Starting phenix.real_space_refine
on Wed Sep 17 15:55:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_26867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_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/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_26867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_26867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_26867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uy8_26867/09_2025/7uy8_26867.cif"
  }
  resolution = 4.5
  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=   0.002
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. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.30, per 1000 atoms: 0.24
  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  - 3.00
        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: 0.88
  Conformation dependent library (CDL) restraints added in 381.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.34
  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: 1.33

  Time building geometry restraints manager: 1.17 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:
        0.00 -     1.70: 12762
        1.70 -     3.39: 255
        3.39 -     5.09: 40
        5.09 -     6.78: 16
        6.78 -     8.48: 6
  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 3.040
  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 3.040
  nonbonded pdb=" OG1 THR C  52 "
            pdb=" OD1 ASN C  72 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OH  TYR B 341 "
            pdb=" O   PHE B 365 "
     model   vdw
     2.245 3.040
  ... (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
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.000
  Find NCS groups from input model:        0.050
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.340
-------------------------------------------------------------------------------
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   9723  Z= 0.131
  Angle     :  0.639   8.479  13085  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 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: -0.66 (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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 252 
 TYR   0.034   0.002   TYR B 260 
 PHE   0.021   0.001   PHE B 174 
 TRP   0.019   0.002   TRP C 318 
 HIS   0.006   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9719)
  covalent geometry    : angle       0.63384 (13079)
  hydrogen bonds       : bond        0.20847 (  366)
  hydrogen bonds       : angle       6.92554 ( 1050)
  metal coordination   : bond        0.00271 (    4)
  metal coordination   : angle       3.91138 (    6)

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1306 ASP cc_start: 0.7482 (p0) cc_final: 0.7038 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1117
  time to fit residues: 18.4432
Evaluate side-chains
  57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 HIS
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
B 425 GLN
B 459 ASN
B 469 ASN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1315 GLN
C 172 HIS
C 228 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.026234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2420 r_free = 0.2420 target = 0.018948 restraints weight = 146658.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.019602 restraints weight = 102115.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.020093 restraints weight = 78874.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.020479 restraints weight = 65041.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2498 r_free = 0.2498 target = 0.020767 restraints weight = 56004.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6424
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9723  Z= 0.249
  Angle     :  0.743   7.810  13085  Z= 0.395
  Chirality :  0.046   0.160   1473
  Planarity :  0.005   0.069   1659
  Dihedral  :  5.283  23.203   1235
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  6.61 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.96 (0.24), residues: 1135
  helix:  0.30 (0.24), residues: 447
  sheet: -1.01 (0.44), residues: 124
  loop : -1.30 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1243 
 TYR   0.028   0.003   TYR B 533 
 PHE   0.025   0.002   PHE C  31 
 TRP   0.019   0.003   TRP C 138 
 HIS   0.008   0.002   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 9719)
  covalent geometry    : angle       0.73516 (13079)
  hydrogen bonds       : bond        0.04759 (  366)
  hydrogen bonds       : angle       5.53080 ( 1050)
  metal coordination   : bond        0.00486 (    4)
  metal coordination   : angle       5.21963 (    6)

*********************** 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
  59 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  426 MET cc_start: 0.8082 (pmm) cc_final: 0.7794 (pmm)
REVERT: B  479 MET cc_start: 0.9221 (mmm) cc_final: 0.8964 (mmp)
REVERT: B  486 PHE cc_start: 0.9640 (m-80) cc_final: 0.9425 (m-80)
REVERT: A 1312 TYR cc_start: 0.9322 (p90) cc_final: 0.9102 (p90)
REVERT: D  231 MET cc_start: 0.8077 (mpp) cc_final: 0.7835 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1012
  time to fit residues: 8.8879
Evaluate side-chains
  41 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    0.0370
   chunk 4 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 113 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 13 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0470
   chunk 83 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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
B 459 ASN
** A1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.038485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.032018 restraints weight = 133130.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.032829 restraints weight = 79678.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.033390 restraints weight = 54804.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.033809 restraints weight = 41278.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.034121 restraints weight = 32793.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.073   9723  Z= 0.114
  Angle     :  0.592   7.997  13085  Z= 0.306
  Chirality :  0.044   0.163   1473
  Planarity :  0.004   0.057   1659
  Dihedral  :  4.756  23.980   1235
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1135
  helix:  0.82 (0.25), residues: 441
  sheet: -1.20 (0.41), residues: 146
  loop : -0.98 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 188 
 TYR   0.019   0.001   TYR B 260 
 PHE   0.016   0.001   PHE B 174 
 TRP   0.018   0.002   TRP C 283 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9719)
  covalent geometry    : angle       0.58459 (13079)
  hydrogen bonds       : bond        0.03826 (  366)
  hydrogen bonds       : angle       4.99957 ( 1050)
  metal coordination   : bond        0.00507 (    4)
  metal coordination   : angle       4.30066 (    6)

