Starting phenix.real_space_refine
on Thu Mar 13 01:34:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2025/7p15_13156.cif"
  }
  resolution = 3.58
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      34      5.49       5
     S      14      5.16       5
     C    5451      2.51       5
     N    1439      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8587
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 553, 4473
          Classifications: {'peptide': 553}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 515}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 3398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3398
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 30, 'TRANS': 385}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLN%COO:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "F"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 699
          Classifications: {'DNA': 32, 'RNA': 2}
          Modifications used: {'rna3p': 2}
          Link IDs: {'rna3p': 33}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 6
    Chain: "F"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'4OI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.26, per 1000 atoms: 0.61
  Number of scatterers: 8587
  At special positions: 0
  Unit cell: (95.06, 104.76, 100.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P      34     15.00
     O    1649      8.00
     N    1439      7.00
     C    5451      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: 2.38
  Conformation dependent library (CDL) restraints added in 918.6 milliseconds
  

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1826

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      38.7% alpha, 13.1% beta
      12 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 3.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 45
    Processing helix  chain 'A' and resid 77 through 83
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.525A  pdb=" N   ARG A 125 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 211
      removed outlier: 3.712A  pdb=" N   ARG A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 276 through 282
      removed outlier: 3.861A  pdb=" N   LEU A 282 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 363 through 384
    Processing helix  chain 'A' and resid 394 through 403
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.792A  pdb=" N   SER A 489 " --> pdb=" O   ALA A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 509
      removed outlier: 4.222A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ILE A 505 " --> pdb=" O   TYR A 501 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ILE A 506 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 543 through 553
      removed outlier: 3.983A  pdb=" N   GLN A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 44
    Processing helix  chain 'B' and resid 77 through 84
    Processing helix  chain 'B' and resid 112 through 118
      removed outlier: 3.831A  pdb=" N   SER B 117 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B 118 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 127
      removed outlier: 4.312A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 175
      removed outlier: 4.054A  pdb=" N   ALA B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 216
    Processing helix  chain 'B' and resid 235 through 239
      removed outlier: 3.532A  pdb=" N   TRP B 239 " --> pdb=" O   PRO B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
    Processing helix  chain 'B' and resid 276 through 282
    Processing helix  chain 'B' and resid 296 through 312
    Processing helix  chain 'B' and resid 363 through 383
    Processing helix  chain 'B' and resid 394 through 402
    Processing helix  chain 'B' and resid 403 through 406
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
      removed outlier: 3.641A  pdb=" N   SER A  48 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63
      removed outlier: 3.802A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331
      removed outlier: 3.725A  pdb=" N   GLN A 330 " --> pdb=" O   THR A 338 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TYR A 354 " --> pdb=" O   TRP A 337 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344
      removed outlier: 4.507A  pdb=" N   GLU A 344 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362
      removed outlier: 3.842A  pdb=" N   THR A 362 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS A 512 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 470
      removed outlier: 3.589A  pdb=" N   LYS A 465 " --> pdb=" O   TYR A 457 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR A 457 " --> pdb=" O   LYS A 465 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 455 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LEU A 452 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN A 447 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY A 456 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 63
    Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 183
      removed outlier: 3.645A  pdb=" N   LEU B 187 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER B 105 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TYR B 232 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 130
    Processing sheet with id=AB3, first strand: chain 'B' and resid 251 through 253
      removed outlier: 3.968A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 350
      removed outlier: 7.450A  pdb=" N   LYS B 347 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   GLN B 343 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 350
