Starting phenix.real_space_refine
on Wed Mar  4 03:25:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7plv_13503/03_2026/7plv_13503.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    6462      2.51       5
     N    1722      2.21       5
     O    1889      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  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: 10139
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 6097
          Classifications: {'peptide': 747}
          Link IDs: {'PTRANS': 27, 'TRANS': 719}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.38, per 1000 atoms: 0.23
  Number of scatterers: 10139
  At special positions: 0
  Unit cell: (103.88, 131.44, 152.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P       2     15.00
     Mg      1     11.99
     O    1889      8.00
     N    1722      7.00
     C    6462      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
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 494.5 milliseconds
  

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
  Number of C-beta restraints generated:  2378

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 14 sheets defined
      55.2% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.200A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 140 through 150
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 164 through 167
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 191 through 207
      removed outlier: 3.645A  pdb=" N   LYS A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASN A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.544A  pdb=" N   ARG A 248 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.251A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
      removed outlier: 4.276A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.967A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 316
      removed outlier: 3.855A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.531A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 3.857A  pdb=" N   HIS A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
    Processing helix  chain 'A' and resid 448 through 479
      removed outlier: 3.552A  pdb=" N   GLN A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 487
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.612A  pdb=" N   LEU A 498 " --> pdb=" O   PRO A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 515
      removed outlier: 3.666A  pdb=" N   LYS A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.598A  pdb=" N   ALA A 524 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.649A  pdb=" N   ASN A 568 " --> pdb=" O   PHE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.743A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 593
      removed outlier: 3.537A  pdb=" N   GLU A 591 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 635 through 652
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.837A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 695
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.766A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 4.353A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.183A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU C 117 " --> pdb=" O   LYS C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 4.077A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 196
      removed outlier: 3.548A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ARG C 196 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 4.276A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
      removed outlier: 3.798A  pdb=" N   GLU C 226 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 237
    Processing helix  chain 'C' and resid 251 through 260
      removed outlier: 4.262A  pdb=" N   PHE C 255 " --> pdb=" O   GLY C 251 " (cutoff:3.500A)
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 273 through 285
      removed outlier: 3.600A  pdb=" N   CYS C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 296
      removed outlier: 3.698A  pdb=" N   ARG C 290 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 4.361A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 319
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 4.602A  pdb=" N   LYS C 336 " --> pdb=" O   PRO C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.762A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 3.789A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16
      removed outlier: 4.661A  pdb=" N   LEU A  42 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LYS A  46 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102
      removed outlier: 3.884A  pdb=" N   GLN A 157 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY A 163 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209
    Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344
      removed outlier: 6.235A  pdb=" N   SER A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382
    Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703
      removed outlier: 3.553A  pdb=" N   SER A 700 " --> pdb=" O   PHE A 751 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32
      removed outlier: 6.706A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   THR C 106 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   CYS C  10 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.470A  pdb=" N   ILE C 151 " --> pdb=" O   VAL C 298 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   SER C 300 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   LEU C 153 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241

    524 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 0.97 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: 1691
        1.32 -     1.44: 2733
        1.44 -     1.56: 5825
        1.56 -     1.69: 3
        1.69 -     1.81: 102
  Bond restraints: 10354
  Sorted by residual:
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.453  0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C   HYP H   6 "
       pdb=" N   ALA H   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.374 -0.045 1.40e-02 5.10e+03 1.03e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.200  0.063 2.00e-02 2.50e+03 9.91e+00
  bond pdb=" CA  TRP H   1 "
       pdb=" C   TRP H   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.468  0.057 2.10e-02 2.27e+03 7.45e+00
  bond pdb=" CE1 HIC C  73 "
       pdb=" NE2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.347  1.400 -0.053 2.00e-02 2.50e+03 7.15e+00
  ... (remaining 10349 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 13739
        2.49 -     4.98: 216
        4.98 -     7.47: 20
        7.47 -     9.96: 5
        9.96 -    12.45: 2
  Bond angle restraints: 13982
  Sorted by residual:
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  111.07   10.63 1.80e+00 3.09e-01 3.49e+01
  angle pdb=" N   HYP H   6 "
        pdb=" CA  HYP H   6 "
        pdb=" CB  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.00  108.87   -5.87 1.10e+00 8.26e-01 2.85e+01
  angle pdb=" CA  EEP H   2 "
        pdb=" CB  EEP H   2 "
        pdb=" CG  EEP H   2 "
      ideal   model   delta    sigma   weight residual
     115.99  103.54   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" CD2 TRP H   1 "
        pdb=" CE2 TRP H   1 "
        pdb=" CZ2 TRP H   1 "
      ideal   model   delta    sigma   weight residual
     122.40  118.25    4.15 1.00e+00 1.00e+00 1.72e+01
  angle pdb=" CA  DTH H   4 "
        pdb=" C   DTH H   4 "
        pdb=" N   CYS H   5 "
      ideal   model   delta    sigma   weight residual
     116.20  123.69   -7.49 2.00e+00 2.50e-01 1.40e+01
  ... (remaining 13977 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.86: 6093
       31.86 -    63.72: 120
       63.72 -    95.58: 38
       95.58 -   127.44: 1
      127.44 -   159.30: 2
  Dihedral angle restraints: 6254
    sinusoidal: 2564
      harmonic: 3690
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   99.30 -159.30     1      2.00e+01 2.50e-03 4.65e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   85.37 -145.37     1      2.00e+01 2.50e-03 4.37e+01
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  177.96  122.04     1      2.00e+01 2.50e-03 3.67e+01
  ... (remaining 6251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1003
       0.041 -    0.081: 378
       0.081 -    0.122: 114
       0.122 -    0.162: 29
       0.162 -    0.203: 4
  Chirality restraints: 1528
  Sorted by residual:
  chirality pdb=" CA  CYS H   5 "
            pdb=" N   CYS H   5 "
            pdb=" C   CYS H   5 "
            pdb=" CB  CYS H   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  GLU A 512 "
            pdb=" N   GLU A 512 "
            pdb=" C   GLU A 512 "
            pdb=" CB  GLU A 512 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" CA  PHE C 255 "
            pdb=" N   PHE C 255 "
            pdb=" C   PHE C 255 "
            pdb=" CB  PHE C 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.56e-01
  ... (remaining 1525 not shown)

  Planarity restraints: 1791
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 213 "   -0.174 9.50e-02 1.11e+02   9.87e-02 4.98e+01
        pdb=" NE  ARG A 213 "    0.050 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 213 "   -0.116 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 213 "    0.041 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 213 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 677 "    0.164 9.50e-02 1.11e+02   9.42e-02 4.69e+01
