Starting phenix.real_space_refine
on Wed Aug  5 08:21:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iol_60744/08_2026/9iol_60744.map"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      40      5.16       5
     C    5631      2.51       5
     N    1530      2.21       5
     O    1789      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4104
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 23, 'TRANS': 488}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3970
          Classifications: {'peptide': 494}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 27, 'TRANS': 466}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 404
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 416
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "M"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 101
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'2OP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'2OP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 2.19, per 1000 atoms: 0.24
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (95.57, 92.7029, 141.444, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P      46     15.00
     O    1789      8.00
     N    1530      7.00
     C    5631      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 299.4 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      39.7% alpha, 20.9% beta
      12 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 48
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 106 through 123
      removed outlier: 3.676A  pdb=" N   ILE A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
    Processing helix  chain 'A' and resid 198 through 222
      removed outlier: 9.357A  pdb=" N   GLU A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 299 through 303
      removed outlier: 4.543A  pdb=" N   THR A 303 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 308
      No H-bonds generated for 'chain 'A' and resid 306 through 308'
    Processing helix  chain 'A' and resid 324 through 332
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 352 through 356
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 3.829A  pdb=" N   LEU A 430 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 461
      removed outlier: 3.582A  pdb=" N   ASP A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 482
      removed outlier: 3.574A  pdb=" N   ILE A 482 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 500
      removed outlier: 3.702A  pdb=" N   GLN A 488 " --> pdb=" O   ASN A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 517
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 526 through 537
    Processing helix  chain 'B' and resid 45 through 50
    Processing helix  chain 'B' and resid 58 through 78
    Processing helix  chain 'B' and resid 112 through 121
    Processing helix  chain 'B' and resid 123 through 136
    Processing helix  chain 'B' and resid 142 through 156
    Processing helix  chain 'B' and resid 179 through 196
    Processing helix  chain 'B' and resid 238 through 251
      removed outlier: 3.935A  pdb=" N   THR B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 314
      No H-bonds generated for 'chain 'B' and resid 312 through 314'
    Processing helix  chain 'B' and resid 330 through 338
      removed outlier: 3.788A  pdb=" N   LYS B 338 " --> pdb=" O   THR B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 356
      No H-bonds generated for 'chain 'B' and resid 354 through 356'
    Processing helix  chain 'B' and resid 377 through 393
      removed outlier: 3.538A  pdb=" N   LEU B 381 " --> pdb=" O   GLY B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
    Processing helix  chain 'B' and resid 455 through 469
    Processing helix  chain 'B' and resid 474 through 478
      removed outlier: 4.159A  pdb=" N   PHE B 478 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 495
      removed outlier: 3.537A  pdb=" N   ARG B 488 " --> pdb=" O   GLN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 519
    Processing helix  chain 'B' and resid 520 through 530
    Processing helix  chain 'M' and resid 9 through 13
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84
      removed outlier: 5.194A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU A  58 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LEU A  83 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ALA A  55 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL A  10 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   VAL A  57 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   LEU A  12 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   PHE A  59 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   MET A  14 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARG A 130 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLN A 162 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ILE A 132 " --> pdb=" O   GLN A 162 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 164 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE A 134 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   TYR A 225 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 165 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253
