Starting phenix.real_space_refine
on Mon Jul 28 15:38:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_13503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_13503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_13503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_13503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2025/7plv_13503.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: 6.56, per 1000 atoms: 0.65
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.15
  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: 3.18

  Time building geometry restraints manager: 2.96 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:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.740
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.400
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (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
 TRP   0.022   0.003   TRP A 374 
 HIS   0.010   0.002   HIS A 418 
 PHE   0.034   0.002   PHE C 255 
 TYR   0.040   0.006   TYR C 306 
 ARG   0.118   0.012   ARG A 213 

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

*********************** 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  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9310 (m-10) cc_final: 0.8758 (m-10)
REVERT: B   66 ASP cc_start: 0.8944 (p0) cc_final: 0.8367 (p0)
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: 0.2603
  time to fit residues: 52.3672
Evaluate side-chains
  85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 97 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 112 optimal weight:    0.3980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 GLN
C 280 ASN
C 296 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.058859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.043077 restraints weight = 45649.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.044695 restraints weight = 21856.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.045786 restraints weight = 13486.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10356  Z= 0.129
  Angle     :  0.615   7.853  13988  Z= 0.322
  Chirality :  0.042   0.229   1528
  Planarity :  0.004   0.052   1789
  Dihedral  :  9.254 158.460   1396
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  5.18 %
    Favored  : 93.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1236
  helix:  0.47 (0.20), residues: 610
  sheet:  0.85 (0.39), residues: 158
  loop :  0.51 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 484 
 HIS   0.009   0.001   HIS A 418 
 PHE   0.026   0.002   PHE C 255 
 TYR   0.018   0.001   TYR A 787 
 ARG   0.004   0.000   ARG C 372 

Details of bonding type rmsd
  link_TRANS           : bond        0.00219 (    2)
  link_TRANS           : angle       0.96876 (    6)
  hydrogen bonds       : bond        0.03931 (  522)
  hydrogen bonds       : angle       4.82242 ( 1470)
  covalent geometry    : bond        0.00281 (10354)
  covalent geometry    : angle       0.61452 (13982)

*********************** 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
  103 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   50 LYS cc_start: 0.9496 (ttpp) cc_final: 0.9233 (ptmm)
REVERT: B   66 ASP cc_start: 0.8852 (p0) cc_final: 0.8375 (p0)
REVERT: B   93 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8974 (t80)
REVERT: A  503 MET cc_start: 0.8624 (mmt) cc_final: 0.8237 (mmt)
REVERT: A  682 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: C   44 MET cc_start: 0.8766 (mtp) cc_final: 0.8426 (ttt)
REVERT: C  236 LEU cc_start: 0.9005 (mt) cc_final: 0.8804 (mp)
  outliers start: 12
  outliers final: 3
  residues processed: 99
  average time/residue: 0.2273
  time to fit residues: 32.4026
Evaluate side-chains
  78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  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 99 optimal weight:    0.0020
   chunk 88 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 111 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.1592

-------------------------------------------------------------------------------
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 705 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.057891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.042217 restraints weight = 45854.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.043794 restraints weight = 22021.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.044864 restraints weight = 13599.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10356  Z= 0.164
  Angle     :  0.577   7.950  13988  Z= 0.298
  Chirality :  0.041   0.157   1528
  Planarity :  0.004   0.057   1789
  Dihedral  :  8.709 158.414   1396
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  6.19 %
    Favored  : 92.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.23), residues: 1236
  helix:  0.98 (0.21), residues: 620
  sheet:  0.77 (0.39), residues: 160
  loop :  0.56 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 484 
 HIS   0.008   0.001   HIS A 418 
 PHE   0.023   0.001   PHE C 255 
 TYR   0.016   0.001   TYR A  50 
 ARG   0.006   0.000   ARG C 290 

Details of bonding type rmsd
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.95071 (    6)
  hydrogen bonds       : bond        0.03692 (  522)
  hydrogen bonds       : angle       4.55596 ( 1470)
  covalent geometry    : bond        0.00366 (10354)
  covalent geometry    : angle       0.57703 (13982)

