Starting phenix.real_space_refine
on Sun Apr 27 16:58:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yho_39290/04_2025/8yho_39290.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    3953      2.51       5
     N    1022      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6206
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 2028
          Classifications: {'peptide': 248}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 245}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2024
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 2, 'TRANS': 244}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2154
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 261}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 4.68, per 1000 atoms: 0.75
  Number of scatterers: 6206
  At special positions: 0
  Unit cell: (83.78, 87.33, 100.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O    1216      8.00
     N    1022      7.00
     C    3953      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: 1.56
  Conformation dependent library (CDL) restraints added in 775.3 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 5 sheets defined
      57.8% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 215 through 224
    Processing helix  chain 'A' and resid 229 through 246
      removed outlier: 3.543A  pdb=" N   ILE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 264
    Processing helix  chain 'A' and resid 270 through 280
      removed outlier: 3.554A  pdb=" N   ARG A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 292
      removed outlier: 3.727A  pdb=" N   ASP A 292 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 317
      removed outlier: 3.560A  pdb=" N   GLU A 303 " --> pdb=" O   ASP A 299 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A 305 " --> pdb=" O   ASN A 301 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   VAL A 313 " --> pdb=" O   SER A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 354
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 3.678A  pdb=" N   THR A 375 " --> pdb=" O   LYS A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 420
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'B' and resid 212 through 214
      No H-bonds generated for 'chain 'B' and resid 212 through 214'
    Processing helix  chain 'B' and resid 215 through 224
    Processing helix  chain 'B' and resid 230 through 246
    Processing helix  chain 'B' and resid 250 through 264
    Processing helix  chain 'B' and resid 269 through 281
    Processing helix  chain 'B' and resid 301 through 317
      removed outlier: 3.790A  pdb=" N   LYS B 305 " --> pdb=" O   ASN B 301 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN B 312 " --> pdb=" O   GLU B 308 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   VAL B 313 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 329
      removed outlier: 3.634A  pdb=" N   ILE B 327 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 354
    Processing helix  chain 'B' and resid 358 through 369
      removed outlier: 5.245A  pdb=" N   THR B 365 " --> pdb=" O   SER B 361 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   LEU B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU B 367 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 377
    Processing helix  chain 'B' and resid 401 through 423
      removed outlier: 3.685A  pdb=" N   ASN B 420 " --> pdb=" O   GLU B 416 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS B 421 " --> pdb=" O   PHE B 417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 173
    Processing helix  chain 'C' and resid 212 through 214
      No H-bonds generated for 'chain 'C' and resid 212 through 214'
    Processing helix  chain 'C' and resid 215 through 224
    Processing helix  chain 'C' and resid 229 through 246
    Processing helix  chain 'C' and resid 250 through 262
    Processing helix  chain 'C' and resid 271 through 282
      removed outlier: 3.645A  pdb=" N   LEU C 281 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 290
      removed outlier: 3.777A  pdb=" N   THR C 288 " --> pdb=" O   THR C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 317
      removed outlier: 3.827A  pdb=" N   VAL C 313 " --> pdb=" O   SER C 309 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY C 317 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 329
    Processing helix  chain 'C' and resid 336 through 344
    Processing helix  chain 'C' and resid 344 through 354
      removed outlier: 3.761A  pdb=" N   LEU C 350 " --> pdb=" O   TYR C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 363
      removed outlier: 3.781A  pdb=" N   SER C 361 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 363 through 369
      removed outlier: 3.736A  pdb=" N   GLU C 367 " --> pdb=" O   SER C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 377
    Processing helix  chain 'C' and resid 401 through 423
      removed outlier: 3.910A  pdb=" N   LEU C 406 " --> pdb=" O   ASP C 402 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE C 407 " --> pdb=" O   ASP C 403 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   THR C 410 " --> pdb=" O   LEU C 406 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS C 422 " --> pdb=" O   GLU C 418 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186
      removed outlier: 6.544A  pdb=" N   ILE A 185 " --> pdb=" O   TYR A 395 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   LYS A 199 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   SER A 396 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   VAL A 201 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 186
      removed outlier: 6.258A  pdb=" N   ILE B 185 " --> pdb=" O   TYR B 395 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   VAL B 201 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 210
      removed outlier: 5.196A  pdb=" N   ILE B 209 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 184 through 186
      removed outlier: 6.480A  pdb=" N   ILE C 185 " --> pdb=" O   TYR C 395 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LYS C 199 " --> pdb=" O   VAL C 394 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   SER C 396 " --> pdb=" O   LYS C 199 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL C 201 " --> pdb=" O   SER C 396 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 210
      removed outlier: 5.359A  pdb=" N   ILE C 209 " --> pdb=" O   GLY C 382 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    265 hydrogen bonds defined for protein.