*********************** 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
  66 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  283 MET cc_start: 0.9597 (ppp) cc_final: 0.9353 (ppp)
REVERT: B  426 MET cc_start: 0.9146 (pmm) cc_final: 0.8764 (pmm)
REVERT: B  464 MET cc_start: 0.9266 (mmt) cc_final: 0.9015 (mmm)
REVERT: A 1306 ASP cc_start: 0.9063 (p0) cc_final: 0.8824 (p0)
REVERT: A 1312 TYR cc_start: 0.9669 (p90) cc_final: 0.9088 (p90)
REVERT: D  152 ARG cc_start: 0.9621 (ppt170) cc_final: 0.9331 (ttp80)
REVERT: D  247 TYR cc_start: 0.8938 (t80) cc_final: 0.8659 (t80)
REVERT: D  267 MET cc_start: 0.9691 (mtm) cc_final: 0.9344 (mtm)
REVERT: C   70 MET cc_start: 0.9189 (mmp) cc_final: 0.8925 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1061
  time to fit residues: 10.0628
Evaluate side-chains
  48 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    0.4980
   chunk 32 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 94 optimal weight:    0.9990
   chunk 71 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 196 HIS
B 425 GLN
A1253 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.036388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.031377 restraints weight = 134128.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.032184 restraints weight = 80250.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.032735 restraints weight = 55182.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.033144 restraints weight = 41273.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.033443 restraints weight = 32770.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   9723  Z= 0.104
  Angle     :  0.553   7.628  13085  Z= 0.287
  Chirality :  0.043   0.148   1473
  Planarity :  0.004   0.051   1659
  Dihedral  :  4.503  23.220   1235
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.26 (0.26), residues: 1135
  helix:  1.08 (0.25), residues: 442
  sheet: -0.76 (0.42), residues: 142
  loop : -1.03 (0.28), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  54 
 TYR   0.016   0.001   TYR B 260 
 PHE   0.014   0.001   PHE B 174 
 TRP   0.009   0.001   TRP C 163 
 HIS   0.004   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9719)
  covalent geometry    : angle       0.54776 (13079)
  hydrogen bonds       : bond        0.03349 (  366)
  hydrogen bonds       : angle       4.68036 ( 1050)
  metal coordination   : bond        0.00422 (    4)
  metal coordination   : angle       3.67703 (    6)

*********************** 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
  65 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  337 MET cc_start: 0.9405 (mpp) cc_final: 0.9182 (mpp)
REVERT: B  426 MET cc_start: 0.9039 (pmm) cc_final: 0.8657 (pmm)
REVERT: B  464 MET cc_start: 0.9484 (mmt) cc_final: 0.9011 (mmm)
REVERT: A 1253 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5422 (pm20)
REVERT: A 1312 TYR cc_start: 0.9648 (p90) cc_final: 0.9074 (p90)
REVERT: A 1327 MET cc_start: 0.8386 (pmm) cc_final: 0.8167 (pmm)
REVERT: D   64 VAL cc_start: 0.9812 (t) cc_final: 0.9004 (t)
REVERT: D  152 ARG cc_start: 0.9604 (ppt170) cc_final: 0.9227 (ttp80)
REVERT: D  247 TYR cc_start: 0.8868 (t80) cc_final: 0.8415 (t80)
REVERT: D  267 MET cc_start: 0.9691 (mtm) cc_final: 0.9303 (mtm)
REVERT: C   70 MET cc_start: 0.9259 (mmp) cc_final: 0.8992 (mmp)
REVERT: C  193 ASP cc_start: 0.9686 (t70) cc_final: 0.9420 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1026
  time to fit residues: 9.7863
Evaluate side-chains
  50 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0000
   chunk 90 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
B 425 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.027530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.020949 restraints weight = 140317.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.021452 restraints weight = 110559.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.021809 restraints weight = 91679.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.022083 restraints weight = 80069.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.022280 restraints weight = 71766.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   9723  Z= 0.110
  Angle     :  0.560   7.226  13085  Z= 0.290
  Chirality :  0.043   0.182   1473
  Planarity :  0.003   0.045   1659
  Dihedral  :  4.502  23.358   1235
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.14 (0.26), residues: 1135
  helix:  1.22 (0.25), residues: 443
  sheet: -0.66 (0.41), residues: 147
  loop : -1.02 (0.28), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1243 
 TYR   0.016   0.001   TYR B 185 
 PHE   0.027   0.001   PHE B 395 
 TRP   0.008   0.001   TRP C 163 
 HIS   0.004   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9719)
  covalent geometry    : angle       0.55453 (13079)
  hydrogen bonds       : bond        0.03249 (  366)
  hydrogen bonds       : angle       4.73451 ( 1050)
  metal coordination   : bond        0.00280 (    4)
  metal coordination   : angle       3.65858 (    6)