      removed outlier: 7.450A  pdb=" N   LYS B 347 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   GLN B 343 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN B 330 " --> pdb=" O   THR B 338 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU B 328 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ALA B 327 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 415 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1379
        1.32 -     1.44: 2448
        1.44 -     1.56: 4961
        1.56 -     1.69: 68
        1.69 -     1.81: 26
  Bond restraints: 8882
  Sorted by residual:
  bond pdb=" O3'  DC F  15 "
       pdb=" P    DT F  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.480  0.127 1.50e-02 4.44e+03 7.19e+01
  bond pdb=" C03 4OI F 101 "
       pdb=" C05 4OI F 101 "
    ideal  model  delta    sigma   weight residual
    1.492  1.610 -0.118 2.00e-02 2.50e+03 3.47e+01
  bond pdb=" O3'  DG F  31 "
       pdb=" P    DG F  32 "
    ideal  model  delta    sigma   weight residual
    1.607  1.681 -0.074 1.50e-02 4.44e+03 2.42e+01
  bond pdb=" C02 4OI F 101 "
       pdb=" N12 4OI F 101 "
    ideal  model  delta    sigma   weight residual
    1.356  1.449 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C02 4OI F 101 "
       pdb=" C03 4OI F 101 "
    ideal  model  delta    sigma   weight residual
    1.498  1.573 -0.075 2.00e-02 2.50e+03 1.41e+01
  ... (remaining 8877 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 12077
        3.54 -     7.08: 117
        7.08 -    10.62: 16
       10.62 -    14.16: 3
       14.16 -    17.70: 2
  Bond angle restraints: 12215
  Sorted by residual:
  angle pdb=" C5'  DA F  21 "
        pdb=" C4'  DA F  21 "
        pdb=" O4'  DA F  21 "
      ideal   model   delta    sigma   weight residual
     109.40  127.10  -17.70 1.50e+00 4.44e-01 1.39e+02
  angle pdb=" C3'  DC F  15 "
        pdb=" O3'  DC F  15 "
        pdb=" P    DT F  16 "
      ideal   model   delta    sigma   weight residual
     120.20  132.96  -12.76 1.50e+00 4.44e-01 7.24e+01
  angle pdb=" N   ASP B 186 "
        pdb=" CA  ASP B 186 "
        pdb=" C   ASP B 186 "
      ideal   model   delta    sigma   weight residual
     109.24  120.86  -11.62 1.63e+00 3.76e-01 5.08e+01
  angle pdb=" C5'  DC F  20 "
        pdb=" C4'  DC F  20 "
        pdb=" O4'  DC F  20 "
      ideal   model   delta    sigma   weight residual
     109.40  119.52  -10.12 1.50e+00 4.44e-01 4.55e+01
  angle pdb=" C5'  DC F  22 "
        pdb=" C4'  DC F  22 "
        pdb=" O4'  DC F  22 "
      ideal   model   delta    sigma   weight residual
     109.40  118.85   -9.45 1.50e+00 4.44e-01 3.97e+01
  ... (remaining 12210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4532
       17.94 -    35.89: 527
       35.89 -    53.83: 130
       53.83 -    71.78: 30
       71.78 -    89.72: 9
  Dihedral angle restraints: 5228
    sinusoidal: 2397
      harmonic: 2831
  Sorted by residual:
  dihedral pdb=" C   TYR A 181 "
           pdb=" N   TYR A 181 "
           pdb=" CA  TYR A 181 "
           pdb=" CB  TYR A 181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.61  -12.99     0      2.50e+00 1.60e-01 2.70e+01
  dihedral pdb=" C   GLU B 169 "
           pdb=" N   GLU B 169 "
           pdb=" CA  GLU B 169 "
           pdb=" CB  GLU B 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.60   10.00     0      2.50e+00 1.60e-01 1.60e+01
  dihedral pdb=" CA  GLU B 344 "
           pdb=" C   GLU B 344 "
           pdb=" N   PRO B 345 "
           pdb=" CA  PRO B 345 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.09  -19.91     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.157: 1303
       0.157 -    0.314: 24
       0.314 -    0.471: 9
       0.471 -    0.628: 2
       0.628 -    0.785: 1
  Chirality restraints: 1339
  Sorted by residual:
  chirality pdb=" C4'  DA F  21 "
            pdb=" C5'  DA F  21 "
            pdb=" O4'  DA F  21 "
            pdb=" C3'  DA F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -1.74   -0.79 2.00e-01 2.50e+01 1.54e+01
  chirality pdb=" C4'  DC F  20 "
            pdb=" C5'  DC F  20 "
            pdb=" O4'  DC F  20 "
            pdb=" C3'  DC F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -1.96   -0.57 2.00e-01 2.50e+01 8.03e+00
  chirality pdb=" C4'  DC F  22 "
            pdb=" C5'  DC F  22 "
            pdb=" O4'  DC F  22 "
            pdb=" C3'  DC F  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.01   -0.51 2.00e-01 2.50e+01 6.62e+00
  ... (remaining 1336 not shown)

  Planarity restraints: 1420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  78 "    0.540 9.50e-02 1.11e+02   2.42e-01 3.58e+01
        pdb=" NE  ARG A  78 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  78 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  78 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 536 "    0.059 5.00e-02 4.00e+02   8.88e-02 1.26e+01
        pdb=" N   PRO A 537 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 537 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 537 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 475 "   -0.016 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   GLN A 475 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLN A 475 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LYS A 476 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1417 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 842
        2.74 -     3.28: 8071
        3.28 -     3.82: 14246
        3.82 -     4.36: 16601
        4.36 -     4.90: 28282
  Nonbonded interactions: 68042
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  80 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP B  17 "
            pdb=" OH  TYR B  56 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   LEU A 486 "
            pdb=" NZ  LYS A 528 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O   LYS A 540 "
