  loop : -1.14 (0.27), residues: 552

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1934
  time to fit residues: 17.1297
Evaluate side-chains
  42 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.143 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5355
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 69 optimal weight:    0.1980
   chunk 67 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   overall best weight:    5.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 440 HIS
** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.5770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9719  Z= 0.302
  Angle     :  0.680   8.290  13079  Z= 0.365
  Chirality :  0.044   0.205   1473
  Planarity :  0.004   0.043   1659
  Dihedral  :  5.351  23.180   1235
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 26.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.52 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.25), residues: 1135
  helix:  0.56 (0.24), residues: 444
  sheet: -1.10 (0.44), residues: 123
  loop : -1.24 (0.27), residues: 568

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2246
  time to fit residues: 17.1380
Evaluate side-chains
  37 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.085 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5046
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.0070
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    2.4006

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.5803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9719  Z= 0.194
  Angle     :  0.585   7.275  13079  Z= 0.306
  Chirality :  0.044   0.184   1473
  Planarity :  0.004   0.041   1659
  Dihedral  :  5.033  22.468   1235
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 20.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1135
  helix:  0.72 (0.25), residues: 444
  sheet: -1.26 (0.41), residues: 136
  loop : -1.05 (0.28), residues: 555

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.2115
  time to fit residues: 15.9677
Evaluate side-chains
  39 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.217 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6342
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 106 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0670
   chunk 67 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0870
   overall best weight:    1.3700

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1352 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.5803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   9719  Z= 0.162
  Angle     :  0.570   8.173  13079  Z= 0.294
  Chirality :  0.044   0.155   1473
  Planarity :  0.003   0.042   1659
  Dihedral  :  4.773  23.304   1235
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.55 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.26), residues: 1135
  helix:  0.83 (0.25), residues: 444
  sheet: -0.99 (0.42), residues: 133
  loop : -1.06 (0.28), residues: 558

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.2288
  time to fit residues: 18.3474
Evaluate side-chains
  40 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.152 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.8253
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 114 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 70 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   9719  Z= 0.154
  Angle     :  0.578   8.868  13079  Z= 0.294
  Chirality :  0.043   0.149   1473
  Planarity :  0.003   0.043   1659
  Dihedral  :  4.612  22.953   1235
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.25), residues: 1135
  helix:  0.85 (0.25), residues: 451
  sheet: -0.84 (0.42), residues: 135
  loop : -1.05 (0.28), residues: 549

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.2639
  time to fit residues: 20.9869
Evaluate side-chains
  42 residues out of total 1089 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.288 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6909
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 84 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** 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 = 0.2690 r_free = 0.2690 target = 0.024906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2447 r_free = 0.2447 target = 0.018891 restraints weight = 148916.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2470 r_free = 0.2470 target = 0.019370 restraints weight = 114203.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2486 r_free = 0.2486 target = 0.019727 restraints weight = 93588.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.6219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9719  Z= 0.198
  Angle     :  0.587   8.123  13079  Z= 0.308
  Chirality :  0.043   0.164   1473
  Planarity :  0.004   0.043   1659
  Dihedral  :  4.791  22.200   1235
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.26), residues: 1135
  helix:  0.90 (0.24), residues: 445
  sheet: -0.88 (0.42), residues: 135
  loop : -0.97 (0.29), residues: 555
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1612.14 seconds
wall clock time: 31 minutes 4.61 seconds (1864.61 seconds total)