        pdb=" NE  ARG A 677 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 677 "    0.112 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 677 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 677 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 196 "    0.125 9.50e-02 1.11e+02   7.29e-02 2.90e+01
        pdb=" NE  ARG C 196 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 196 "    0.089 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 196 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 196 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1788 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 13
        2.37 -     3.00: 5420
        3.00 -     3.63: 14892
        3.63 -     4.27: 22403
        4.27 -     4.90: 37983
  Nonbonded interactions: 80711
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.732 3.620
  nonbonded pdb=" OH  TYR C 218 "
            pdb=" OE2 GLU C 226 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" NH2 ARG B  37 "
            pdb=" O   PRO B  43 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" OD1 ASN C 128 "
            pdb=" NZ  LYS C 359 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O   ASN C  92 "
            pdb=" NH1 ARG C  95 "
     model   vdw
     2.218 3.120
  ... (remaining 80706 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:             3.070
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.740
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
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      :  0.005   0.119  10356  Z= 0.216
  Angle     :  0.812  12.450  13988  Z= 0.483
  Chirality :  0.048   0.203   1528
  Planarity :  0.008   0.124   1789
  Dihedral  : 15.024 159.301   3870
  Min Nonbonded Distance : 1.732

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.54 (0.21), residues: 1236
  helix: -1.60 (0.17), residues: 611
  sheet:  0.34 (0.36), residues: 162
  loop : -0.39 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.118   0.012   ARG A 213 
 TYR   0.040   0.006   TYR C 306 
 PHE   0.034   0.002   PHE C 255 
 TRP   0.022   0.003   TRP A 374 
 HIS   0.010   0.002   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (10354)
  covalent geometry    : angle       0.80758 (13982)
  hydrogen bonds       : bond        0.14107 (  522)
  hydrogen bonds       : angle       6.78962 ( 1470)
  link_TRANS           : bond        0.00704 (    2)
  link_TRANS           : angle       3.99435 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9310 (m-10) cc_final: 0.8754 (m-10)
REVERT: B   66 ASP cc_start: 0.8944 (p0) cc_final: 0.8371 (p0)
REVERT: B   93 PHE cc_start: 0.8972 (m-80) cc_final: 0.8177 (m-80)
REVERT: C   44 MET cc_start: 0.7946 (mtp) cc_final: 0.7737 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1117
  time to fit residues: 22.5493
Evaluate side-chains
  86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
A  81 HIS
A 264 GLN
A 283 ASN
A 463 GLN
A 464 GLN
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
C  59 GLN
C 162 ASN
C 280 ASN
C 296 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.058384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.042658 restraints weight = 45946.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.044250 restraints weight = 21943.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.045340 restraints weight = 13543.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.046103 restraints weight = 9687.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.046651 restraints weight = 7604.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10356  Z= 0.147
  Angle     :  0.638   9.032  13988  Z= 0.332
  Chirality :  0.043   0.237   1528
  Planarity :  0.004   0.053   1789
  Dihedral  :  9.326 158.682   1396
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.08 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.57 (0.23), residues: 1236
  helix:  0.42 (0.20), residues: 610
  sheet:  0.71 (0.38), residues: 168
  loop :  0.47 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  95 
 TYR   0.019   0.001   TYR A 787 
 PHE   0.027   0.002   PHE C 255 
 TRP   0.016   0.002   TRP A 484 
 HIS   0.010   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10354)
  covalent geometry    : angle       0.63746 (13982)
  hydrogen bonds       : bond        0.04025 (  522)
  hydrogen bonds       : angle       4.92853 ( 1470)
  link_TRANS           : bond        0.00198 (    2)
  link_TRANS           : angle       1.03447 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   50 LYS cc_start: 0.9487 (ttpp) cc_final: 0.9219 (ptmm)
REVERT: A   62 LEU cc_start: 0.9124 (tt) cc_final: 0.8711 (mp)
REVERT: A  445 GLU cc_start: 0.7939 (pm20) cc_final: 0.7620 (pm20)
REVERT: A  503 MET cc_start: 0.8614 (mmt) cc_final: 0.8241 (mmt)