      removed outlier: 6.913A  pdb=" N   VAL A 361 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 9.917A  pdb=" N   ASN A 359 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 8.771A  pdb=" N   ASN A 359 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
      removed outlier: 11.930A  pdb=" N   TYR A 421 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 10.122A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 11.031A  pdb=" N   LEU A 419 " --> pdb=" O   VAL A 361 " (cutoff:3.500A)
      removed outlier: 9.948A  pdb=" N   LYS A 363 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
      removed outlier: 10.850A  pdb=" N   GLU A 417 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
      removed outlier: 8.960A  pdb=" N   MET A 389 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLY A 344 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ARG A 394 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   VAL A 342 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ALA A 396 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   PHE A 340 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 280
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 297
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322
    Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA7, first strand: chain 'A' and resid 540 through 541
    Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 109
      removed outlier: 7.161A  pdb=" N   LEU B 105 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   PHE B  87 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   GLU B 107 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   VAL B  85 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP B  43 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B 164 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 8.724A  pdb=" N   ASP B 201 " --> pdb=" O   LYS B 164 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE B 166 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   MET B 203 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 168 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262
      removed outlier: 7.825A  pdb=" N   VAL B 394 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   PHE B 350 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 348 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 420
      removed outlier: 6.882A  pdb=" N   GLU B 419 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1428
        1.29 -     1.42: 2464
        1.42 -     1.55: 5244
        1.55 -     1.69: 89
        1.69 -     1.82: 67
  Bond restraints: 9292
  Sorted by residual:
  bond pdb=" CB  GLN B 320 "
       pdb=" CG  GLN B 320 "
    ideal  model  delta    sigma   weight residual
    1.520  1.340  0.180 3.00e-02 1.11e+03 3.59e+01
  bond pdb=" CZ  ARG B 318 "
       pdb=" NH2 ARG B 318 "
    ideal  model  delta    sigma   weight residual
    1.330  1.259  0.071 1.30e-02 5.92e+03 3.00e+01
  bond pdb=" O14 IHP B 801 "
       pdb=" P4  IHP B 801 "
    ideal  model  delta    sigma   weight residual
    1.671  1.571  0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" C5'  DC C   1 "
       pdb=" C4'  DC C   1 "
    ideal  model  delta    sigma   weight residual
    1.512  1.544 -0.032 7.00e-03 2.04e+04 2.15e+01
  bond pdb=" C4   DC D  13 "
       pdb=" N4   DC D  13 "
    ideal  model  delta    sigma   weight residual
    1.335  1.293  0.042 9.00e-03 1.23e+04 2.15e+01
  ... (remaining 9287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.09: 12382
        4.09 -     8.18: 315
        8.18 -    12.27: 10
       12.27 -    16.36: 1
       16.36 -    20.45: 1
  Bond angle restraints: 12709
  Sorted by residual:
  angle pdb=" CB  GLN B 320 "
        pdb=" CG  GLN B 320 "
        pdb=" CD  GLN B 320 "
      ideal   model   delta    sigma   weight residual
     112.60  133.05  -20.45 1.70e+00 3.46e-01 1.45e+02
  angle pdb=" O2   DT C  14 "
        pdb=" C2   DT C  14 "
        pdb=" N3   DT C  14 "
      ideal   model   delta    sigma   weight residual
     122.30  117.00    5.30 6.00e-01 2.78e+00 7.81e+01
  angle pdb=" C5   DA D   7 "
        pdb=" C6   DA D   7 "
        pdb=" N1   DA D   7 "
      ideal   model   delta    sigma   weight residual
     117.70  121.92   -4.22 5.00e-01 4.00e+00 7.12e+01
  angle pdb=" C5   DA C  17 "
        pdb=" C6   DA C  17 "
        pdb=" N1   DA C  17 "
      ideal   model   delta    sigma   weight residual
     117.70  121.87   -4.17 5.00e-01 4.00e+00 6.97e+01
  angle pdb=" N6   DA D   1 "
        pdb=" C6   DA D   1 "
        pdb=" N1   DA D   1 "
      ideal   model   delta    sigma   weight residual
     118.60  113.76    4.84 6.00e-01 2.78e+00 6.52e+01
  ... (remaining 12704 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.39: 5110
       23.39 -    46.77: 372