*********************** 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
  88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   50 LYS cc_start: 0.9481 (ttpp) cc_final: 0.9252 (ptmm)
REVERT: B   66 ASP cc_start: 0.8841 (p0) cc_final: 0.8392 (p0)
REVERT: B   93 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8935 (t80)
REVERT: A  445 GLU cc_start: 0.7950 (pm20) cc_final: 0.7693 (pm20)
REVERT: A  478 MET cc_start: 0.9462 (tpp) cc_final: 0.8937 (tpp)
REVERT: A  503 MET cc_start: 0.8583 (mmt) cc_final: 0.8214 (mmt)
REVERT: C   44 MET cc_start: 0.8837 (mtp) cc_final: 0.8558 (tpp)
REVERT: C  125 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7808 (mp0)
REVERT: C  305 MET cc_start: 0.8811 (mmm) cc_final: 0.8464 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 86
  average time/residue: 0.2254
  time to fit residues: 28.9107
Evaluate side-chains
  74 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  735 LEU
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  193 LEU
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 88 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:   20.0000
   chunk 105 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   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 638 HIS
** 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 = 0.3297 r_free = 0.3297 target = 0.058201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.042176 restraints weight = 45822.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.043792 restraints weight = 21864.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.044887 restraints weight = 13494.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10356  Z= 0.129
  Angle     :  0.546   8.915  13988  Z= 0.277
  Chirality :  0.040   0.160   1528
  Planarity :  0.004   0.056   1789
  Dihedral  :  8.505 157.950   1396
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1236
  helix:  1.33 (0.21), residues: 620
  sheet:  0.80 (0.39), residues: 160
  loop :  0.60 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 484 
 HIS   0.006   0.001   HIS A 418 
 PHE   0.020   0.001   PHE C 255 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00100 (    2)
  link_TRANS           : angle       0.88360 (    6)
  hydrogen bonds       : bond        0.03295 (  522)
  hydrogen bonds       : angle       4.34407 ( 1470)
  covalent geometry    : bond        0.00291 (10354)
  covalent geometry    : angle       0.54604 (13982)

*********************** 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
  87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ASP cc_start: 0.8870 (p0) cc_final: 0.8422 (p0)
REVERT: B   93 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8935 (t80)
REVERT: A  132 MET cc_start: 0.8063 (ttm) cc_final: 0.7708 (tpt)
REVERT: A  177 MET cc_start: 0.8364 (ptt) cc_final: 0.8146 (ppp)
REVERT: A  305 MET cc_start: 0.8736 (tpp) cc_final: 0.8237 (tpp)
REVERT: A  445 GLU cc_start: 0.8011 (pm20) cc_final: 0.7808 (pm20)
REVERT: A  478 MET cc_start: 0.9481 (tpp) cc_final: 0.8927 (tpp)
REVERT: A  484 TRP cc_start: 0.7755 (m-10) cc_final: 0.7471 (m-90)
REVERT: A  503 MET cc_start: 0.8580 (mmt) cc_final: 0.8243 (mmt)
REVERT: C  123 MET cc_start: 0.9362 (tpp) cc_final: 0.9140 (mmm)
REVERT: C  125 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7817 (mp0)
REVERT: C  167 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8466 (mp0)
REVERT: C  305 MET cc_start: 0.8783 (mmm) cc_final: 0.8431 (mmm)
  outliers start: 12
  outliers final: 4
  residues processed: 85
  average time/residue: 0.2182
  time to fit residues: 28.0230
Evaluate side-chains
  75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
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 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  250 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0000
   chunk 86 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3286 r_free = 0.3286 target = 0.057756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.042071 restraints weight = 45656.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.043628 restraints weight = 21944.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.044696 restraints weight = 13571.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3190

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= 0.154
  Angle     :  0.557   8.898  13988  Z= 0.281
  Chirality :  0.041   0.194   1528
  Planarity :  0.004   0.057   1789
  Dihedral  :  8.442 156.945   1396
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.04 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1236
  helix:  1.43 (0.21), residues: 625
  sheet:  0.86 (0.39), residues: 158
  loop :  0.55 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.006   0.001   HIS A 418 
 PHE   0.019   0.001   PHE C 255 
 TYR   0.014   0.001   TYR A 259 
 ARG   0.002   0.000   ARG A 779 

Details of bonding type rmsd
  link_TRANS           : bond        0.00086 (    2)
  link_TRANS           : angle       0.78873 (    6)
  hydrogen bonds       : bond        0.03340 (  522)
  hydrogen bonds       : angle       4.32779 ( 1470)
  covalent geometry    : bond        0.00348 (10354)
  covalent geometry    : angle       0.55685 (13982)