REVERT: A  682 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: C   44 MET cc_start: 0.8712 (mtp) cc_final: 0.8392 (ttt)
REVERT: C  123 MET cc_start: 0.9429 (tpp) cc_final: 0.8889 (mmm)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 0.0918
  time to fit residues: 13.1627
Evaluate side-chains
  73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  535 CYS
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain C residue  211 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 113 optimal weight:    0.3980
   chunk 67 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 GLN
C 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.058357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.042431 restraints weight = 46232.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.044023 restraints weight = 22154.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.045123 restraints weight = 13716.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.045848 restraints weight = 9788.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.046366 restraints weight = 7755.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10356  Z= 0.132
  Angle     :  0.571   7.904  13988  Z= 0.293
  Chirality :  0.041   0.147   1528
  Planarity :  0.004   0.057   1789
  Dihedral  :  8.718 158.903   1396
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  6.75 %
    Favored  : 92.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.17 (0.24), residues: 1236
  helix:  1.05 (0.21), residues: 616
  sheet:  0.76 (0.38), residues: 160
  loop :  0.63 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 712 
 TYR   0.017   0.001   TYR A 787 
 PHE   0.022   0.001   PHE C 255 
 TRP   0.015   0.001   TRP A 484 
 HIS   0.008   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10354)
  covalent geometry    : angle       0.57058 (13982)
  hydrogen bonds       : bond        0.03571 (  522)
  hydrogen bonds       : angle       4.52001 ( 1470)
  link_TRANS           : bond        0.00147 (    2)
  link_TRANS           : angle       0.99026 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9239 (ptmm)
REVERT: B   66 ASP cc_start: 0.8770 (p0) cc_final: 0.8568 (p0)
REVERT: B   93 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.9006 (t80)
REVERT: A   62 LEU cc_start: 0.9142 (tt) cc_final: 0.8728 (mp)
REVERT: A  132 MET cc_start: 0.8018 (ttm) cc_final: 0.7626 (tpt)
REVERT: A  445 GLU cc_start: 0.7975 (pm20) cc_final: 0.7695 (pm20)
REVERT: A  478 MET cc_start: 0.9430 (tpp) cc_final: 0.8971 (tpp)
REVERT: A  503 MET cc_start: 0.8540 (mmt) cc_final: 0.8203 (mmt)
REVERT: A  682 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8965 (mm)
REVERT: C   44 MET cc_start: 0.8788 (mtp) cc_final: 0.8526 (tpp)
REVERT: C  123 MET cc_start: 0.9413 (tpp) cc_final: 0.9087 (mmm)
REVERT: C  125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7743 (mp0)
REVERT: C  236 LEU cc_start: 0.8860 (mp) cc_final: 0.8637 (mt)
REVERT: C  305 MET cc_start: 0.8758 (mmm) cc_final: 0.8409 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0861
  time to fit residues: 11.0324
Evaluate side-chains
  72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 410 ASN
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.057525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.041538 restraints weight = 46357.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.043140 restraints weight = 22111.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.044223 restraints weight = 13624.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.044945 restraints weight = 9742.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.045447 restraints weight = 7705.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10356  Z= 0.158
  Angle     :  0.557   8.070  13988  Z= 0.285
  Chirality :  0.041   0.148   1528
  Planarity :  0.004   0.057   1789
  Dihedral  :  8.398 158.735   1396
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  6.93 %
    Favored  : 91.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.37 (0.24), residues: 1236
  helix:  1.30 (0.21), residues: 622
  sheet:  0.83 (0.39), residues: 160
  loop :  0.59 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 542 
 TYR   0.016   0.001   TYR A 787 
 PHE   0.020   0.001   PHE C 255 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.007   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10354)
  covalent geometry    : angle       0.55681 (13982)
  hydrogen bonds       : bond        0.03461 (  522)
  hydrogen bonds       : angle       4.41896 ( 1470)
  link_TRANS           : bond        0.00024 (    2)
  link_TRANS           : angle       0.85986 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.342 
Fit side-chains
REVERT: B   66 ASP cc_start: 0.8828 (p0) cc_final: 0.8526 (p0)