    786 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: 1.59

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1169
        1.32 -     1.44: 1504
        1.44 -     1.56: 3586
        1.56 -     1.68: 5
        1.68 -     1.81: 27
  Bond restraints: 6291
  Sorted by residual:
  bond pdb=" N   LYS C 294 "
       pdb=" CA  LYS C 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.570 -0.113 1.29e-02 6.01e+03 7.68e+01
  bond pdb=" CA  LYS C 294 "
       pdb=" C   LYS C 294 "
    ideal  model  delta    sigma   weight residual
    1.523  1.630 -0.107 1.34e-02 5.57e+03 6.40e+01
  bond pdb=" C   THR C 284 "
       pdb=" O   THR C 284 "
    ideal  model  delta    sigma   weight residual
    1.234  1.311 -0.077 1.07e-02 8.73e+03 5.16e+01
  bond pdb=" N   ASP C 287 "
       pdb=" CA  ASP C 287 "
    ideal  model  delta    sigma   weight residual
    1.458  1.372  0.086 1.30e-02 5.92e+03 4.39e+01
  bond pdb=" CA  GLU C 303 "
       pdb=" C   GLU C 303 "
    ideal  model  delta    sigma   weight residual
    1.523  1.465  0.059 1.30e-02 5.92e+03 2.04e+01
  ... (remaining 6286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.56: 8303
        4.56 -     9.13: 137
        9.13 -    13.69: 15
       13.69 -    18.26: 1
       18.26 -    22.82: 4
  Bond angle restraints: 8460
  Sorted by residual:
  angle pdb=" N   ASP C 287 "
        pdb=" CA  ASP C 287 "
        pdb=" C   ASP C 287 "
      ideal   model   delta    sigma   weight residual
     113.55   90.73   22.82 1.26e+00 6.30e-01 3.28e+02
  angle pdb=" CA  LYS C 294 "
        pdb=" C   LYS C 294 "
        pdb=" O   LYS C 294 "
      ideal   model   delta    sigma   weight residual
     120.51  140.28  -19.77 1.43e+00 4.89e-01 1.91e+02
  angle pdb=" C   LYS C 290 "
        pdb=" N   TYR C 291 "
        pdb=" CA  TYR C 291 "
      ideal   model   delta    sigma   weight residual
     122.67  104.33   18.34 1.59e+00 3.96e-01 1.33e+02
  angle pdb=" N   ILE C 286 "
        pdb=" CA  ILE C 286 "
        pdb=" C   ILE C 286 "
      ideal   model   delta    sigma   weight residual
     112.80  101.23   11.57 1.15e+00 7.56e-01 1.01e+02
  angle pdb=" N   LYS C 294 "
        pdb=" CA  LYS C 294 "
        pdb=" C   LYS C 294 "
      ideal   model   delta    sigma   weight residual
     110.80  132.15  -21.35 2.13e+00 2.20e-01 1.00e+02
  ... (remaining 8455 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 3532
       17.00 -    34.01: 262
       34.01 -    51.01: 37
       51.01 -    68.02: 14
       68.02 -    85.02: 6
  Dihedral angle restraints: 3851
    sinusoidal: 1609
      harmonic: 2242
  Sorted by residual:
  dihedral pdb=" CA  GLY C 296 "
           pdb=" C   GLY C 296 "
           pdb=" N   ASN C 297 "
           pdb=" CA  ASN C 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  103.43   76.57     0      5.00e+00 4.00e-02 2.35e+02
  dihedral pdb=" CA  ASN C 297 "
           pdb=" C   ASN C 297 "
           pdb=" N   MET C 298 "
           pdb=" CA  MET C 298 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -114.55  -65.45     0      5.00e+00 4.00e-02 1.71e+02
  dihedral pdb=" CA  SER C 293 "
           pdb=" C   SER C 293 "
           pdb=" N   LYS C 294 "
           pdb=" CA  LYS C 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.39   54.61     0      5.00e+00 4.00e-02 1.19e+02
  ... (remaining 3848 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.185: 948
       0.185 -    0.370: 18
       0.370 -    0.554: 0
       0.554 -    0.739: 2
       0.739 -    0.924: 1
  Chirality restraints: 969
  Sorted by residual:
  chirality pdb=" CA  LYS C 294 "
            pdb=" N   LYS C 294 "
            pdb=" C   LYS C 294 "
            pdb=" CB  LYS C 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.59    0.92 2.00e-01 2.50e+01 2.13e+01
  chirality pdb=" CA  TYR C 291 "
            pdb=" N   TYR C 291 "
            pdb=" C   TYR C 291 "
            pdb=" CB  TYR C 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  SER C 293 "
            pdb=" N   SER C 293 "
            pdb=" C   SER C 293 "
            pdb=" CB  SER C 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.88    0.63 2.00e-01 2.50e+01 9.92e+00
  ... (remaining 966 not shown)

  Planarity restraints: 1076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 377 "    0.026 2.00e-02 2.50e+03   2.71e-02 1.29e+01
        pdb=" CG  PHE B 377 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 377 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 377 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 377 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 377 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 377 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 227 "   -0.017 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   GLU C 227 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLU C 227 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LEU C 228 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 281 "    0.017 2.00e-02 2.50e+03   3.41e-02 1.17e+01