       46.77 -    70.15: 121
       70.15 -    93.54: 14
       93.54 -   116.92: 4
  Dihedral angle restraints: 5621
    sinusoidal: 2627
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C   LEU A 108 "
           pdb=" N   LEU A 108 "
           pdb=" CA  LEU A 108 "
           pdb=" CB  LEU A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.02   14.42     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" CA  LYS A 413 "
           pdb=" C   LYS A 413 "
           pdb=" N   HIS A 414 "
           pdb=" CA  HIS A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.25   28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  GLU B  91 "
           pdb=" C   GLU B  91 "
           pdb=" N   LYS B  92 "
           pdb=" CA  LYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.09   25.91     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5618 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1154
       0.107 -    0.215: 241
       0.215 -    0.322: 31
       0.322 -    0.429: 2
       0.429 -    0.536: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  LEU A 108 "
            pdb=" N   LEU A 108 "
            pdb=" C   LEU A 108 "
            pdb=" CB  LEU A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" CA  PHE B 159 "
            pdb=" N   PHE B 159 "
            pdb=" C   PHE B 159 "
            pdb=" CB  PHE B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.94e+00
  chirality pdb=" CG  LEU B  57 "
            pdb=" CB  LEU B  57 "
            pdb=" CD1 LEU B  57 "
            pdb=" CD2 LEU B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.20   -0.39 2.00e-01 2.50e+01 3.76e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA D   1 "    0.355 2.00e-02 2.50e+03   1.51e-01 6.30e+02
        pdb=" N9   DA D   1 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8   DA D   1 "   -0.095 2.00e-02 2.50e+03
        pdb=" N7   DA D   1 "   -0.097 2.00e-02 2.50e+03
        pdb=" C5   DA D   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" C6   DA D   1 "    0.028 2.00e-02 2.50e+03
        pdb=" N6   DA D   1 "    0.242 2.00e-02 2.50e+03
        pdb=" N1   DA D   1 "    0.030 2.00e-02 2.50e+03
        pdb=" C2   DA D   1 "   -0.053 2.00e-02 2.50e+03
        pdb=" N3   DA D   1 "   -0.114 2.00e-02 2.50e+03
        pdb=" C4   DA D   1 "   -0.133 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  14 "   -0.188 2.00e-02 2.50e+03   1.22e-01 3.72e+02
        pdb=" N1   DT C  14 "    0.121 2.00e-02 2.50e+03
        pdb=" C2   DT C  14 "    0.141 2.00e-02 2.50e+03
        pdb=" O2   DT C  14 "   -0.141 2.00e-02 2.50e+03
        pdb=" N3   DT C  14 "    0.128 2.00e-02 2.50e+03
        pdb=" C4   DT C  14 "    0.022 2.00e-02 2.50e+03
        pdb=" O4   DT C  14 "   -0.155 2.00e-02 2.50e+03
        pdb=" C5   DT C  14 "    0.035 2.00e-02 2.50e+03
        pdb=" C7   DT C  14 "   -0.073 2.00e-02 2.50e+03
        pdb=" C6   DT C  14 "    0.108 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC C   7 "   -0.155 2.00e-02 2.50e+03   8.46e-02 1.61e+02
        pdb=" N1   DC C   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DC C   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DC C   7 "    0.119 2.00e-02 2.50e+03
        pdb=" N3   DC C   7 "   -0.036 2.00e-02 2.50e+03
        pdb=" C4   DC C   7 "   -0.028 2.00e-02 2.50e+03
        pdb=" N4   DC C   7 "   -0.081 2.00e-02 2.50e+03
        pdb=" C5   DC C   7 "    0.077 2.00e-02 2.50e+03
        pdb=" C6   DC C   7 "    0.109 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1288
        2.79 -     3.31: 9097
        3.31 -     3.84: 14986
        3.84 -     4.37: 17397
        4.37 -     4.90: 28012
  Nonbonded interactions: 70780
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 324 "
            pdb=" OD2 ASP A 327 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR A  61 "
            pdb=" O   GLY A  63 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LYS B 265 "
            pdb=" NZ  LYS B 265 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   GLY A  17 "
            pdb=" OG  SER A  21 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ILE A 197 "
            pdb=" NZ  LYS A 202 "
     model   vdw
     2.345 3.120
  ... (remaining 70775 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.020
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
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      :  0.012   0.180   9293  Z= 0.789
  Angle     :  1.679  20.454  12709  Z= 1.258
  Chirality :  0.087   0.536   1430
  Planarity :  0.017   0.173   1482
  Dihedral  : 18.011 116.920   3667
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.85 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.24), residues: 1007
  helix: -0.29 (0.25), residues: 354
  sheet:  0.52 (0.38), residues: 156
  loop : -0.57 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 165 
 TYR   0.111   0.015   TYR B 217 
 PHE   0.060   0.010   PHE A 409 
 TRP   0.077   0.016   TRP A 276 
 HIS   0.014   0.003   HIS B 360 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01179 /  0.79 ( 9292)