*********************** 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
  85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9331 (m-10) cc_final: 0.8881 (m-10)
REVERT: B   66 ASP cc_start: 0.8847 (p0) cc_final: 0.8440 (p0)
REVERT: B   93 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8943 (t80)
REVERT: A  132 MET cc_start: 0.8021 (ttm) cc_final: 0.7704 (tpt)
REVERT: A  478 MET cc_start: 0.9442 (tpp) cc_final: 0.9124 (tpp)
REVERT: A  503 MET cc_start: 0.8603 (mmt) cc_final: 0.8281 (mmt)
REVERT: A  682 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8943 (mm)
REVERT: C  123 MET cc_start: 0.9324 (tpp) cc_final: 0.8917 (mmm)
REVERT: C  125 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7794 (mp0)
REVERT: C  167 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8516 (mp0)
REVERT: C  305 MET cc_start: 0.8761 (mmm) cc_final: 0.8386 (mmm)
  outliers start: 14
  outliers final: 4
  residues processed: 84
  average time/residue: 0.2015
  time to fit residues: 25.6743
Evaluate side-chains
  76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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 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  250 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 120 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 113 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   chunk 109 optimal weight:    0.8980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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**
C 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.058131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.042443 restraints weight = 45586.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.044052 restraints weight = 21790.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.045164 restraints weight = 13391.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3367

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= 0.111
  Angle     :  0.538   9.674  13988  Z= 0.269
  Chirality :  0.040   0.195   1528
  Planarity :  0.003   0.055   1789
  Dihedral  :  8.340 156.158   1396
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  7.95 %
    Favored  : 90.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.24), residues: 1236
  helix:  1.58 (0.21), residues: 622
  sheet:  0.82 (0.38), residues: 158
  loop :  0.60 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  79 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.020   0.001   PHE B  12 
 TYR   0.011   0.001   TYR A 259 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00137 (    2)
  link_TRANS           : angle       0.85557 (    6)
  hydrogen bonds       : bond        0.03147 (  522)
  hydrogen bonds       : angle       4.19394 ( 1470)
  covalent geometry    : bond        0.00253 (10354)
  covalent geometry    : angle       0.53769 (13982)

*********************** 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
  86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9500 (m-10) cc_final: 0.9220 (m-10)
REVERT: B   93 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8964 (t80)
REVERT: A  132 MET cc_start: 0.8018 (ttm) cc_final: 0.7738 (tpp)
REVERT: A  478 MET cc_start: 0.9419 (tpp) cc_final: 0.9101 (tpp)
REVERT: A  503 MET cc_start: 0.8580 (mmt) cc_final: 0.8260 (mmt)
REVERT: A  564 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8707 (t80)
REVERT: A  682 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8928 (mm)
REVERT: C  123 MET cc_start: 0.9298 (tpp) cc_final: 0.8935 (mmm)
REVERT: C  125 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7772 (mp0)
REVERT: C  167 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8556 (mp0)
REVERT: C  227 MET cc_start: 0.8992 (tpt) cc_final: 0.8731 (tpt)
REVERT: C  305 MET cc_start: 0.8778 (mmm) cc_final: 0.8420 (mmm)
  outliers start: 13
  outliers final: 5
  residues processed: 84
  average time/residue: 0.2233
  time to fit residues: 28.0802
Evaluate side-chains
  77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  564 PHE
Chi-restraints excluded: chain A residue  682 LEU
Chi-restraints excluded: chain A residue  782 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  250 ILE
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 54 optimal weight:    0.0170
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6020

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.058429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.042735 restraints weight = 45694.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.044356 restraints weight = 21806.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.045455 restraints weight = 13435.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10356  Z= 0.108
  Angle     :  0.541  10.796  13988  Z= 0.270
  Chirality :  0.041   0.191   1528
  Planarity :  0.003   0.055   1789
  Dihedral  :  8.247 154.913   1396
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1236
  helix:  1.69 (0.21), residues: 621
  sheet:  0.87 (0.38), residues: 158
  loop :  0.64 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.016   0.001   PHE C 255 
 TYR   0.011   0.001   TYR A 259 
 ARG   0.001   0.000   ARG A 542 

Details of bonding type rmsd
  link_TRANS           : bond        0.00138 (    2)
  link_TRANS           : angle       0.86613 (    6)
  hydrogen bonds       : bond        0.03072 (  522)
  hydrogen bonds       : angle       4.13561 ( 1470)
  covalent geometry    : bond        0.00246 (10354)
  covalent geometry    : angle       0.54053 (13982)