        pdb=" C   LEU C 281 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LEU C 281 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASP C 282 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1073 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1134
        2.74 -     3.28: 6381
        3.28 -     3.82: 10706
        3.82 -     4.36: 13455
        4.36 -     4.90: 21649
  Nonbonded interactions: 53325
  Sorted by model distance:
  nonbonded pdb=" N   ASP C 287 "
            pdb=" N   THR C 288 "
     model   vdw
     2.200 2.560
  nonbonded pdb=" O   LEU A 350 "
            pdb=" OG  SER A 353 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" N   ILE C 286 "
            pdb=" N   ASP C 287 "
     model   vdw
     2.223 2.560
  nonbonded pdb=" O   PHE B 306 "
            pdb=" OG  SER B 309 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   SER B 361 "
            pdb=" OG  SER C 324 "
     model   vdw
     2.265 3.040
  ... (remaining 53320 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 179 through 294 or resid 296 through 318 or resid 321 thro \ 
ugh 428))
  selection = (chain 'B' and (resid 179 through 327 or resid 329 through 428))
  selection = (chain 'C' and (resid 179 through 294 or resid 296 through 327 or resid 329 thro \ 
ugh 428))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.730
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.870
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  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:11.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
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      :  0.018   0.142   6291  Z= 0.815
  Angle     :  1.523  22.821   8460  Z= 0.893
  Chirality :  0.083   0.924    969
  Planarity :  0.007   0.039   1076
  Dihedral  : 12.890  85.019   2387
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  8.21 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  6.35 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.55 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.81 (0.23), residues: 743
  helix: -3.43 (0.16), residues: 419
  sheet: -2.92 (0.74), residues: 25
  loop : -2.59 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP A 253 
 HIS   0.014   0.002   HIS B 184 
 PHE   0.059   0.005   PHE B 377 
 TYR   0.032   0.005   TYR B 240 
 ARG   0.015   0.003   ARG C 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27660 (  265)
  hydrogen bonds       : angle       9.83133 (  786)
  covalent geometry    : bond        0.01792 ( 6291)
  covalent geometry    : angle       1.52251 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  263 TYR cc_start: 0.8383 (t80) cc_final: 0.8059 (t80)
REVERT: B  287 ASP cc_start: 0.8590 (t0) cc_final: 0.8375 (OUTLIER)
REVERT: B  291 TYR cc_start: 0.7465 (t80) cc_final: 0.6969 (t80)
REVERT: B  308 GLU cc_start: 0.8886 (tt0) cc_final: 0.8563 (tm-30)
REVERT: B  312 ASN cc_start: 0.7863 (p0) cc_final: 0.7544 (p0)
REVERT: B  362 TYR cc_start: 0.8374 (m-80) cc_final: 0.8008 (m-80)
REVERT: B  395 TYR cc_start: 0.8749 (m-10) cc_final: 0.8507 (m-10)
REVERT: B  405 LEU cc_start: 0.9260 (tt) cc_final: 0.9045 (tm)
REVERT: C  240 TYR cc_start: 0.8757 (m-80) cc_final: 0.8539 (m-80)
REVERT: C  291 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6544 (t80)
  outliers start: 13
  outliers final: 3
  residues processed: 140
  average time/residue: 1.2209
  time to fit residues: 179.2698
Evaluate side-chains
  74 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain C residue  291 TYR
Chi-restraints excluded: chain C residue  321 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
B 180 ASN
B 213 ASN
B 221 ASN
B 242 ASN
B 246 ASN
B 338 ASN
C 174 ASN
** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 297 ASN
C 372 ASN
C 379 ASN
C 420 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.135526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.098439 restraints weight = 12858.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 3.60
r_work: 0.3408 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6291  Z= 0.173
  Angle     :  0.745   9.379   8460  Z= 0.392
  Chirality :  0.045   0.221    969
  Planarity :  0.004   0.025   1076
  Dihedral  :  7.077  45.285    803
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.65 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 11.85 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.27), residues: 743
  helix: -1.56 (0.21), residues: 432
  sheet: -3.38 (0.68), residues: 30
  loop : -2.31 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 253 
 HIS   0.003   0.001   HIS A 184 
 PHE   0.027   0.002   PHE B 306 
 TYR   0.026   0.002   TYR A 291 
 ARG   0.004   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  265)
  hydrogen bonds       : angle       5.43908 (  786)