  covalent geometry    : angle       1.67864 /  1.26 (12709)
  hydrogen bonds       : bond        0.15671 / 10.71 (  403)
  hydrogen bonds       : angle       7.91297 /  5.55 ( 1092)
  Misc. bond           : bond        0.01948 /  1.03 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9320 (mmt) cc_final: 0.8968 (mmm)
REVERT: A  208 VAL cc_start: 0.9637 (t) cc_final: 0.9428 (t)
REVERT: A  292 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7806 (tm-30)
REVERT: A  427 MET cc_start: 0.9567 (tmm) cc_final: 0.9040 (tmm)
REVERT: A  461 MET cc_start: 0.9015 (mpp) cc_final: 0.8790 (mmp)
REVERT: B   41 LEU cc_start: 0.9299 (mm) cc_final: 0.9076 (mm)
REVERT: B   62 MET cc_start: 0.9120 (tpp) cc_final: 0.8805 (tpp)
REVERT: B   68 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9225 (mm-40)
REVERT: B  287 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8898 (mmmt)
REVERT: B  488 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8961 (tpp80)
REVERT: B  514 MET cc_start: 0.9705 (mtp) cc_final: 0.9173 (mtp)
REVERT: B  518 LEU cc_start: 0.9683 (mt) cc_final: 0.9448 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 90
  average time/residue: 0.0917
  time to fit residues: 11.6137
Evaluate side-chains
  69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 GLU
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  488 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 162 GLN
A 432 GLN
A 517 ASN
B  68 GLN
B 152 ASN
B 176 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.058737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.040403 restraints weight = 43260.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 4.92
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9293  Z= 0.193
  Angle     :  0.733   6.716  12709  Z= 0.397
  Chirality :  0.046   0.225   1430
  Planarity :  0.004   0.058   1482
  Dihedral  : 19.621 104.450   1568
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.92 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1007
  helix:  0.56 (0.27), residues: 356
  sheet:  0.28 (0.37), residues: 164
  loop : -0.52 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG M   9 
 TYR   0.022   0.002   TYR A 264 
 PHE   0.017   0.002   PHE A  31 
 TRP   0.018   0.002   TRP A 247 
 HIS   0.005   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.19 ( 9292)
  covalent geometry    : angle       0.73346 /  0.40 (12709)
  hydrogen bonds       : bond        0.06989 /  5.06 (  403)
  hydrogen bonds       : angle       6.13246 /  4.31 ( 1092)
  Misc. bond           : bond        0.00065 /  0.03 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9379 (mmt) cc_final: 0.9068 (mmm)
REVERT: A  115 MET cc_start: 0.9742 (tpp) cc_final: 0.9486 (tmm)
REVERT: A  427 MET cc_start: 0.9612 (tmm) cc_final: 0.9069 (tmm)
REVERT: A  461 MET cc_start: 0.9099 (mpp) cc_final: 0.8840 (mmp)
REVERT: B   62 MET cc_start: 0.9170 (tpp) cc_final: 0.8728 (tpp)
REVERT: B   68 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.9340 (mt0)
REVERT: B  203 MET cc_start: 0.9398 (mmp) cc_final: 0.9034 (mmp)
REVERT: B  287 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8914 (mmmt)
REVERT: B  518 LEU cc_start: 0.9710 (mt) cc_final: 0.9478 (mt)
  outliers start: 15
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0707
  time to fit residues: 7.9746
Evaluate side-chains
  68 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 101 optimal weight:   20.0000
   chunk 84 optimal weight:    0.5980
   chunk 52 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    3.0786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.058473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.040045 restraints weight = 44167.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 4.89
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9293  Z= 0.190
  Angle     :  0.659   6.752  12709  Z= 0.353
  Chirality :  0.043   0.161   1430
  Planarity :  0.004   0.053   1482
  Dihedral  : 19.436 103.248   1557
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.01 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.25), residues: 1007
  helix:  0.89 (0.27), residues: 355
  sheet:  0.17 (0.38), residues: 167
  loop : -0.48 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 399 
 TYR   0.016   0.002   TYR A 264 
 PHE   0.019   0.002   PHE A  31 
 TRP   0.011   0.001   TRP A 247 
 HIS   0.005   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.19 ( 9292)
  covalent geometry    : angle       0.65882 /  0.35 (12709)
  hydrogen bonds       : bond        0.05765 /  4.13 (  403)
  hydrogen bonds       : angle       5.64259 /  3.98 ( 1092)
  Misc. bond           : bond        0.00041 /  0.02 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9373 (mmt) cc_final: 0.9059 (mmm)
REVERT: A  427 MET cc_start: 0.9648 (tmm) cc_final: 0.9088 (tmm)
REVERT: A  461 MET cc_start: 0.9165 (mpp) cc_final: 0.8799 (mmp)
REVERT: B  287 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8864 (mmmt)
REVERT: B  518 LEU cc_start: 0.9680 (mt) cc_final: 0.9439 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 74