            pdb=" OG  SER B 280 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR B 253 "
            pdb=" OD1 ASP B 256 "
     model   vdw
     2.290 3.040
  ... (remaining 68037 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.130
  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:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.220
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
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      :  0.006   0.127   8882  Z= 0.346
  Angle     :  0.940  17.698  12215  Z= 0.557
  Chirality :  0.071   0.785   1339
  Planarity :  0.009   0.242   1420
  Dihedral  : 16.286  89.724   3402
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.75 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.15 (0.26), residues: 963
  helix:  0.33 (0.27), residues: 352
  sheet: -1.34 (0.45), residues: 132
  loop : -1.40 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 414 
 HIS   0.003   0.001   HIS A 208 
 PHE   0.021   0.002   PHE A  77 
 TYR   0.027   0.002   TYR B 339 
 ARG   0.004   0.001   ARG B 125 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 THR cc_start: 0.7879 (m) cc_final: 0.7417 (m)
REVERT: A  232 TYR cc_start: 0.8293 (m-10) cc_final: 0.7963 (m-10)
REVERT: A  537 PRO cc_start: 0.8730 (Cg_exo) cc_final: 0.8498 (Cg_endo)
REVERT: B   22 LYS cc_start: 0.7901 (tttm) cc_final: 0.7601 (pttt)
REVERT: B  185 ASP cc_start: 0.6693 (m-30) cc_final: 0.6230 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 127
  average time/residue: 0.2205
  time to fit residues: 38.0980
Evaluate side-chains
  95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 75 optimal weight:   30.0000
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
** B 340 GLN ** 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 = 0.4404 r_free = 0.4404 target = 0.207003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.169064 restraints weight = 10047.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.170160 restraints weight = 8539.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.172830 restraints weight = 6665.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8882  Z= 0.192
  Angle     :  0.580   7.682  12215  Z= 0.307
  Chirality :  0.043   0.170   1339
  Planarity :  0.005   0.059   1420
  Dihedral  : 13.967  59.680   1388
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  6.78 %
    Favored  : 92.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.67 (0.27), residues: 963
  helix:  0.87 (0.28), residues: 353
  sheet: -1.02 (0.45), residues: 143
  loop : -1.27 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 414 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.012   0.002   PHE B 124 
 TYR   0.021   0.002   TYR A 319 
 ARG   0.003   0.001   ARG A 307 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 2.176 
Fit side-chains
REVERT: A  339 TYR cc_start: 0.7440 (m-10) cc_final: 0.7034 (m-10)
REVERT: B   22 LYS cc_start: 0.7925 (tttm) cc_final: 0.7594 (pttt)
REVERT: B  357 MET cc_start: 0.6110 (tpp) cc_final: 0.5848 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 112
  average time/residue: 0.2048
  time to fit residues: 33.0955
Evaluate side-chains
  96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 71 optimal weight:   20.0000
   chunk 23 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 74 optimal weight:   30.0000
   chunk 39 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 55 optimal weight:   40.0000
   chunk 47 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
B 340 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.209639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.172058 restraints weight = 10134.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.173165 restraints weight = 8371.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.175714 restraints weight = 6518.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8882  Z= 0.156
  Angle     :  0.530   6.550  12215  Z= 0.279
  Chirality :  0.042   0.172   1339
  Planarity :  0.004   0.047   1420
  Dihedral  : 13.881  59.976   1388
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.47 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.21 (0.27), residues: 963
  helix:  1.35 (0.28), residues: 347
  sheet: -0.83 (0.43), residues: 149
  loop : -1.03 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 402 
 HIS   0.004   0.001   HIS B 198 
 PHE   0.011   0.001   PHE A  77 
 TYR   0.017   0.001   TYR A 319 
 ARG   0.003   0.000   ARG A  83 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  339 TYR cc_start: 0.7262 (m-10) cc_final: 0.6328 (m-10)
REVERT: A  340 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7664 (mp10)
REVERT: B   22 LYS cc_start: 0.7903 (tttm) cc_final: 0.7576 (pttt)
  outliers start: 11
  outliers final: 7
  residues processed: 125
  average time/residue: 0.1930
  time to fit residues: 34.6093
Evaluate side-chains
  108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.200177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.161674 restraints weight = 10213.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.162522 restraints weight = 8887.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164247 restraints weight = 7273.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8882  Z= 0.414
  Angle     :  0.716  10.651  12215  Z= 0.374
  Chirality :  0.048   0.169   1339
  Planarity :  0.006   0.046   1420
  Dihedral  : 14.462  59.881   1386
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.93 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.75 (0.27), residues: 963
  helix:  0.75 (0.28), residues: 345
  sheet: -1.34 (0.44), residues: 141
  loop : -1.13 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 402 
 HIS   0.005   0.002   HIS A 315 
 PHE   0.031   0.003   PHE A 160 
 TYR   0.030   0.003   TYR A 232 