  covalent geometry    : bond        0.00391 ( 6291)
  covalent geometry    : angle       0.74547 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8694 (m-30) cc_final: 0.8291 (t0)
REVERT: A  256 CYS cc_start: 0.9171 (m) cc_final: 0.8925 (m)
REVERT: A  290 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8872 (tmmt)
REVERT: A  395 TYR cc_start: 0.7662 (m-80) cc_final: 0.7261 (m-80)
REVERT: B  189 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (m90)
REVERT: B  218 ASP cc_start: 0.8484 (m-30) cc_final: 0.8251 (m-30)
REVERT: B  263 TYR cc_start: 0.8578 (t80) cc_final: 0.8307 (t80)
REVERT: B  274 ARG cc_start: 0.9146 (ttp-110) cc_final: 0.8795 (ptm-80)
REVERT: B  291 TYR cc_start: 0.8117 (t80) cc_final: 0.7618 (t80)
REVERT: C  217 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7470 (tp40)
REVERT: C  236 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8190 (mmm)
REVERT: C  252 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8542 (pp20)
REVERT: C  298 MET cc_start: 0.7492 (pmm) cc_final: 0.6892 (ttm)
REVERT: C  406 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7451 (tm)
  outliers start: 24
  outliers final: 3
  residues processed: 128
  average time/residue: 1.2671
  time to fit residues: 171.4167
Evaluate side-chains
  84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  189 HIS
Chi-restraints excluded: chain C residue  236 MET
Chi-restraints excluded: chain C residue  252 GLU
Chi-restraints excluded: chain C residue  269 ASP
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 52 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 205 ASN
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.134546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.096082 restraints weight = 12827.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 3.71
r_work: 0.3421 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6291  Z= 0.151
  Angle     :  0.706  11.844   8460  Z= 0.358
  Chirality :  0.043   0.199    969
  Planarity :  0.003   0.019   1076
  Dihedral  :  5.963  32.095    797
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.46 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.82 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.30), residues: 743
  helix: -0.63 (0.24), residues: 437
  sheet: -3.06 (0.73), residues: 30
  loop : -1.80 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 253 
 HIS   0.002   0.001   HIS B 184 
 PHE   0.022   0.002   PHE B 306 
 TYR   0.017   0.002   TYR A 362 
 ARG   0.009   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03565 (  265)
  hydrogen bonds       : angle       4.89671 (  786)
  covalent geometry    : bond        0.00350 ( 6291)
  covalent geometry    : angle       0.70593 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8719 (m-30) cc_final: 0.8290 (t0)
REVERT: A  256 CYS cc_start: 0.9175 (m) cc_final: 0.8944 (m)
REVERT: A  298 MET cc_start: 0.4786 (pmm) cc_final: 0.4527 (pmm)
REVERT: A  363 SER cc_start: 0.8935 (m) cc_final: 0.8310 (t)
REVERT: A  395 TYR cc_start: 0.7576 (m-80) cc_final: 0.7266 (m-80)
REVERT: A  402 ASP cc_start: 0.8596 (m-30) cc_final: 0.8290 (p0)
REVERT: B  189 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.7778 (m90)
REVERT: B  263 TYR cc_start: 0.8521 (t80) cc_final: 0.8282 (t80)
REVERT: B  291 TYR cc_start: 0.7986 (t80) cc_final: 0.7242 (t80)
REVERT: C  205 ASN cc_start: 0.9030 (m-40) cc_final: 0.8669 (m110)
REVERT: C  236 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8615 (mmm)
REVERT: C  305 LYS cc_start: 0.9344 (mmtm) cc_final: 0.9088 (mmtm)
REVERT: C  406 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7351 (tm)
REVERT: C  414 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8028 (mttt)
  outliers start: 23
  outliers final: 3
  residues processed: 108
  average time/residue: 0.9950
  time to fit residues: 113.9956
Evaluate side-chains
  82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  189 HIS
Chi-restraints excluded: chain B residue  287 ASP
Chi-restraints excluded: chain C residue  236 MET
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Chi-restraints excluded: chain C residue  414 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0870
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:   30.0000
   chunk 38 optimal weight:    0.0870
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.135711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.098318 restraints weight = 12937.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.67
r_work: 0.3471 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6291  Z= 0.137
  Angle     :  0.690   9.496   8460  Z= 0.346
  Chirality :  0.043   0.221    969
  Planarity :  0.003   0.019   1076
  Dihedral  :  5.523  29.012    797
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.37 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.30), residues: 743
  helix: -0.18 (0.24), residues: 440
