Starting phenix.real_space_refine
on Tue Mar  3 20:08:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_13156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_13156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_13156.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_13156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p15_13156/03_2026/7p15_13156.map"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'TRP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'GLN%COO:plan1': 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: 1.99, per 1000 atoms: 0.23
  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: 0.66
  Conformation dependent library (CDL) restraints added in 288.2 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: 0.77
  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: 1.33

  Time building geometry restraints manager: 0.90 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:             0.180
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     9.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.870
-------------------------------------------------------------------------------
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= 0.329
  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 : 8.99
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG B 125 
 TYR   0.027   0.002   TYR B 339 
 PHE   0.021   0.002   PHE A  77 
 TRP   0.047   0.002   TRP B 414 
 HIS   0.003   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 8882)
  covalent geometry    : angle       0.93980 (12215)
  hydrogen bonds       : bond        0.17860 (  331)
  hydrogen bonds       : angle       7.26020 (  880)

*********************** 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  : 0.295 
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: 0.7600 (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: 0.0981
  time to fit residues: 17.0854
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  : 0.314 
-------------------------------------------------------------------------------
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 49 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0970
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 161 GLN
A 258 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.208233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.171241 restraints weight = 10199.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.171613 restraints weight = 9414.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.172715 restraints weight = 7826.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.173198 restraints weight = 6833.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.174799 restraints weight = 5936.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8882  Z= 0.121
  Angle     :  0.567   7.863  12215  Z= 0.301
  Chirality :  0.043   0.170   1339
  Planarity :  0.005   0.058   1420
  Dihedral  : 13.917  59.593   1388
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  6.67 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.27), residues: 963
  helix:  0.95 (0.28), residues: 353
  sheet: -0.91 (0.45), residues: 143
  loop : -1.25 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 143 
 TYR   0.020   0.001   TYR A 319 
 PHE   0.012   0.001   PHE B 124 
 TRP   0.019   0.001   TRP B 414 
 HIS   0.002   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8882)
  covalent geometry    : angle       0.56729 (12215)
  hydrogen bonds       : bond        0.04005 (  331)
  hydrogen bonds       : angle       4.80755 (  880)

*********************** 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
  115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   10 VAL cc_start: 0.8306 (p) cc_final: 0.7914 (m)
REVERT: A  339 TYR cc_start: 0.7433 (m-10) cc_final: 0.6905 (m-10)
REVERT: B   22 LYS cc_start: 0.7903 (tttm) cc_final: 0.7556 (pttt)
REVERT: B  357 MET cc_start: 0.6180 (tpp) cc_final: 0.5916 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 113
  average time/residue: 0.0880
  time to fit residues: 14.1156
Evaluate side-chains
  97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 ILE
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 12 optimal weight:   20.0000
   chunk 2 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 19 optimal weight:   40.0000
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0370
   chunk 73 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 64 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.4462

-------------------------------------------------------------------------------
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
B 340 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.209876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.173429 restraints weight = 10011.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.175296 restraints weight = 8308.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.177150 restraints weight = 6688.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.177351 restraints weight = 5468.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.177600 restraints weight = 4811.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.1563

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= 0.108
  Angle     :  0.527   6.539  12215  Z= 0.277
  Chirality :  0.042   0.168   1339
  Planarity :  0.004   0.049   1420
  Dihedral  : 13.810  59.829   1386
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.12 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.27), residues: 963
  helix:  1.42 (0.28), residues: 347
  sheet: -0.77 (0.44), residues: 149
  loop : -1.01 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 143 
 TYR   0.016   0.001   TYR A 319 
 PHE   0.012   0.001   PHE A  77 
 TRP   0.017   0.001   TRP A 402 
 HIS   0.004   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8882)
  covalent geometry    : angle       0.52749 (12215)
  hydrogen bonds       : bond        0.03298 (  331)
  hydrogen bonds       : angle       4.39835 (  880)