 ARG   0.003   0.000   ARG B 125 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  340 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (mp10)
REVERT: A  356 ARG cc_start: 0.7320 (tpt-90) cc_final: 0.7084 (tpt-90)
REVERT: B   22 LYS cc_start: 0.7902 (tttm) cc_final: 0.7481 (pttt)
  outliers start: 17
  outliers final: 14
  residues processed: 121
  average time/residue: 0.2351
  time to fit residues: 40.0712
Evaluate side-chains
  110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  380 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 14 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 15 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
A 306 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.204165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.165439 restraints weight = 10099.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.169587 restraints weight = 8970.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.171124 restraints weight = 6457.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8882  Z= 0.230
  Angle     :  0.584   7.077  12215  Z= 0.307
  Chirality :  0.043   0.173   1339
  Planarity :  0.005   0.044   1420
  Dihedral  : 14.219  59.746   1386
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.50 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.39 (0.27), residues: 963
  helix:  1.17 (0.28), residues: 340
  sheet: -1.23 (0.41), residues: 155
  loop : -0.94 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.013   0.001   PHE A 160 
 TYR   0.025   0.002   TYR A 232 
 ARG   0.003   0.000   ARG B 125 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8170 (t60) cc_final: 0.7453 (t60)
REVERT: A  340 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7773 (mp10)
REVERT: B   22 LYS cc_start: 0.7930 (tttm) cc_final: 0.7502 (pttt)
  outliers start: 11
  outliers final: 9
  residues processed: 113
  average time/residue: 0.2077
  time to fit residues: 32.9227
Evaluate side-chains
  108 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  344 GLU
Chi-restraints excluded: chain B residue  380 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 14 optimal weight:    0.0000
   chunk 71 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0570
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0000
   overall best weight:    2.0110

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.206749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.168845 restraints weight = 9987.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170493 restraints weight = 8513.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172197 restraints weight = 6588.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8882  Z= 0.175
  Angle     :  0.536   6.703  12215  Z= 0.282
  Chirality :  0.042   0.172   1339
  Planarity :  0.004   0.043   1420
  Dihedral  : 14.018  59.881   1386
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.20 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.05 (0.27), residues: 963
  helix:  1.42 (0.28), residues: 341
  sheet: -0.90 (0.44), residues: 143
  loop : -0.79 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 212 
 HIS   0.002   0.001   HIS A 208 
 PHE   0.009   0.001   PHE A 130 
 TYR   0.018   0.001   TYR A 232 
 ARG   0.002   0.000   ARG B 211 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 TYR cc_start: 0.7272 (m-10) cc_final: 0.6649 (m-10)
REVERT: A  340 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7645 (mp10)
REVERT: B   22 LYS cc_start: 0.7879 (tttm) cc_final: 0.7495 (pttt)
  outliers start: 15
  outliers final: 8
  residues processed: 128
  average time/residue: 0.2305
  time to fit residues: 40.4489
Evaluate side-chains
  112 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:    0.0970
   chunk 97 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 75 optimal weight:   30.0000
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    4.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
A 306 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.203307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.165042 restraints weight = 10157.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.167115 restraints weight = 8753.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.168761 restraints weight = 6624.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8882  Z= 0.276
  Angle     :  0.608   7.321  12215  Z= 0.320
  Chirality :  0.044   0.171   1339
  Planarity :  0.005   0.073   1420
  Dihedral  : 14.215  59.530   1386
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.02 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.25 (0.27), residues: 963
  helix:  1.25 (0.29), residues: 339
  sheet: -1.09 (0.44), residues: 138
  loop : -0.88 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 212 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.018   0.002   PHE A 160 
 TYR   0.029   0.002   TYR A 232 
 ARG   0.016   0.001   ARG B 125 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A  339 TYR cc_start: 0.7381 (m-10) cc_final: 0.6956 (m-10)
REVERT: A  340 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7828 (mp10)
REVERT: B   22 LYS cc_start: 0.7904 (tttm) cc_final: 0.7503 (pttt)
  outliers start: 12
  outliers final: 10
  residues processed: 117
  average time/residue: 0.2265
  time to fit residues: 37.0652
Evaluate side-chains
  115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 10 optimal weight:    0.0020
   chunk 57 optimal weight:    4.9990
   chunk 75 optimal weight:   30.0000
   chunk 5 optimal weight:    0.1980
   chunk 73 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0670
   chunk 95 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    0.6530

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 258 GLN