REVERT: B   93 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.9027 (t80)
REVERT: A  132 MET cc_start: 0.8053 (ttm) cc_final: 0.7713 (tpt)
REVERT: A  305 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8467 (tpp)
REVERT: A  478 MET cc_start: 0.9442 (tpp) cc_final: 0.8898 (tpp)
REVERT: A  484 TRP cc_start: 0.7644 (m-10) cc_final: 0.7342 (m-90)
REVERT: A  503 MET cc_start: 0.8581 (mmt) cc_final: 0.8245 (mmt)
REVERT: A  682 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8893 (mm)
REVERT: C  123 MET cc_start: 0.9396 (tpp) cc_final: 0.8865 (mmm)
REVERT: C  125 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7802 (mp0)
REVERT: C  167 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8466 (mp0)
REVERT: C  227 MET cc_start: 0.9037 (tpt) cc_final: 0.8754 (tpt)
  outliers start: 15
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0822
  time to fit residues: 10.1699
Evaluate side-chains
  74 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Chi-restraints excluded: chain C residue  211 ASP
Chi-restraints excluded: chain C residue  250 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.057894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.041932 restraints weight = 45923.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.043534 restraints weight = 22067.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.044621 restraints weight = 13680.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.045326 restraints weight = 9810.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.045849 restraints weight = 7790.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10356  Z= 0.129
  Angle     :  0.553   9.954  13988  Z= 0.277
  Chirality :  0.041   0.176   1528
  Planarity :  0.004   0.056   1789
  Dihedral  :  8.244 158.310   1396
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  8.23 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.51 (0.24), residues: 1236
  helix:  1.42 (0.21), residues: 625
  sheet:  0.97 (0.39), residues: 158
  loop :  0.60 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 290 
 TYR   0.015   0.001   TYR A 787 
 PHE   0.018   0.001   PHE C 255 
 TRP   0.013   0.001   TRP C  79 
 HIS   0.006   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10354)
  covalent geometry    : angle       0.55260 (13982)
  hydrogen bonds       : bond        0.03283 (  522)
  hydrogen bonds       : angle       4.29459 ( 1470)
  link_TRANS           : bond        0.00046 (    2)
  link_TRANS           : angle       0.84070 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9358 (m-10) cc_final: 0.8921 (m-10)
REVERT: B   66 ASP cc_start: 0.8849 (p0) cc_final: 0.8542 (p0)
REVERT: B   93 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.9001 (t80)
REVERT: A   62 LEU cc_start: 0.9147 (tt) cc_final: 0.8768 (mp)
REVERT: A  132 MET cc_start: 0.7955 (ttm) cc_final: 0.7670 (tpt)
REVERT: A  177 MET cc_start: 0.8280 (ptt) cc_final: 0.8071 (ppp)
REVERT: A  305 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8456 (tpp)
REVERT: A  478 MET cc_start: 0.9395 (tpp) cc_final: 0.9109 (tpp)
REVERT: A  503 MET cc_start: 0.8552 (mmt) cc_final: 0.8249 (mmt)
REVERT: A  564 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8665 (t80)
REVERT: C  123 MET cc_start: 0.9347 (tpp) cc_final: 0.8860 (mmm)
REVERT: C  125 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7753 (mp0)
REVERT: C  167 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8337 (mp0)
  outliers start: 17
  outliers final: 4
  residues processed: 84
  average time/residue: 0.0803
  time to fit residues: 10.5661
Evaluate side-chains
  73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Chi-restraints excluded: chain C residue  269 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 60 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 HIS
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.057583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.041991 restraints weight = 46180.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.043576 restraints weight = 22006.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.044668 restraints weight = 13550.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.045418 restraints weight = 9622.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.045919 restraints weight = 7555.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10356  Z= 0.136
  Angle     :  0.558  10.884  13988  Z= 0.277
  Chirality :  0.041   0.184   1528
  Planarity :  0.003   0.056   1789
  Dihedral  :  8.235 159.073   1396
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.78 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.54 (0.24), residues: 1236
  helix:  1.49 (0.21), residues: 626
  sheet:  0.91 (0.39), residues: 158