  average time/residue: 0.0777
  time to fit residues: 8.6460
Evaluate side-chains
  71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    0.0000
   chunk 1 optimal weight:   20.0000
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 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 = 0.3413 r_free = 0.3413 target = 0.059051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.040530 restraints weight = 43934.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 4.93
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9293  Z= 0.142
  Angle     :  0.633   8.192  12709  Z= 0.333
  Chirality :  0.042   0.164   1430
  Planarity :  0.004   0.048   1482
  Dihedral  : 19.336 100.910   1554
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.21 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.26), residues: 1007
  helix:  1.11 (0.27), residues: 355
  sheet:  0.30 (0.39), residues: 165
  loop : -0.41 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M   9 
 TYR   0.015   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A  31 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.004   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 ( 9292)
  covalent geometry    : angle       0.63305 /  0.33 (12709)
  hydrogen bonds       : bond        0.05295 /  3.80 (  403)
  hydrogen bonds       : angle       5.33811 /  3.78 ( 1092)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9536 (tpp) cc_final: 0.9193 (tpp)
REVERT: A  427 MET cc_start: 0.9657 (tmm) cc_final: 0.9137 (tmm)
REVERT: A  461 MET cc_start: 0.9174 (mpp) cc_final: 0.8774 (mmp)
REVERT: B   62 MET cc_start: 0.9262 (ttm) cc_final: 0.8844 (tpp)
REVERT: B  203 MET cc_start: 0.9423 (mmp) cc_final: 0.8780 (mmp)
REVERT: B  518 LEU cc_start: 0.9655 (mt) cc_final: 0.9422 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0765
  time to fit residues: 8.7362
Evaluate side-chains
  73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 100 optimal weight:   40.0000
   chunk 96 optimal weight:    1.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 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 = 0.3405 r_free = 0.3405 target = 0.058842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.040172 restraints weight = 44410.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 4.94
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9293  Z= 0.164
  Angle     :  0.643   7.915  12709  Z= 0.336
  Chirality :  0.042   0.185   1430
  Planarity :  0.004   0.078   1482
  Dihedral  : 19.269  99.231   1554
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.67 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.26), residues: 1007
  helix:  1.37 (0.28), residues: 354
  sheet:  0.31 (0.39), residues: 166
  loop : -0.42 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M   9 
 TYR   0.013   0.001   TYR A 264 
 PHE   0.019   0.001   PHE A  31 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.005   0.001   HIS B 176 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 ( 9292)
  covalent geometry    : angle       0.64322 /  0.34 (12709)
  hydrogen bonds       : bond        0.05301 /  3.77 (  403)
  hydrogen bonds       : angle       5.23504 /  3.71 ( 1092)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9499 (tpp) cc_final: 0.9249 (tpp)
REVERT: A  427 MET cc_start: 0.9655 (tmm) cc_final: 0.9159 (tmm)
REVERT: A  461 MET cc_start: 0.9181 (tpp) cc_final: 0.8782 (mmp)
REVERT: B   62 MET cc_start: 0.9301 (ttm) cc_final: 0.8800 (tpp)
REVERT: B  497 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8916 (pp)
REVERT: B  518 LEU cc_start: 0.9663 (mt) cc_final: 0.9432 (mt)
  outliers start: 18
  outliers final: 13
  residues processed: 78
  average time/residue: 0.0699
  time to fit residues: 8.5512
Evaluate side-chains
  78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  497 LEU
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 66 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 100 optimal weight:   40.0000
   chunk 94 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0000
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    2.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 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 = 0.3403 r_free = 0.3403 target = 0.058665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.040272 restraints weight = 43900.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 4.86
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9293  Z= 0.151
  Angle     :  0.655  12.649  12709  Z= 0.335
  Chirality :  0.042   0.177   1430
  Planarity :  0.003   0.049   1482
  Dihedral  : 19.181  97.021   1554
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.43 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 1007
  helix:  1.43 (0.28), residues: 355
  sheet:  0.40 (0.39), residues: 164
  loop : -0.38 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 517 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.018   0.001   PHE A  31 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.005   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 9292)