  sheet: -2.87 (0.77), residues: 30
  loop : -1.77 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 253 
 HIS   0.002   0.000   HIS B 184 
 PHE   0.031   0.002   PHE B 377 
 TYR   0.016   0.002   TYR A 362 
 ARG   0.003   0.000   ARG C 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  265)
  hydrogen bonds       : angle       4.71598 (  786)
  covalent geometry    : bond        0.00317 ( 6291)
  covalent geometry    : angle       0.68979 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 1.019 
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  206 ASP cc_start: 0.8703 (m-30) cc_final: 0.8306 (t0)
REVERT: A  256 CYS cc_start: 0.9166 (m) cc_final: 0.8936 (m)
REVERT: A  298 MET cc_start: 0.4989 (pmm) cc_final: 0.4606 (pmm)
REVERT: A  363 SER cc_start: 0.8953 (m) cc_final: 0.8323 (t)
REVERT: A  395 TYR cc_start: 0.7587 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  402 ASP cc_start: 0.8528 (m-30) cc_final: 0.8266 (p0)
REVERT: B  181 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8618 (mt)
REVERT: B  189 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7814 (m90)
REVERT: B  291 TYR cc_start: 0.7929 (t80) cc_final: 0.7128 (t80)
REVERT: B  362 TYR cc_start: 0.8511 (m-80) cc_final: 0.8132 (m-80)
REVERT: B  376 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8398 (ttp80)
REVERT: C  192 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (m-80)
REVERT: C  205 ASN cc_start: 0.9045 (m-40) cc_final: 0.8683 (m110)
REVERT: C  240 TYR cc_start: 0.8820 (m-80) cc_final: 0.8589 (m-80)
REVERT: C  298 MET cc_start: 0.6693 (pmm) cc_final: 0.5943 (tpp)
REVERT: C  406 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7230 (tm)
  outliers start: 28
  outliers final: 4
  residues processed: 108
  average time/residue: 0.8887
  time to fit residues: 102.9578
Evaluate side-chains
  86 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  189 HIS
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  192 TYR
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0270
   chunk 8 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0060
   chunk 45 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0770
   chunk 65 optimal weight:    0.2980
   overall best weight:    0.2012

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.138298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.101571 restraints weight = 12796.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 3.72
r_work: 0.3534 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6291  Z= 0.114
  Angle     :  0.665   9.093   8460  Z= 0.334
  Chirality :  0.042   0.197    969
  Planarity :  0.003   0.020   1076
  Dihedral  :  5.075  25.221    797
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.78 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.31), residues: 743
  helix:  0.21 (0.25), residues: 442
  sheet: -2.59 (0.82), residues: 30
  loop : -1.64 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 253 
 HIS   0.002   0.000   HIS B 184 
 PHE   0.023   0.001   PHE B 306 
 TYR   0.014   0.002   TYR A 362 
 ARG   0.009   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  265)
  hydrogen bonds       : angle       4.51398 (  786)
  covalent geometry    : bond        0.00254 ( 6291)
  covalent geometry    : angle       0.66505 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 1.369 
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: A  206 ASP cc_start: 0.8649 (m-30) cc_final: 0.8270 (t0)
REVERT: A  256 CYS cc_start: 0.9170 (m) cc_final: 0.8940 (m)
REVERT: A  298 MET cc_start: 0.4942 (pmm) cc_final: 0.4514 (pmm)
REVERT: A  363 SER cc_start: 0.8808 (m) cc_final: 0.8245 (t)
REVERT: A  384 ASN cc_start: 0.8472 (m-40) cc_final: 0.8001 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8862 (m) cc_final: 0.8390 (p)
REVERT: A  395 TYR cc_start: 0.7675 (m-80) cc_final: 0.7352 (m-80)
REVERT: B  181 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8625 (mt)
REVERT: B  218 ASP cc_start: 0.8282 (m-30) cc_final: 0.7924 (m-30)
REVERT: B  236 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8497 (mtp)
REVERT: B  291 TYR cc_start: 0.7405 (t80) cc_final: 0.6958 (t80)
REVERT: B  393 ILE cc_start: 0.8817 (mt) cc_final: 0.8579 (tp)
REVERT: C  192 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7771 (m-80)
REVERT: C  205 ASN cc_start: 0.9027 (m-40) cc_final: 0.8669 (m110)
REVERT: C  236 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8490 (mmm)
REVERT: C  298 MET cc_start: 0.6350 (pmm) cc_final: 0.5705 (tpp)
REVERT: C  406 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7109 (tm)
  outliers start: 28
  outliers final: 5
  residues processed: 114
  average time/residue: 1.0268
  time to fit residues: 125.3955
Evaluate side-chains
  85 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  192 TYR
Chi-restraints excluded: chain C residue  236 MET
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 49 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0060