  loop :  0.57 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 290 
 TYR   0.013   0.001   TYR A 259 
 PHE   0.018   0.001   PHE C 255 
 TRP   0.010   0.001   TRP C  79 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10354)
  covalent geometry    : angle       0.55794 (13982)
  hydrogen bonds       : bond        0.03241 (  522)
  hydrogen bonds       : angle       4.24534 ( 1470)
  link_TRANS           : bond        0.00154 (    2)
  link_TRANS           : angle       0.77226 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9475 (m-10) cc_final: 0.9074 (m-10)
REVERT: B   66 ASP cc_start: 0.8917 (p0) cc_final: 0.8596 (p0)
REVERT: B   93 PHE cc_start: 0.9198 (m-80) cc_final: 0.8981 (t80)
REVERT: A   62 LEU cc_start: 0.9162 (tt) cc_final: 0.8827 (mp)
REVERT: A  132 MET cc_start: 0.7971 (ttm) cc_final: 0.7699 (tpt)
REVERT: A  305 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8432 (tpp)
REVERT: A  478 MET cc_start: 0.9364 (tpp) cc_final: 0.9046 (tpp)
REVERT: A  503 MET cc_start: 0.8545 (mmt) cc_final: 0.8255 (mmt)
REVERT: A  564 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8617 (t80)
REVERT: C  123 MET cc_start: 0.9342 (tpp) cc_final: 0.8844 (mmm)
REVERT: C  125 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7772 (mp0)
REVERT: C  167 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8345 (mp0)
REVERT: C  227 MET cc_start: 0.9006 (tpt) cc_final: 0.8766 (tpt)
REVERT: C  305 MET cc_start: 0.8811 (mmm) cc_final: 0.8380 (mmm)
REVERT: H    1 TRP cc_start: 0.8669 (m100) cc_final: 0.8120 (m100)
  outliers start: 12
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0789
  time to fit residues: 9.7155
Evaluate side-chains
  73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Chi-restraints excluded: chain C residue  269 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0770
   chunk 96 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.058001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.042374 restraints weight = 45304.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.043977 restraints weight = 21678.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.045082 restraints weight = 13279.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.045830 restraints weight = 9451.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.046292 restraints weight = 7415.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10356  Z= 0.108
  Angle     :  0.548  11.264  13988  Z= 0.270
  Chirality :  0.040   0.182   1528
  Planarity :  0.003   0.055   1789
  Dihedral  :  8.148 159.148   1396
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.87 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.68 (0.24), residues: 1236
  helix:  1.62 (0.21), residues: 634
  sheet:  0.92 (0.38), residues: 158
  loop :  0.62 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 290 
 TYR   0.014   0.001   TYR A 787 
 PHE   0.016   0.001   PHE C 255 
 TRP   0.009   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10354)
  covalent geometry    : angle       0.54752 (13982)
  hydrogen bonds       : bond        0.03086 (  522)
  hydrogen bonds       : angle       4.14140 ( 1470)
  link_TRANS           : bond        0.00132 (    2)
  link_TRANS           : angle       0.85020 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.8932 (p0) cc_final: 0.8641 (p0)
REVERT: B   93 PHE cc_start: 0.9196 (m-80) cc_final: 0.8985 (t80)
REVERT: A   62 LEU cc_start: 0.9181 (tt) cc_final: 0.8843 (mp)
REVERT: A  305 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (tpp)
REVERT: A  503 MET cc_start: 0.8534 (mmt) cc_final: 0.8266 (mmt)
REVERT: A  564 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8539 (t80)
REVERT: C  123 MET cc_start: 0.9292 (tpp) cc_final: 0.8934 (mmm)
REVERT: C  125 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7757 (mp0)
REVERT: C  167 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8388 (mp0)
REVERT: C  227 MET cc_start: 0.8942 (tpt) cc_final: 0.8683 (tpt)
REVERT: C  305 MET cc_start: 0.8786 (mmm) cc_final: 0.8387 (mmm)
REVERT: H    1 TRP cc_start: 0.8681 (m100) cc_final: 0.8133 (m100)
  outliers start: 12
  outliers final: 2
  residues processed: 80
  average time/residue: 0.0913
  time to fit residues: 11.1320
Evaluate side-chains
  73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 103 optimal weight:    0.2980
   chunk 102 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 74 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.058021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.042344 restraints weight = 45422.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.043934 restraints weight = 21877.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.045010 restraints weight = 13487.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.045720 restraints weight = 9641.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.046267 restraints weight = 7642.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10356  Z= 0.118