*********************** 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
  81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 1.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8971 (t80)
REVERT: A  132 MET cc_start: 0.8027 (ttm) cc_final: 0.7746 (tpp)
REVERT: A  177 MET cc_start: 0.8474 (tmm) cc_final: 0.8234 (ppp)
REVERT: A  478 MET cc_start: 0.9408 (tpp) cc_final: 0.8830 (tpp)
REVERT: A  484 TRP cc_start: 0.7622 (m-10) cc_final: 0.7239 (m-90)
REVERT: A  503 MET cc_start: 0.8569 (mmt) cc_final: 0.8294 (mmt)
REVERT: A  564 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8584 (t80)
REVERT: C  123 MET cc_start: 0.9262 (tpp) cc_final: 0.8916 (mmm)
REVERT: C  125 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: C  167 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8373 (mp0)
REVERT: C  227 MET cc_start: 0.8962 (tpt) cc_final: 0.8686 (tpt)
REVERT: C  305 MET cc_start: 0.8776 (mmm) cc_final: 0.8416 (mmm)
  outliers start: 11
  outliers final: 3
  residues processed: 79
  average time/residue: 0.2849
  time to fit residues: 34.2467
Evaluate side-chains
  72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 1.752 
-------------------------------------------------------------------------------
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  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  250 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.058153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.042401 restraints weight = 45841.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.044016 restraints weight = 21882.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.045104 restraints weight = 13497.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3622

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= 0.121
  Angle     :  0.556  12.156  13988  Z= 0.276
  Chirality :  0.041   0.188   1528
  Planarity :  0.003   0.056   1789
  Dihedral  :  8.217 152.622   1396
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.52 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.24), residues: 1236
  helix:  1.75 (0.21), residues: 622
  sheet:  0.79 (0.38), residues: 155
  loop :  0.61 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.016   0.001   PHE B   4 
 TYR   0.012   0.001   TYR A 259 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00095 (    2)
  link_TRANS           : angle       0.84652 (    6)
  hydrogen bonds       : bond        0.03066 (  522)
  hydrogen bonds       : angle       4.13662 ( 1470)
  covalent geometry    : bond        0.00276 (10354)
  covalent geometry    : angle       0.55557 (13982)

*********************** 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
  78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8070 (m-80) cc_final: 0.7664 (m-80)
REVERT: B   93 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8970 (t80)
REVERT: A  132 MET cc_start: 0.8024 (ttm) cc_final: 0.7745 (tpp)
REVERT: A  177 MET cc_start: 0.8449 (tmm) cc_final: 0.8198 (ppp)
REVERT: A  503 MET cc_start: 0.8593 (mmt) cc_final: 0.8310 (mmt)
REVERT: A  564 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8628 (t80)
REVERT: C  123 MET cc_start: 0.9264 (tpp) cc_final: 0.8911 (mmm)
REVERT: C  125 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7741 (mp0)
REVERT: C  167 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8393 (mp0)
REVERT: C  305 MET cc_start: 0.8776 (mmm) cc_final: 0.8415 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 77
  average time/residue: 0.3035
  time to fit residues: 35.1969
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  : 1.323 
-------------------------------------------------------------------------------
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  564 PHE
Chi-restraints excluded: chain A residue  782 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  250 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 75 optimal weight:    0.3980
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.058533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.042407 restraints weight = 46219.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.044056 restraints weight = 22034.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.045167 restraints weight = 13603.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3736

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= 0.109
  Angle     :  0.560  12.865  13988  Z= 0.274
  Chirality :  0.040   0.185   1528
  Planarity :  0.003   0.055   1789
  Dihedral  :  8.053 147.447   1396
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  9.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.24), residues: 1236
  helix:  1.81 (0.21), residues: 622
  sheet:  0.82 (0.39), residues: 155
  loop :  0.59 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 781 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.022   0.001   PHE B  12 
 TYR   0.011   0.001   TYR A 259 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00129 (    2)
  link_TRANS           : angle       0.84586 (    6)
  hydrogen bonds       : bond        0.02980 (  522)
  hydrogen bonds       : angle       4.07917 ( 1470)
  covalent geometry    : bond        0.00248 (10354)
  covalent geometry    : angle       0.56006 (13982)