  covalent geometry    : angle       0.65488 /  0.33 (12709)
  hydrogen bonds       : bond        0.05022 /  3.58 (  403)
  hydrogen bonds       : angle       5.13325 /  3.64 ( 1092)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8268 (t)
REVERT: A  427 MET cc_start: 0.9658 (tmm) cc_final: 0.9152 (tmm)
REVERT: A  461 MET cc_start: 0.9174 (tpp) cc_final: 0.8909 (mmp)
REVERT: B   62 MET cc_start: 0.9293 (ttm) cc_final: 0.8763 (tpp)
REVERT: B  203 MET cc_start: 0.9460 (mmp) cc_final: 0.8929 (mmp)
REVERT: B  518 LEU cc_start: 0.9645 (mt) cc_final: 0.9421 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0704
  time to fit residues: 8.5790
Evaluate side-chains
  81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0980
   chunk 92 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0670
   chunk 67 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.0324

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.058775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.040302 restraints weight = 44501.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 4.94
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9293  Z= 0.144
  Angle     :  0.650  12.170  12709  Z= 0.330
  Chirality :  0.042   0.286   1430
  Planarity :  0.003   0.049   1482
  Dihedral  : 19.084  94.793   1554
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.98 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 1007
  helix:  1.46 (0.28), residues: 355
  sheet:  0.40 (0.40), residues: 160
  loop : -0.39 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.021   0.001   PHE A 227 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 9292)
  covalent geometry    : angle       0.64970 /  0.33 (12709)
  hydrogen bonds       : bond        0.04869 /  3.47 (  403)
  hydrogen bonds       : angle       5.08391 /  3.62 ( 1092)
  Misc. bond           : bond        0.00011 /  0.01 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (t)
REVERT: A   14 MET cc_start: 0.9583 (tpp) cc_final: 0.8915 (tpp)
REVERT: A  427 MET cc_start: 0.9663 (tmm) cc_final: 0.9179 (tmm)
REVERT: A  461 MET cc_start: 0.9178 (tpp) cc_final: 0.8727 (mmp)
REVERT: B   62 MET cc_start: 0.9270 (ttm) cc_final: 0.8715 (tpp)
REVERT: B  203 MET cc_start: 0.9489 (mmp) cc_final: 0.8984 (mmp)
REVERT: B  518 LEU cc_start: 0.9646 (mt) cc_final: 0.9426 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0710
  time to fit residues: 8.0231
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 90 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 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 = 0.3411 r_free = 0.3411 target = 0.059157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.040537 restraints weight = 44372.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 4.99
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9293  Z= 0.131
  Angle     :  0.662  11.380  12709  Z= 0.335
  Chirality :  0.042   0.211   1430
  Planarity :  0.003   0.048   1482
  Dihedral  : 18.994  92.719   1554
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.52 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.26), residues: 1007
  helix:  1.50 (0.28), residues: 354
  sheet:  0.42 (0.40), residues: 160
  loop : -0.38 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 400 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.021   0.001   PHE A 227 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 382 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 9292)
  covalent geometry    : angle       0.66239 /  0.34 (12709)
  hydrogen bonds       : bond        0.04746 /  3.37 (  403)
  hydrogen bonds       : angle       5.03508 /  3.57 ( 1092)
  Misc. bond           : bond        0.00012 /  0.01 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8411 (t)
REVERT: A   14 MET cc_start: 0.9557 (tpp) cc_final: 0.9214 (tpp)
REVERT: A  427 MET cc_start: 0.9653 (tmm) cc_final: 0.9214 (tmm)
REVERT: A  461 MET cc_start: 0.9181 (tpp) cc_final: 0.8720 (mmp)
REVERT: B   62 MET cc_start: 0.9252 (ttm) cc_final: 0.8692 (tpp)
REVERT: B  203 MET cc_start: 0.9497 (mmp) cc_final: 0.8972 (mmp)
REVERT: B  518 LEU cc_start: 0.9628 (mt) cc_final: 0.9404 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0696
  time to fit residues: 8.0071
Evaluate side-chains
  79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 97 optimal weight:    0.1980
   chunk 20 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    2.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 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 = 0.3399 r_free = 0.3399 target = 0.058564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.040108 restraints weight = 44186.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 4.89
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9293  Z= 0.169
  Angle     :  0.702  23.028  12709  Z= 0.349
  Chirality :  0.042   0.222   1430
  Planarity :  0.003   0.050   1482
  Dihedral  : 18.921  90.840   1554
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.63 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1007