*********************** 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
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  339 TYR cc_start: 0.7241 (m-10) cc_final: 0.6358 (m-10)
REVERT: A  340 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7676 (mp10)
REVERT: A  356 ARG cc_start: 0.7240 (tpt-90) cc_final: 0.7040 (tpt-90)
REVERT: B   22 LYS cc_start: 0.7916 (tttm) cc_final: 0.7571 (pttt)
  outliers start: 11
  outliers final: 7
  residues processed: 121
  average time/residue: 0.0882
  time to fit residues: 15.2179
Evaluate side-chains
  107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 30 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 8 optimal weight:    7.9990
   chunk 49 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0020
   chunk 1 optimal weight:    1.9990
   chunk 89 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   overall best weight:    4.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 306 ASN
** 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 = 0.4377 r_free = 0.4377 target = 0.203605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.164709 restraints weight = 10322.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.166449 restraints weight = 8729.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.168901 restraints weight = 6599.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.168716 restraints weight = 5085.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.169299 restraints weight = 5027.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8882  Z= 0.184
  Angle     :  0.619   8.722  12215  Z= 0.324
  Chirality :  0.045   0.164   1339
  Planarity :  0.005   0.044   1420
  Dihedral  : 14.121  59.986   1386
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.70 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.27), residues: 963
  helix:  1.12 (0.28), residues: 346
  sheet: -1.16 (0.43), residues: 149
  loop : -1.04 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 143 
 TYR   0.019   0.002   TYR B 339 
 PHE   0.022   0.002   PHE A 160 
 TRP   0.021   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 8882)
  covalent geometry    : angle       0.61862 (12215)
  hydrogen bonds       : bond        0.04265 (  331)
  hydrogen bonds       : angle       4.58110 (  880)

*********************** 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
  113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  339 TYR cc_start: 0.7499 (m-10) cc_final: 0.7129 (m-10)
REVERT: B   22 LYS cc_start: 0.7915 (tttm) cc_final: 0.7500 (pttt)
  outliers start: 13
  outliers final: 10
  residues processed: 109
  average time/residue: 0.0865
  time to fit residues: 13.4793
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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  380 ILE
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  497 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  276 VAL
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 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 = 0.4366 r_free = 0.4366 target = 0.202258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.164400 restraints weight = 10207.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.164373 restraints weight = 9372.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.167099 restraints weight = 7707.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.167117 restraints weight = 5744.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.167614 restraints weight = 5212.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8882  Z= 0.200
  Angle     :  0.628   8.253  12215  Z= 0.330
  Chirality :  0.045   0.164   1339
  Planarity :  0.005   0.047   1420
  Dihedral  : 14.314  59.889   1386
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.98 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.27), residues: 963
  helix:  0.98 (0.28), residues: 345
  sheet: -1.34 (0.42), residues: 147
  loop : -1.04 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 125 
 TYR   0.020   0.002   TYR B 339 
 PHE   0.022   0.002   PHE A 160 
 TRP   0.022   0.002   TRP A 402 
 HIS   0.004   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8882)
  covalent geometry    : angle       0.62827 (12215)
  hydrogen bonds       : bond        0.04283 (  331)
  hydrogen bonds       : angle       4.63485 (  880)

*********************** 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
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8217 (t60) cc_final: 0.7596 (t60)
REVERT: A  340 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7885 (mp10)
REVERT: B   22 LYS cc_start: 0.7924 (tttm) cc_final: 0.7510 (pttt)
  outliers start: 17
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0903
  time to fit residues: 15.5854
Evaluate side-chains
  110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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  290 THR
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 45 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 19 optimal weight:   40.0000
   chunk 17 optimal weight:    1.9990
   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 161 GLN
A 258 GLN
** 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 = 0.4385 r_free = 0.4385 target = 0.204308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.165581 restraints weight = 10116.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.167621 restraints weight = 8660.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.169814 restraints weight = 6528.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.170123 restraints weight = 4959.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170404 restraints weight = 4596.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.1909

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= 0.144
  Angle     :  0.572   7.078  12215  Z= 0.300
  Chirality :  0.043   0.165   1339
  Planarity :  0.005   0.046   1420
  Dihedral  : 14.175  59.807   1386
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.32 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.27), residues: 963
  helix:  1.16 (0.28), residues: 346
  sheet: -1.33 (0.42), residues: 149
  loop : -0.96 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 211 
 TYR   0.016   0.002   TYR B 339 
 PHE   0.012   0.001   PHE A 160 
 TRP   0.023   0.001   TRP B 212 
 HIS   0.003   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8882)
  covalent geometry    : angle       0.57161 (12215)
  hydrogen bonds       : bond        0.03722 (  331)
  hydrogen bonds       : angle       4.47705 (  880)