*********************** 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
  81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8183 (m-80) cc_final: 0.7970 (m-10)
REVERT: B   61 LYS cc_start: 0.7603 (mmmt) cc_final: 0.6618 (pttt)
REVERT: B   93 PHE cc_start: 0.9246 (m-80) cc_final: 0.9000 (t80)
REVERT: A  132 MET cc_start: 0.8070 (ttm) cc_final: 0.7758 (tpp)
REVERT: A  177 MET cc_start: 0.8463 (tmm) cc_final: 0.8183 (ppp)
REVERT: A  478 MET cc_start: 0.9271 (tpp) cc_final: 0.8933 (tpp)
REVERT: A  503 MET cc_start: 0.8611 (mmt) cc_final: 0.8328 (mmt)
REVERT: A  564 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8590 (t80)
REVERT: C   82 MET cc_start: 0.8883 (tpt) cc_final: 0.8536 (tpt)
REVERT: C  123 MET cc_start: 0.9238 (tpp) cc_final: 0.8917 (mmm)
REVERT: C  125 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7724 (mp0)
REVERT: C  167 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8408 (mp0)
REVERT: C  227 MET cc_start: 0.8993 (tpt) cc_final: 0.8786 (tpt)
REVERT: C  305 MET cc_start: 0.8787 (mmm) cc_final: 0.8422 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 81
  average time/residue: 0.2339
  time to fit residues: 28.0318
Evaluate side-chains
  75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue   81 HIS
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  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3299 r_free = 0.3299 target = 0.058261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.042091 restraints weight = 46295.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.043712 restraints weight = 22306.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.044816 restraints weight = 13831.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.3791

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= 0.129
  Angle     :  0.590  13.397  13988  Z= 0.287
  Chirality :  0.041   0.182   1528
  Planarity :  0.003   0.056   1789
  Dihedral  :  7.965 143.186   1396
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.07 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1236
  helix:  1.80 (0.21), residues: 626
  sheet:  0.82 (0.39), residues: 155
  loop :  0.47 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  86 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.020   0.001   PHE B  12 
 TYR   0.013   0.001   TYR A 259 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00079 (    2)
  link_TRANS           : angle       0.83744 (    6)
  hydrogen bonds       : bond        0.03061 (  522)
  hydrogen bonds       : angle       4.10903 ( 1470)
  covalent geometry    : bond        0.00292 (10354)
  covalent geometry    : angle       0.59028 (13982)

********************** 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
  79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.8154 (m-80) cc_final: 0.7949 (m-10)
REVERT: B   93 PHE cc_start: 0.9247 (m-80) cc_final: 0.9006 (t80)
REVERT: A  132 MET cc_start: 0.8016 (ttm) cc_final: 0.7737 (tpp)
REVERT: A  177 MET cc_start: 0.8457 (tmm) cc_final: 0.8120 (tmm)
REVERT: A  478 MET cc_start: 0.9270 (tpp) cc_final: 0.8953 (tpp)
REVERT: A  503 MET cc_start: 0.8596 (mmt) cc_final: 0.8295 (mmt)
REVERT: A  564 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8630 (t80)
REVERT: C  123 MET cc_start: 0.9289 (tpp) cc_final: 0.8914 (mmm)
REVERT: C  125 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7737 (mp0)
REVERT: C  167 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8420 (mp0)
REVERT: C  227 MET cc_start: 0.8985 (tpt) cc_final: 0.8782 (tpt)
REVERT: C  305 MET cc_start: 0.8781 (mmm) cc_final: 0.8416 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 79
  average time/residue: 0.2469
  time to fit residues: 30.5208
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  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue   81 HIS
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  125 GLU
Chi-restraints excluded: chain C residue  167 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.0470
   chunk 5 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 110 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6480

-------------------------------------------------------------------------------
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 = 0.3305 r_free = 0.3305 target = 0.058490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.042332 restraints weight = 45991.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.043965 restraints weight = 21959.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.045032 restraints weight = 13575.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10356  Z= 0.114
  Angle     :  0.589  13.330  13988  Z= 0.286
  Chirality :  0.041   0.180   1528
  Planarity :  0.003   0.056   1789
  Dihedral  :  7.845 138.552   1396
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.44 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.24), residues: 1236
  helix:  1.82 (0.21), residues: 625
  sheet:  0.82 (0.39), residues: 155
  loop :  0.46 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  86 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.018   0.001   PHE B  12 
 TYR   0.011   0.001   TYR A 259 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00118 (    2)
  link_TRANS           : angle       0.84463 (    6)
  hydrogen bonds       : bond        0.03010 (  522)
  hydrogen bonds       : angle       4.07349 ( 1470)
  covalent geometry    : bond        0.00261 (10354)
  covalent geometry    : angle       0.58906 (13982)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3688.79 seconds
wall clock time: 67 minutes 22.53 seconds (4042.53 seconds total)