  Angle     :  0.567  12.003  13988  Z= 0.276
  Chirality :  0.041   0.200   1528
  Planarity :  0.003   0.055   1789
  Dihedral  :  8.113 158.406   1396
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.06 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.73 (0.24), residues: 1236
  helix:  1.71 (0.21), residues: 633
  sheet:  0.90 (0.38), residues: 155
  loop :  0.59 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.012   0.001   TYR A 787 
 PHE   0.015   0.001   PHE C 255 
 TRP   0.009   0.001   TRP A 781 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10354)
  covalent geometry    : angle       0.56653 (13982)
  hydrogen bonds       : bond        0.03064 (  522)
  hydrogen bonds       : angle       4.12133 ( 1470)
  link_TRANS           : bond        0.00092 (    2)
  link_TRANS           : angle       0.83969 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.8953 (p0) cc_final: 0.8679 (p0)
REVERT: A   62 LEU cc_start: 0.9173 (tt) cc_final: 0.8850 (mp)
REVERT: A  177 MET cc_start: 0.8413 (tmm) cc_final: 0.8190 (ppp)
REVERT: A  305 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (tpp)
REVERT: A  478 MET cc_start: 0.9167 (tpp) cc_final: 0.8842 (tpp)
REVERT: A  503 MET cc_start: 0.8541 (mmt) cc_final: 0.8310 (mmm)
REVERT: A  564 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8588 (t80)
REVERT: C   47 MET cc_start: 0.8209 (tpp) cc_final: 0.7934 (tpp)
REVERT: C  123 MET cc_start: 0.9283 (tpp) cc_final: 0.8823 (mmm)
REVERT: C  167 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8380 (mp0)
REVERT: C  305 MET cc_start: 0.8784 (mmm) cc_final: 0.8386 (mmm)
  outliers start: 9
  outliers final: 3
  residues processed: 75
  average time/residue: 0.0831
  time to fit residues: 9.7413
Evaluate side-chains
  72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  167 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0770
   chunk 120 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 116 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0470
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.058614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.042558 restraints weight = 45917.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.044200 restraints weight = 21906.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.045316 restraints weight = 13507.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.046065 restraints weight = 9659.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.046565 restraints weight = 7618.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10356  Z= 0.101
  Angle     :  0.558  12.880  13988  Z= 0.270
  Chirality :  0.040   0.207   1528
  Planarity :  0.003   0.054   1789
  Dihedral  :  8.035 155.846   1396
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.43 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.81 (0.24), residues: 1236
  helix:  1.78 (0.21), residues: 633
  sheet:  0.93 (0.38), residues: 155
  loop :  0.60 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.013   0.001   TYR A 787 
 PHE   0.023   0.001   PHE B  12 
 TRP   0.010   0.001   TRP A 781 
 HIS   0.004   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10354)
  covalent geometry    : angle       0.55814 (13982)
  hydrogen bonds       : bond        0.02955 (  522)
  hydrogen bonds       : angle       4.04539 ( 1470)
  link_TRANS           : bond        0.00143 (    2)
  link_TRANS           : angle       0.85154 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.8947 (p0) cc_final: 0.8475 (p0)
REVERT: B   68 GLU cc_start: 0.9054 (mp0) cc_final: 0.8806 (mp0)
REVERT: B   93 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8596 (t80)
REVERT: A   62 LEU cc_start: 0.9167 (tt) cc_final: 0.8679 (mp)
REVERT: A  177 MET cc_start: 0.8409 (tmm) cc_final: 0.8147 (ppp)
REVERT: A  305 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8450 (tpp)
REVERT: A  478 MET cc_start: 0.9202 (tpp) cc_final: 0.8833 (tpp)
REVERT: A  503 MET cc_start: 0.8555 (mmt) cc_final: 0.8302 (mmm)
REVERT: A  564 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8480 (t80)
REVERT: C   44 MET cc_start: 0.8711 (tpp) cc_final: 0.8434 (tpp)
REVERT: C   47 MET cc_start: 0.8218 (tpp) cc_final: 0.7938 (tpp)
REVERT: C   82 MET cc_start: 0.8841 (tpt) cc_final: 0.8452 (tpt)
REVERT: C  123 MET cc_start: 0.9262 (tpp) cc_final: 0.8836 (mmm)
REVERT: C  167 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8379 (mp0)
REVERT: C  227 MET cc_start: 0.8961 (tpt) cc_final: 0.8757 (tpt)
REVERT: C  305 MET cc_start: 0.8799 (mmm) cc_final: 0.8373 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0978