   chunk 51 optimal weight:    8.9990
   chunk 57 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0370
   overall best weight:    0.7678

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.135368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.096962 restraints weight = 12808.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 3.71
r_work: 0.3479 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6291  Z= 0.161
  Angle     :  0.726  10.277   8460  Z= 0.355
  Chirality :  0.044   0.204    969
  Planarity :  0.003   0.029   1076
  Dihedral  :  5.019  24.733    797
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 18.05 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.31), residues: 743
  helix:  0.28 (0.25), residues: 446
  sheet: -2.32 (0.85), residues: 30
  loop : -1.33 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 219 
 HIS   0.001   0.000   HIS A 182 
 PHE   0.034   0.002   PHE B 377 
 TYR   0.014   0.002   TYR A 362 
 ARG   0.005   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  265)
  hydrogen bonds       : angle       4.61277 (  786)
  covalent geometry    : bond        0.00381 ( 6291)
  covalent geometry    : angle       0.72643 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8670 (m-30) cc_final: 0.8304 (t0)
REVERT: A  256 CYS cc_start: 0.9181 (m) cc_final: 0.8956 (m)
REVERT: A  298 MET cc_start: 0.5103 (pmm) cc_final: 0.4653 (pmm)
REVERT: A  363 SER cc_start: 0.8886 (m) cc_final: 0.8283 (t)
REVERT: A  384 ASN cc_start: 0.8564 (m-40) cc_final: 0.8077 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8909 (m) cc_final: 0.8455 (p)
REVERT: A  395 TYR cc_start: 0.7732 (m-80) cc_final: 0.7407 (m-80)
REVERT: B  181 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (mt)
REVERT: B  236 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mtp)
REVERT: B  291 TYR cc_start: 0.7362 (t80) cc_final: 0.7084 (t80)
REVERT: B  362 TYR cc_start: 0.8550 (m-80) cc_final: 0.8229 (m-80)
REVERT: B  393 ILE cc_start: 0.8810 (mt) cc_final: 0.8545 (tp)
REVERT: C  192 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.8064 (m-80)
REVERT: C  205 ASN cc_start: 0.9035 (m-40) cc_final: 0.8655 (m110)
REVERT: C  231 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7825 (tp)
REVERT: C  298 MET cc_start: 0.6264 (pmm) cc_final: 0.5796 (tmm)
REVERT: C  406 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7451 (tm)
  outliers start: 27
  outliers final: 6
  residues processed: 98
  average time/residue: 0.9484
  time to fit residues: 99.5979
Evaluate side-chains
  78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  192 TYR
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  287 ASP
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0020
   chunk 16 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   overall best weight:    0.8190

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.135203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.097388 restraints weight = 12862.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.66
r_work: 0.3462 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6291  Z= 0.167
  Angle     :  0.733  10.079   8460  Z= 0.361
  Chirality :  0.045   0.209    969
  Planarity :  0.003   0.026   1076
  Dihedral  :  4.952  24.476    797
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.76 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.31), residues: 743
  helix:  0.30 (0.25), residues: 441
  sheet: -2.20 (0.87), residues: 30
  loop : -1.43 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 219 
 HIS   0.001   0.000   HIS A 182 
 PHE   0.032   0.002   PHE B 306 
 TYR   0.024   0.002   TYR C 362 
 ARG   0.006   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  265)
  hydrogen bonds       : angle       4.67347 (  786)
  covalent geometry    : bond        0.00393 ( 6291)
  covalent geometry    : angle       0.73264 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8674 (m-30) cc_final: 0.8334 (t0)
REVERT: A  256 CYS cc_start: 0.9207 (m) cc_final: 0.8972 (m)
REVERT: A  298 MET cc_start: 0.5027 (pmm) cc_final: 0.4643 (pmm)
REVERT: A  344 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8566 (mp)
REVERT: A  363 SER cc_start: 0.8882 (m) cc_final: 0.8261 (t)
REVERT: A  384 ASN cc_start: 0.8617 (m-40) cc_final: 0.8153 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8921 (m) cc_final: 0.8475 (p)
REVERT: B  181 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8638 (mt)
REVERT: B  236 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8548 (mtp)
REVERT: B  362 TYR cc_start: 0.8550 (m-80) cc_final: 0.8259 (m-80)
REVERT: B  395 TYR cc_start: 0.8082 (m-10) cc_final: 0.7835 (m-10)
REVERT: C  174 ASN cc_start: 0.4279 (OUTLIER) cc_final: 0.3534 (t0)
REVERT: C  192 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7960 (m-80)
REVERT: C  205 ASN cc_start: 0.9061 (m-40) cc_final: 0.8684 (m110)