*********************** 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
  61 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  426 MET cc_start: 0.9073 (pmm) cc_final: 0.8679 (pmm)
REVERT: B  464 MET cc_start: 0.9404 (mmt) cc_final: 0.9009 (mmm)
REVERT: A 1312 TYR cc_start: 0.9738 (p90) cc_final: 0.9229 (p90)
REVERT: A 1327 MET cc_start: 0.8430 (pmm) cc_final: 0.8216 (pmm)
REVERT: A 1369 ASP cc_start: 0.9666 (t70) cc_final: 0.9301 (m-30)
REVERT: D  152 ARG cc_start: 0.9600 (ppt170) cc_final: 0.9220 (ttp80)
REVERT: D  247 TYR cc_start: 0.8902 (t80) cc_final: 0.8470 (t80)
REVERT: D  267 MET cc_start: 0.9653 (mtm) cc_final: 0.9271 (mtm)
REVERT: D  285 ARG cc_start: 0.9496 (mmp80) cc_final: 0.9174 (mmp-170)
REVERT: C   70 MET cc_start: 0.9236 (mmp) cc_final: 0.8863 (mmp)
REVERT: C  193 ASP cc_start: 0.9680 (t70) cc_final: 0.9450 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1032
  time to fit residues: 9.2298
Evaluate side-chains
  47 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0470
   chunk 61 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    3.6084

-------------------------------------------------------------------------------
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 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 425 GLN
** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 348 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.025538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2462 r_free = 0.2462 target = 0.019420 restraints weight = 147524.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2483 r_free = 0.2483 target = 0.019912 restraints weight = 114493.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2498 r_free = 0.2498 target = 0.020257 restraints weight = 93666.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2509 r_free = 0.2509 target = 0.020522 restraints weight = 81008.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.020682 restraints weight = 72130.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.2511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.4734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9723  Z= 0.181
  Angle     :  0.627   8.891  13085  Z= 0.331
  Chirality :  0.043   0.175   1473
  Planarity :  0.004   0.046   1659
  Dihedral  :  4.887  23.061   1235
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.25), residues: 1135
  helix:  1.07 (0.24), residues: 455
  sheet: -0.95 (0.41), residues: 144
  loop : -1.09 (0.28), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1243 
 TYR   0.018   0.002   TYR B 533 
 PHE   0.032   0.002   PHE D 104 
 TRP   0.016   0.002   TRP C 138 
 HIS   0.006   0.002   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9719)
  covalent geometry    : angle       0.61948 (13079)
  hydrogen bonds       : bond        0.03592 (  366)
  hydrogen bonds       : angle       4.89324 ( 1050)
  metal coordination   : bond        0.00298 (    4)
  metal coordination   : angle       4.71169 (    6)