  time to fit residues: 12.3202
Evaluate side-chains
  77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  167 GLU
Chi-restraints excluded: chain C residue  269 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 115 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.057831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.041814 restraints weight = 45947.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.043432 restraints weight = 22146.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.044532 restraints weight = 13675.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.045255 restraints weight = 9857.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.045678 restraints weight = 7815.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10356  Z= 0.145
  Angle     :  0.593  13.256  13988  Z= 0.290
  Chirality :  0.041   0.200   1528
  Planarity :  0.003   0.056   1789
  Dihedral  :  8.034 152.314   1396
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  9.70 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.75 (0.24), residues: 1236
  helix:  1.77 (0.21), residues: 634
  sheet:  0.92 (0.38), residues: 155
  loop :  0.50 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.015   0.001   TYR A 787 
 PHE   0.019   0.001   PHE B  12 
 TRP   0.023   0.001   TRP C  86 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10354)
  covalent geometry    : angle       0.59255 (13982)
  hydrogen bonds       : bond        0.03148 (  522)
  hydrogen bonds       : angle       4.11068 ( 1470)
  link_TRANS           : bond        0.00032 (    2)
  link_TRANS           : angle       0.83786 (    6)

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

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

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2472 Ramachandran restraints generated.
    1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.8970 (p0) cc_final: 0.8716 (p0)
REVERT: B   93 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8591 (t80)
REVERT: A   62 LEU cc_start: 0.9132 (tt) cc_final: 0.8823 (mp)
REVERT: A  177 MET cc_start: 0.8397 (tmm) cc_final: 0.8063 (tmm)
REVERT: A  305 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8464 (tpp)
REVERT: A  478 MET cc_start: 0.9202 (tpp) cc_final: 0.8859 (tpp)
REVERT: A  503 MET cc_start: 0.8573 (mmt) cc_final: 0.8276 (mmt)
REVERT: A  564 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8614 (t80)
REVERT: C  123 MET cc_start: 0.9361 (tpp) cc_final: 0.8839 (mmm)
REVERT: C  167 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8396 (mp0)
REVERT: C  305 MET cc_start: 0.8810 (mmm) cc_final: 0.8384 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 73
  average time/residue: 0.0865
  time to fit residues: 9.6756
Evaluate side-chains
  73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 PHE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  564 PHE
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain C residue  101 HIS
Chi-restraints excluded: chain C residue  167 GLU
Chi-restraints excluded: chain C residue  269 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0270
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0980
   chunk 106 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.058722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.043025 restraints weight = 45517.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.044652 restraints weight = 21700.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.045751 restraints weight = 13349.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.046540 restraints weight = 9491.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.047045 restraints weight = 7414.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10356  Z= 0.099
  Angle     :  0.581  13.096  13988  Z= 0.279
  Chirality :  0.040   0.194   1528
  Planarity :  0.003   0.053   1789
  Dihedral  :  7.942 147.136   1396
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.17 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.80 (0.24), residues: 1236
  helix:  1.84 (0.21), residues: 635
  sheet:  0.91 (0.38), residues: 155
  loop :  0.49 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.017   0.001   TYR A 787 
 PHE   0.019   0.001   PHE B  12 
 TRP   0.020   0.001   TRP C  86 
 HIS   0.004   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10354)
  covalent geometry    : angle       0.58071 (13982)
  hydrogen bonds       : bond        0.02898 (  522)
  hydrogen bonds       : angle       4.01780 ( 1470)
  link_TRANS           : bond        0.00171 (    2)
  link_TRANS           : angle       0.83789 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1791.58 seconds
wall clock time: 31 minutes 39.91 seconds (1899.91 seconds total)