REVERT: C  231 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7845 (tp)
REVERT: C  298 MET cc_start: 0.6258 (pmm) cc_final: 0.5773 (tmm)
REVERT: C  305 LYS cc_start: 0.9234 (mttp) cc_final: 0.8997 (mptp)
REVERT: C  406 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7454 (tm)
  outliers start: 23
  outliers final: 6
  residues processed: 93
  average time/residue: 0.8251
  time to fit residues: 82.7460
Evaluate side-chains
  80 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  192 TYR
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  287 ASP
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    0.0770
   chunk 70 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 69 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.136220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.099123 restraints weight = 12878.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 3.63
r_work: 0.3492 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6291  Z= 0.147
  Angle     :  0.730  10.702   8460  Z= 0.359
  Chirality :  0.044   0.265    969
  Planarity :  0.003   0.026   1076
  Dihedral  :  4.855  25.259    797
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.89 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.31), residues: 743
  helix:  0.24 (0.24), residues: 453
  sheet: -2.08 (0.90), residues: 30
  loop : -1.27 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 182 
 PHE   0.035   0.002   PHE B 306 
 TYR   0.014   0.001   TYR A 362 
 ARG   0.005   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  265)
  hydrogen bonds       : angle       4.70032 (  786)
  covalent geometry    : bond        0.00345 ( 6291)
  covalent geometry    : angle       0.72997 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8670 (m-30) cc_final: 0.8363 (t0)
REVERT: A  256 CYS cc_start: 0.9182 (m) cc_final: 0.8949 (m)
REVERT: A  298 MET cc_start: 0.5024 (pmm) cc_final: 0.4647 (pmm)
REVERT: A  323 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7645 (pp)
REVERT: A  363 SER cc_start: 0.8851 (m) cc_final: 0.8258 (t)
REVERT: A  384 ASN cc_start: 0.8648 (m-40) cc_final: 0.8189 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8921 (m) cc_final: 0.8494 (p)
REVERT: A  395 TYR cc_start: 0.7697 (m-80) cc_final: 0.7377 (m-80)
REVERT: B  181 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8649 (mt)
REVERT: B  236 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8529 (mtp)
REVERT: B  395 TYR cc_start: 0.8074 (m-10) cc_final: 0.7785 (m-10)
REVERT: B  423 MET cc_start: 0.9154 (mpp) cc_final: 0.8780 (tpt)
REVERT: C  174 ASN cc_start: 0.4237 (OUTLIER) cc_final: 0.3481 (t0)
REVERT: C  192 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7874 (m-80)
REVERT: C  205 ASN cc_start: 0.9043 (m-40) cc_final: 0.8659 (m110)
REVERT: C  231 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7719 (tp)
REVERT: C  298 MET cc_start: 0.6152 (pmm) cc_final: 0.5746 (tmm)
REVERT: C  305 LYS cc_start: 0.9249 (mttp) cc_final: 0.8977 (mptp)
REVERT: C  406 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7481 (tm)
  outliers start: 21
  outliers final: 6
  residues processed: 89
  average time/residue: 1.2131
  time to fit residues: 118.1705
Evaluate side-chains
  83 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  192 TYR
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 44 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN
** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.132049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092331 restraints weight = 12937.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 3.75
r_work: 0.3380 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6291  Z= 0.251
  Angle     :  0.811  12.175   8460  Z= 0.399
  Chirality :  0.047   0.329    969
  Planarity :  0.004   0.044   1076
  Dihedral  :  5.030  23.787    797
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.59 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.31), residues: 743
  helix:  0.08 (0.24), residues: 455
  sheet: -2.04 (0.90), residues: 30
  loop : -1.24 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 219 
 HIS   0.002   0.000   HIS A 182 
 PHE   0.043   0.002   PHE B 306 
 TYR   0.023   0.002   TYR C 240 
 ARG   0.007   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  265)
  hydrogen bonds       : angle       4.86123 (  786)
  covalent geometry    : bond        0.00596 ( 6291)
  covalent geometry    : angle       0.81129 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 ASP cc_start: 0.8716 (m-30) cc_final: 0.8431 (t0)
REVERT: A  256 CYS cc_start: 0.9183 (m) cc_final: 0.8845 (t)
REVERT: A  298 MET cc_start: 0.5298 (pmm) cc_final: 0.4883 (pmm)
REVERT: A  323 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7839 (pp)
REVERT: A  363 SER cc_start: 0.9047 (m) cc_final: 0.8420 (t)