A 306 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.209698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.172201 restraints weight = 10118.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.174713 restraints weight = 8268.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.176145 restraints weight = 6100.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8882  Z= 0.154
  Angle     :  0.525   6.342  12215  Z= 0.277
  Chirality :  0.041   0.169   1339
  Planarity :  0.005   0.061   1420
  Dihedral  : 13.876  59.598   1386
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.02 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.27), residues: 963
  helix:  1.68 (0.29), residues: 333
  sheet: -0.78 (0.43), residues: 141
  loop : -0.67 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 212 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.011   0.001   PHE A 130 
 TYR   0.013   0.001   TYR B 342 
 ARG   0.008   0.000   ARG B 125 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7622 (mp10)
REVERT: B   22 LYS cc_start: 0.7872 (tttm) cc_final: 0.7476 (pttt)
REVERT: B  356 ARG cc_start: 0.5920 (ptm160) cc_final: 0.5633 (ttm170)
  outliers start: 13
  outliers final: 6
  residues processed: 132
  average time/residue: 0.2199
  time to fit residues: 39.9874
Evaluate side-chains
  113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
A 306 ASN
** A 373 GLN ** 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 = 0.4397 r_free = 0.4397 target = 0.205683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.169312 restraints weight = 10109.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.170559 restraints weight = 8292.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.171893 restraints weight = 7482.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8882  Z= 0.223
  Angle     :  0.592  13.996  12215  Z= 0.305
  Chirality :  0.043   0.173   1339
  Planarity :  0.005   0.065   1420
  Dihedral  : 14.008  59.665   1386
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.61 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.02 (0.27), residues: 963
  helix:  1.42 (0.29), residues: 343
  sheet: -0.96 (0.43), residues: 141
  loop : -0.74 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 212 
 HIS   0.002   0.001   HIS B 208 
 PHE   0.012   0.001   PHE A 160 
 TYR   0.022   0.002   TYR A 232 
 ARG   0.007   0.001   ARG B 211 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 TYR cc_start: 0.7285 (m-10) cc_final: 0.6576 (m-10)
REVERT: A  340 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7698 (mp10)
REVERT: B   22 LYS cc_start: 0.7910 (tttm) cc_final: 0.7510 (pttt)
  outliers start: 11
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2134
  time to fit residues: 34.1235
Evaluate side-chains
  113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 98 optimal weight:   20.0000
   chunk 86 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
A 306 ASN
** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.201015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.164877 restraints weight = 10367.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.164378 restraints weight = 8924.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.166076 restraints weight = 8500.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8882  Z= 0.359
  Angle     :  0.698  12.015  12215  Z= 0.363
  Chirality :  0.047   0.172   1339
  Planarity :  0.006   0.088   1420
  Dihedral  : 14.444  60.884   1386
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.61 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.50 (0.27), residues: 963
  helix:  0.92 (0.28), residues: 341
  sheet: -1.16 (0.46), residues: 127
  loop : -0.97 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 212 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.024   0.002   PHE A 160 
 TYR   0.037   0.002   TYR A 232 
 ARG   0.007   0.001   ARG B 211 

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

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

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1926 Ramachandran restraints generated.
    963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8165 (t60) cc_final: 0.7466 (t60)
REVERT: A  340 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7865 (mp10)
REVERT: B   22 LYS cc_start: 0.7886 (tttm) cc_final: 0.7465 (pttt)
  outliers start: 12
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1908
  time to fit residues: 30.7912
Evaluate side-chains
  111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  189 VAL
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0970
   chunk 9 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 258 GLN
A 306 ASN
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.208915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.171509 restraints weight = 10099.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.173286 restraints weight = 8399.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.174473 restraints weight = 7122.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8882  Z= 0.166
  Angle     :  0.567  11.434  12215  Z= 0.295
  Chirality :  0.042   0.175   1339
  Planarity :  0.005   0.054   1420
  Dihedral  : 13.995  59.662   1386
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.31 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.06 (0.27), residues: 963
  helix:  1.43 (0.29), residues: 347
  sheet: -0.97 (0.42), residues: 141
  loop : -0.84 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 212 
 HIS   0.002   0.001   HIS A 198 
 PHE   0.014   0.001   PHE A 130 
 TYR   0.019   0.001   TYR B 115 
 ARG   0.008   0.000   ARG B 211 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2397.46 seconds
wall clock time: 43 minutes 56.60 seconds (2636.60 seconds total)