*********************** 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
  114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8153 (t60) cc_final: 0.7430 (t60)
REVERT: A  232 TYR cc_start: 0.7835 (m-10) cc_final: 0.7613 (m-10)
REVERT: A  339 TYR cc_start: 0.7398 (m-10) cc_final: 0.6977 (m-10)
REVERT: A  340 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7742 (mp10)
REVERT: B   22 LYS cc_start: 0.7914 (tttm) cc_final: 0.7497 (pttt)
  outliers start: 12
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0843
  time to fit residues: 13.3936
Evaluate side-chains
  110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  276 VAL
Chi-restraints excluded: chain B residue  290 THR
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 84 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0770
   chunk 82 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 97 optimal weight:   20.0000
   chunk 21 optimal weight:   20.0000
   chunk 56 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    5.8146

-------------------------------------------------------------------------------
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 = 0.4356 r_free = 0.4356 target = 0.201260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.164220 restraints weight = 10355.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.166273 restraints weight = 8287.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.167849 restraints weight = 6799.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.167873 restraints weight = 5037.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.167982 restraints weight = 5168.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8882  Z= 0.212
  Angle     :  0.641   7.942  12215  Z= 0.336
  Chirality :  0.045   0.166   1339
  Planarity :  0.005   0.049   1420
  Dihedral  : 14.425  59.867   1386
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.91 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.27), residues: 963
  helix:  0.99 (0.28), residues: 339
  sheet: -1.36 (0.41), residues: 153
  loop : -0.98 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 199 
 TYR   0.021   0.002   TYR B 339 
 PHE   0.022   0.002   PHE A 160 
 TRP   0.027   0.002   TRP B 212 
 HIS   0.004   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 8882)
  covalent geometry    : angle       0.64141 (12215)
  hydrogen bonds       : bond        0.04419 (  331)
  hydrogen bonds       : angle       4.67711 (  880)

*********************** 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
  116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8216 (t60) cc_final: 0.7565 (t60)
REVERT: A  340 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7885 (mp10)
REVERT: B   22 LYS cc_start: 0.7916 (tttm) cc_final: 0.7464 (pttt)
  outliers start: 16
  outliers final: 14
  residues processed: 112
  average time/residue: 0.0890
  time to fit residues: 14.3931
Evaluate side-chains
  115 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  254 VAL
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 82 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 90 optimal weight:    5.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
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
B 373 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.205276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.167859 restraints weight = 10024.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.167862 restraints weight = 8815.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.170159 restraints weight = 7499.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170713 restraints weight = 5576.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.171227 restraints weight = 5045.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8882  Z= 0.128
  Angle     :  0.559   7.442  12215  Z= 0.293
  Chirality :  0.043   0.168   1339
  Planarity :  0.005   0.047   1420
  Dihedral  : 14.166  59.353   1386
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.27), residues: 963
  helix:  1.26 (0.28), residues: 341
  sheet: -1.03 (0.43), residues: 143
  loop : -0.86 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 199 
 TYR   0.015   0.001   TYR B 342 
 PHE   0.013   0.001   PHE A 130 
 TRP   0.028   0.001   TRP B 212 
 HIS   0.003   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8882)
  covalent geometry    : angle       0.55909 (12215)
  hydrogen bonds       : bond        0.03490 (  331)
  hydrogen bonds       : angle       4.42770 (  880)

*********************** 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
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 TRP cc_start: 0.8113 (t60) cc_final: 0.7447 (t60)
REVERT: A  232 TYR cc_start: 0.7898 (m-10) cc_final: 0.7650 (m-10)
REVERT: A  339 TYR cc_start: 0.7400 (m-10) cc_final: 0.6863 (m-10)
REVERT: A  340 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7768 (mp10)
REVERT: B   22 LYS cc_start: 0.7919 (tttm) cc_final: 0.7529 (pttt)
REVERT: B  125 ARG cc_start: 0.6720 (tpp80) cc_final: 0.6480 (tpp80)
  outliers start: 15
  outliers final: 9
  residues processed: 122
  average time/residue: 0.0891
  time to fit residues: 15.4640
Evaluate side-chains
  116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  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  290 THR
Chi-restraints excluded: chain B residue  344 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 83 optimal weight:   30.0000
   chunk 32 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 94 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.208178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.172186 restraints weight = 10051.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.173492 restraints weight = 7964.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.175755 restraints weight = 6635.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.175697 restraints weight = 4959.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.176282 restraints weight = 4784.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.2242