REVERT: A  384 ASN cc_start: 0.8798 (m-40) cc_final: 0.8323 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8940 (m) cc_final: 0.8523 (p)
REVERT: B  181 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8719 (mt)
REVERT: B  236 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8569 (mtp)
REVERT: B  395 TYR cc_start: 0.8274 (m-10) cc_final: 0.8021 (m-10)
REVERT: B  423 MET cc_start: 0.9167 (mpp) cc_final: 0.8774 (tpt)
REVERT: C  174 ASN cc_start: 0.4319 (OUTLIER) cc_final: 0.3547 (t0)
REVERT: C  205 ASN cc_start: 0.9071 (m-40) cc_final: 0.8666 (m110)
REVERT: C  298 MET cc_start: 0.6156 (pmm) cc_final: 0.5756 (tmm)
REVERT: C  406 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7518 (tm)
  outliers start: 13
  outliers final: 5
  residues processed: 81
  average time/residue: 0.9727
  time to fit residues: 84.5676
Evaluate side-chains
  71 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   chunk 49 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.136144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.098878 restraints weight = 13021.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 3.66
r_work: 0.3487 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6291  Z= 0.144
  Angle     :  0.775  12.659   8460  Z= 0.371
  Chirality :  0.044   0.314    969
  Planarity :  0.003   0.062   1076
  Dihedral  :  4.878  26.527    797
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.58 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.31), residues: 743
  helix:  0.22 (0.24), residues: 453
  sheet: -1.95 (0.93), residues: 30
  loop : -1.10 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 253 
 HIS   0.001   0.000   HIS B 182 
 PHE   0.044   0.002   PHE B 306 
 TYR   0.014   0.002   TYR A 362 
 ARG   0.020   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  265)
  hydrogen bonds       : angle       4.77814 (  786)
  covalent geometry    : bond        0.00339 ( 6291)
  covalent geometry    : angle       0.77496 ( 8460)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.815 
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  206 ASP cc_start: 0.8657 (m-30) cc_final: 0.8372 (t0)
REVERT: A  256 CYS cc_start: 0.9191 (m) cc_final: 0.8947 (m)
REVERT: A  298 MET cc_start: 0.5110 (pmm) cc_final: 0.4685 (pmm)
REVERT: A  323 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7519 (pp)
REVERT: A  363 SER cc_start: 0.8874 (m) cc_final: 0.8244 (t)
REVERT: A  384 ASN cc_start: 0.8676 (m-40) cc_final: 0.8236 (OUTLIER)
REVERT: A  386 THR cc_start: 0.8906 (m) cc_final: 0.8484 (p)
REVERT: B  181 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (mt)
REVERT: B  236 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8286 (mmm)
REVERT: B  362 TYR cc_start: 0.8450 (m-80) cc_final: 0.8215 (m-80)
REVERT: B  376 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8614 (ttp80)
REVERT: B  395 TYR cc_start: 0.8153 (m-10) cc_final: 0.7795 (m-10)
REVERT: B  423 MET cc_start: 0.9171 (mpp) cc_final: 0.8799 (tpt)
REVERT: C  174 ASN cc_start: 0.4168 (OUTLIER) cc_final: 0.3425 (t0)
REVERT: C  205 ASN cc_start: 0.9039 (m-40) cc_final: 0.8645 (m110)
REVERT: C  236 MET cc_start: 0.8801 (mmm) cc_final: 0.8534 (mmm)
REVERT: C  298 MET cc_start: 0.5853 (pmm) cc_final: 0.5523 (tmm)
REVERT: C  406 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7477 (tm)
  outliers start: 13
  outliers final: 6
  residues processed: 81
  average time/residue: 0.7866
  time to fit residues: 68.9165
Evaluate side-chains
  79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  236 MET
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain C residue  174 ASN
Chi-restraints excluded: chain C residue  252 GLU
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 1 optimal weight:    0.3980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.135905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.098428 restraints weight = 12905.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 3.68
r_work: 0.3470 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6291  Z= 0.150
  Angle     :  0.777  12.362   8460  Z= 0.373
  Chirality :  0.045   0.318    969
  Planarity :  0.003   0.049   1076
  Dihedral  :  4.786  25.449    797
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.44 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.31), residues: 743
  helix:  0.38 (0.24), residues: 447
  sheet: -1.85 (0.95), residues: 30
  loop : -1.08 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 253 
 HIS   0.001   0.000   HIS B 182 
 PHE   0.044   0.002   PHE B 306 
 TYR   0.014   0.002   TYR A 362 
 ARG   0.017   0.001   ARG A 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  265)
  hydrogen bonds       : angle       4.71421 (  786)
  covalent geometry    : bond        0.00358 ( 6291)
  covalent geometry    : angle       0.77693 ( 8460)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5358.62 seconds
wall clock time: 95 minutes 38.51 seconds (5738.51 seconds total)