  helix:  1.43 (0.28), residues: 355
  sheet:  0.38 (0.40), residues: 160
  loop : -0.39 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 318 
 TYR   0.010   0.001   TYR B 217 
 PHE   0.024   0.001   PHE A 227 
 TRP   0.004   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 414 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 ( 9292)
  covalent geometry    : angle       0.70195 /  0.35 (12709)
  hydrogen bonds       : bond        0.04837 /  3.40 (  403)
  hydrogen bonds       : angle       5.08778 /  3.62 ( 1092)
  Misc. bond           : bond        0.00010 /  0.01 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 CYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (t)
REVERT: A   14 MET cc_start: 0.9559 (tpp) cc_final: 0.9234 (tpp)
REVERT: A  427 MET cc_start: 0.9669 (tmm) cc_final: 0.9217 (tmm)
REVERT: A  461 MET cc_start: 0.9190 (tpp) cc_final: 0.8775 (mpp)
REVERT: B   62 MET cc_start: 0.9273 (ttm) cc_final: 0.8839 (tpp)
REVERT: B  203 MET cc_start: 0.9516 (mmp) cc_final: 0.8993 (mmp)
REVERT: B  287 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8758 (mmmt)
REVERT: B  518 LEU cc_start: 0.9622 (mt) cc_final: 0.9386 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 74
  average time/residue: 0.0784
  time to fit residues: 8.6613
Evaluate side-chains
  79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  447 THR
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0470
   chunk 81 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0060
   chunk 102 optimal weight:   20.0000
   chunk 89 optimal weight:    0.0270
   chunk 17 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.3152

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 511 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.060075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.041724 restraints weight = 43442.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 4.93
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9293  Z= 0.117
  Angle     :  0.722  20.782  12709  Z= 0.349
  Chirality :  0.043   0.247   1430
  Planarity :  0.003   0.047   1482
  Dihedral  : 18.783  86.664   1554
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.07 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.26), residues: 1007
  helix:  1.43 (0.28), residues: 354
  sheet:  0.42 (0.40), residues: 160
  loop : -0.29 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 318 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.025   0.001   PHE A 227 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.002   0.001   HIS B 486 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 ( 9292)
  covalent geometry    : angle       0.72224 /  0.35 (12709)
  hydrogen bonds       : bond        0.04357 /  3.06 (  403)
  hydrogen bonds       : angle       4.92386 /  3.50 ( 1092)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.9560 (tpp) cc_final: 0.9221 (tpp)
REVERT: A  212 MET cc_start: 0.9331 (pmm) cc_final: 0.8990 (pmm)
REVERT: A  427 MET cc_start: 0.9646 (tmm) cc_final: 0.9240 (tmm)
REVERT: A  461 MET cc_start: 0.9160 (tpp) cc_final: 0.8769 (mmp)
REVERT: B   62 MET cc_start: 0.9208 (ttm) cc_final: 0.8626 (tpp)
REVERT: B  203 MET cc_start: 0.9535 (mmp) cc_final: 0.9042 (mmp)
REVERT: B  287 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8719 (mmmt)
REVERT: B  348 MET cc_start: 0.8840 (mmm) cc_final: 0.8402 (mtt)
REVERT: B  518 LEU cc_start: 0.9585 (mt) cc_final: 0.9351 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0722
  time to fit residues: 7.9228
Evaluate side-chains
  76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue   41 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  498 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.059144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.040809 restraints weight = 43908.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 4.94
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
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   0.041   9293  Z= 0.150
  Angle     :  0.700  18.176  12709  Z= 0.346
  Chirality :  0.042   0.247   1430
  Planarity :  0.003   0.049   1482
  Dihedral  : 18.707  84.846   1554
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.63 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.26), residues: 1007
  helix:  1.51 (0.28), residues: 355
  sheet:  0.41 (0.41), residues: 160
  loop : -0.31 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 318 
 TYR   0.009   0.001   TYR B 217 
 PHE   0.027   0.001   PHE A  31 
 TRP   0.004   0.001   TRP A 247 
 HIS   0.002   0.001   HIS A 414 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.15 ( 9292)
  covalent geometry    : angle       0.69987 /  0.35 (12709)
  hydrogen bonds       : bond        0.04463 /  3.10 (  403)
  hydrogen bonds       : angle       4.93583 /  3.51 ( 1092)
  Misc. bond           : bond        0.00007 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1402.55 seconds
wall clock time: 24 minutes 50.85 seconds (1490.85 seconds total)