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= 0.109
  Angle     :  0.553  14.731  12215  Z= 0.283
  Chirality :  0.042   0.165   1339
  Planarity :  0.005   0.073   1420
  Dihedral  : 14.021  59.988   1386
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.19 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.27), residues: 963
  helix:  1.35 (0.29), residues: 344
  sheet: -0.88 (0.44), residues: 134
  loop : -0.81 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 211 
 TYR   0.014   0.001   TYR B 342 
 PHE   0.015   0.001   PHE A 130 
 TRP   0.031   0.001   TRP B 212 
 HIS   0.002   0.001   HIS A 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8882)
  covalent geometry    : angle       0.55253 (12215)
  hydrogen bonds       : bond        0.03088 (  331)
  hydrogen bonds       : angle       4.32138 (  880)

*********************** 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
  128 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 TYR cc_start: 0.7247 (m-10) cc_final: 0.6566 (m-10)
REVERT: A  340 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7572 (mp10)
REVERT: B   22 LYS cc_start: 0.7889 (tttm) cc_final: 0.7465 (pttt)
  outliers start: 10
  outliers final: 5
  residues processed: 125
  average time/residue: 0.0911
  time to fit residues: 16.2115
Evaluate side-chains
  116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    0.0470
   chunk 2 optimal weight:   20.0000
   chunk 76 optimal weight:    4.9990
   chunk 67 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 4 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.9084

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.207998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.171781 restraints weight = 9992.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.173084 restraints weight = 7921.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175359 restraints weight = 6600.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.175335 restraints weight = 4942.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.175936 restraints weight = 4763.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8882  Z= 0.119
  Angle     :  0.565  12.064  12215  Z= 0.293
  Chirality :  0.042   0.167   1339
  Planarity :  0.005   0.062   1420
  Dihedral  : 14.009  59.841   1386
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.27), residues: 963
  helix:  1.37 (0.29), residues: 345
  sheet: -0.80 (0.44), residues: 134
  loop : -0.76 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 125 
 TYR   0.024   0.001   TYR A 232 
 PHE   0.015   0.001   PHE A 130 
 TRP   0.030   0.001   TRP B 212 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8882)
  covalent geometry    : angle       0.56471 (12215)
  hydrogen bonds       : bond        0.03214 (  331)
  hydrogen bonds       : angle       4.31153 (  880)

********************** 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
  123 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7120 (pt)
REVERT: A  339 TYR cc_start: 0.7196 (m-10) cc_final: 0.6470 (m-10)
REVERT: A  340 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7640 (mp10)
REVERT: B   22 LYS cc_start: 0.7889 (tttm) cc_final: 0.7481 (pttt)
  outliers start: 10
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1032
  time to fit residues: 16.8551
Evaluate side-chains
  113 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
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  344 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 25 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:   40.0000
   chunk 63 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 51 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   overall best weight:    5.9188

-------------------------------------------------------------------------------
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 = 0.4363 r_free = 0.4363 target = 0.202125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.165248 restraints weight = 10140.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.166375 restraints weight = 8446.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.168464 restraints weight = 6979.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.168412 restraints weight = 5342.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.168857 restraints weight = 5093.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   8882  Z= 0.217
  Angle     :  0.670  11.478  12215  Z= 0.349
  Chirality :  0.046   0.171   1339
  Planarity :  0.005   0.061   1420
  Dihedral  : 14.363  60.583   1386
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 963
  helix:  1.08 (0.29), residues: 337
  sheet: -0.98 (0.43), residues: 139
  loop : -0.92 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 125 
 TYR   0.025   0.002   TYR A 232 
 PHE   0.020   0.002   PHE A 160 
 TRP   0.029   0.002   TRP B 212 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 8882)
  covalent geometry    : angle       0.67031 (12215)
  hydrogen bonds       : bond        0.04336 (  331)
  hydrogen bonds       : angle       4.62571 (  880)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1267.86 seconds
wall clock time: 22 minutes 42.74 seconds (1362.74 seconds total)