*********************** 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
  54 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  486 PHE cc_start: 0.9190 (m-80) cc_final: 0.8882 (m-80)
REVERT: A 1247 ASP cc_start: 0.9416 (p0) cc_final: 0.9104 (t0)
REVERT: A 1312 TYR cc_start: 0.9717 (p90) cc_final: 0.9188 (p90)
REVERT: A 1369 ASP cc_start: 0.9719 (t70) cc_final: 0.9393 (m-30)
REVERT: D  152 ARG cc_start: 0.9560 (ppt170) cc_final: 0.9169 (ttp80)
REVERT: D  222 MET cc_start: 0.9206 (ppp) cc_final: 0.8990 (ppp)
REVERT: D  267 MET cc_start: 0.9665 (mtm) cc_final: 0.9335 (mtp)
REVERT: C   70 MET cc_start: 0.9281 (mmp) cc_final: 0.8953 (mmp)
REVERT: C  193 ASP cc_start: 0.9682 (t70) cc_final: 0.9432 (m-30)
REVERT: C  258 MET cc_start: 0.7918 (tpt) cc_final: 0.7638 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1082
  time to fit residues: 8.5266
Evaluate side-chains
  43 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 81 optimal weight:    0.4980
   chunk 93 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 113 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 199 GLN
B 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.026684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2500 r_free = 0.2500 target = 0.020255 restraints weight = 140522.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2523 r_free = 0.2523 target = 0.020792 restraints weight = 108810.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.021156 restraints weight = 88578.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.021452 restraints weight = 76415.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.021691 restraints weight = 67891.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.066   9723  Z= 0.104
  Angle     :  0.570   6.526  13085  Z= 0.290
  Chirality :  0.044   0.185   1473
  Planarity :  0.003   0.045   1659
  Dihedral  :  4.532  22.979   1235
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.11 (0.26), residues: 1135
  helix:  1.28 (0.25), residues: 453
  sheet: -0.92 (0.41), residues: 142
  loop : -0.99 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1243 
 TYR   0.015   0.001   TYR B 185 
 PHE   0.027   0.001   PHE D 104 
 TRP   0.010   0.001   TRP C 163 
 HIS   0.006   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9719)
  covalent geometry    : angle       0.56226 (13079)
  hydrogen bonds       : bond        0.03123 (  366)
  hydrogen bonds       : angle       4.63830 ( 1050)
  metal coordination   : bond        0.00250 (    4)
  metal coordination   : angle       4.47061 (    6)

*********************** 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
  60 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  234 MET cc_start: 0.4360 (mmt) cc_final: 0.4154 (mmp)
REVERT: B  426 MET cc_start: 0.8888 (pmm) cc_final: 0.8657 (pmm)
REVERT: B  464 MET cc_start: 0.9395 (mmt) cc_final: 0.8941 (mmm)
REVERT: A 1306 ASP cc_start: 0.9248 (p0) cc_final: 0.9038 (p0)
REVERT: A 1312 TYR cc_start: 0.9696 (p90) cc_final: 0.9163 (p90)
REVERT: A 1369 ASP cc_start: 0.9693 (t70) cc_final: 0.9378 (m-30)
REVERT: D   64 VAL cc_start: 0.9789 (t) cc_final: 0.9130 (t)
REVERT: D  152 ARG cc_start: 0.9597 (ppt170) cc_final: 0.9175 (ttp80)
REVERT: D  222 MET cc_start: 0.9202 (ppp) cc_final: 0.8998 (ppp)
REVERT: D  247 TYR cc_start: 0.8900 (t80) cc_final: 0.8467 (t80)
REVERT: D  267 MET cc_start: 0.9632 (mtm) cc_final: 0.9328 (mtp)
REVERT: D  285 ARG cc_start: 0.9534 (mmp80) cc_final: 0.9237 (mmp-170)
REVERT: C   70 MET cc_start: 0.9220 (mmp) cc_final: 0.8889 (mmp)
REVERT: C  193 ASP cc_start: 0.9710 (t70) cc_final: 0.9476 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1037
  time to fit residues: 8.9879
Evaluate side-chains
  48 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    0.0770
   chunk 67 optimal weight:    0.0570
   chunk 65 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   overall best weight:    2.4262

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

Flipped N/Q/H residues before XYZ refinement:
B 247 ASN
B 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.025699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2471 r_free = 0.2471 target = 0.019507 restraints weight = 144395.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2491 r_free = 0.2491 target = 0.019983 restraints weight = 111845.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.020347 restraints weight = 92223.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.2517 r_free = 0.2517 target = 0.020623 restraints weight = 79403.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.020783 restraints weight = 70766.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9723  Z= 0.135
  Angle     :  0.582   7.400  13085  Z= 0.300
  Chirality :  0.043   0.181   1473
  Planarity :  0.004   0.044   1659
  Dihedral  :  4.592  22.528   1235
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.12 (0.26), residues: 1135
  helix:  1.23 (0.25), residues: 456
  sheet: -0.92 (0.41), residues: 142
  loop : -0.98 (0.29), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1243 
 TYR   0.014   0.001   TYR B 533 
 PHE   0.030   0.002   PHE D 104 
 TRP   0.009   0.001   TRP C 138 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9719)
  covalent geometry    : angle       0.57401 (13079)
  hydrogen bonds       : bond        0.03183 (  366)
  hydrogen bonds       : angle       4.70359 ( 1050)
  metal coordination   : bond        0.00205 (    4)
  metal coordination   : angle       4.47009 (    6)

*********************** 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
  57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  327 MET cc_start: 0.9058 (ppp) cc_final: 0.8748 (ppp)
REVERT: B  337 MET cc_start: 0.9446 (mpp) cc_final: 0.9245 (mpp)
REVERT: B  361 LEU cc_start: 0.9858 (mp) cc_final: 0.9644 (pt)
REVERT: B  486 PHE cc_start: 0.9308 (m-80) cc_final: 0.8965 (m-80)
REVERT: A 1247 ASP cc_start: 0.9284 (p0) cc_final: 0.8983 (t0)
REVERT: A 1312 TYR cc_start: 0.9707 (p90) cc_final: 0.9135 (p90)
REVERT: A 1342 MET cc_start: 0.8353 (ppp) cc_final: 0.7702 (ppp)
REVERT: A 1369 ASP cc_start: 0.9709 (t70) cc_final: 0.9388 (m-30)
REVERT: D   64 VAL cc_start: 0.9561 (t) cc_final: 0.9114 (t)
REVERT: D   68 MET cc_start: 0.9427 (mmp) cc_final: 0.9138 (mmm)
REVERT: D  267 MET cc_start: 0.9640 (mtm) cc_final: 0.9322 (mtp)
REVERT: D  285 ARG cc_start: 0.9548 (mmp80) cc_final: 0.9257 (mmp-170)
REVERT: C   70 MET cc_start: 0.9460 (mmp) cc_final: 0.9039 (mmp)
REVERT: C  155 ASP cc_start: 0.9447 (m-30) cc_final: 0.9243 (m-30)
REVERT: C  193 ASP cc_start: 0.9705 (t70) cc_final: 0.9473 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1062
  time to fit residues: 8.6574
Evaluate side-chains
  46 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   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 425 GLN
B 491 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.024657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2438 r_free = 0.2438 target = 0.018872 restraints weight = 158098.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.019331 restraints weight = 121889.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.2471 r_free = 0.2471 target = 0.019614 restraints weight = 100095.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2484 r_free = 0.2484 target = 0.019904 restraints weight = 87483.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2493 r_free = 0.2493 target = 0.020114 restraints weight = 77379.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.5657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9723  Z= 0.190
  Angle     :  0.657   8.189  13085  Z= 0.344
  Chirality :  0.045   0.203   1473
  Planarity :  0.004   0.044   1659
  Dihedral  :  5.026  23.939   1235
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.39 (0.25), residues: 1135
  helix:  0.99 (0.24), residues: 450
  sheet: -0.99 (0.42), residues: 141
  loop : -1.11 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1243 
 TYR   0.021   0.002   TYR C 186 
 PHE   0.025   0.002   PHE B 395 
 TRP   0.022   0.002   TRP C 283 
 HIS   0.006   0.002   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 9719)
  covalent geometry    : angle       0.64557 (13079)
  hydrogen bonds       : bond        0.03568 (  366)
  hydrogen bonds       : angle       5.00513 ( 1050)
  metal coordination   : bond        0.00366 (    4)
  metal coordination   : angle       5.75810 (    6)

*********************** 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 to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  426 MET cc_start: 0.8984 (pmm) cc_final: 0.8722 (pmm)
REVERT: B  486 PHE cc_start: 0.9323 (m-80) cc_final: 0.8991 (m-80)
REVERT: A 1247 ASP cc_start: 0.9318 (p0) cc_final: 0.9000 (t0)
REVERT: A 1312 TYR cc_start: 0.9720 (p90) cc_final: 0.9198 (p90)
REVERT: A 1369 ASP cc_start: 0.9722 (t70) cc_final: 0.9410 (m-30)
REVERT: D  222 MET cc_start: 0.9204 (ppp) cc_final: 0.8997 (ppp)
REVERT: D  267 MET cc_start: 0.9651 (mtm) cc_final: 0.9280 (mtm)
REVERT: C   70 MET cc_start: 0.9481 (mmp) cc_final: 0.9116 (mmp)
REVERT: C  155 ASP cc_start: 0.9596 (m-30) cc_final: 0.9376 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0916
  time to fit residues: 7.5352
Evaluate side-chains
  41 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 100 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 425 GLN
B 557 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.025437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2466 r_free = 0.2466 target = 0.019432 restraints weight = 151036.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2486 r_free = 0.2486 target = 0.019916 restraints weight = 114956.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2503 r_free = 0.2503 target = 0.020314 restraints weight = 92985.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.020599 restraints weight = 79511.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.020762 restraints weight = 70320.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   9723  Z= 0.113
  Angle     :  0.595   8.243  13085  Z= 0.301
  Chirality :  0.044   0.177   1473
  Planarity :  0.003   0.045   1659
  Dihedral  :  4.664  22.658   1235
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  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 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: -0.24 (0.26), residues: 1135
  helix:  1.14 (0.25), residues: 456
  sheet: -0.95 (0.41), residues: 141
  loop : -1.07 (0.28), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1243 
 TYR   0.013   0.001   TYR B 260 
 PHE   0.021   0.001   PHE B 395 
 TRP   0.010   0.001   TRP C 138 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9719)
  covalent geometry    : angle       0.58334 (13079)
  hydrogen bonds       : bond        0.03090 (  366)
  hydrogen bonds       : angle       4.83512 ( 1050)
  metal coordination   : bond        0.00187 (    4)
  metal coordination   : angle       5.50749 (    6)

********************** 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
  55 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1247 ASP cc_start: 0.9307 (p0) cc_final: 0.8991 (t0)
REVERT: A 1312 TYR cc_start: 0.9690 (p90) cc_final: 0.9155 (p90)
REVERT: A 1369 ASP cc_start: 0.9707 (t70) cc_final: 0.9393 (m-30)
REVERT: D   64 VAL cc_start: 0.9767 (t) cc_final: 0.9147 (t)
REVERT: D  222 MET cc_start: 0.9161 (ppp) cc_final: 0.8957 (ppp)
REVERT: D  267 MET cc_start: 0.9615 (mtm) cc_final: 0.9310 (mtp)
REVERT: C   70 MET cc_start: 0.9492 (mmp) cc_final: 0.9056 (mmp)
REVERT: C  193 ASP cc_start: 0.9694 (t0) cc_final: 0.9393 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0998
  time to fit residues: 8.1945
Evaluate side-chains
  45 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 112 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:   30.0000
   chunk 33 optimal weight:    9.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.024167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2428 r_free = 0.2428 target = 0.018653 restraints weight = 162358.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2449 r_free = 0.2449 target = 0.019100 restraints weight = 124127.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2464 r_free = 0.2464 target = 0.019441 restraints weight = 101415.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.019670 restraints weight = 86729.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.019900 restraints weight = 77583.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.6198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9723  Z= 0.226
  Angle     :  0.699   9.193  13085  Z= 0.366
  Chirality :  0.045   0.212   1473
  Planarity :  0.004   0.043   1659
  Dihedral  :  5.208  23.658   1235
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.60 (0.25), residues: 1135
  helix:  0.78 (0.24), residues: 455
  sheet: -0.98 (0.41), residues: 136
  loop : -1.24 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1243 
 TYR   0.021   0.002   TYR C 186 
 PHE   0.024   0.002   PHE B 395 
 TRP   0.023   0.003   TRP C 283 
 HIS   0.006   0.002   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 9719)
  covalent geometry    : angle       0.68647 (13079)
  hydrogen bonds       : bond        0.03745 (  366)
  hydrogen bonds       : angle       5.17750 ( 1050)
  metal coordination   : bond        0.00489 (    4)
  metal coordination   : angle       6.28117 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1440.50 seconds
wall clock time: 25 minutes 59.05 seconds (1559.05 seconds total)