Starting phenix.real_space_refine
on Thu Oct 22 22:37:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wdt_65905/10_2026/9wdt_65905.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4040      2.51       5
     N    1164      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6434
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3183
          Classifications: {'peptide': 420}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 399}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3183
          Classifications: {'peptide': 420}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 399}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 68
          Unusual residues: {'WV2': 2}
          Classifications: {'undetermined': 2, 'water': 4}
          Link IDs: {None: 5}
  Time building chain proxies: 1.44, per 1000 atoms: 0.22
  Number of scatterers: 6434
  At special positions: 0
  Unit cell: (71.4, 85.85, 116.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1194      8.00
     N    1164      7.00
     C    4040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 367.1 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1552

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      52.6% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 75
      removed outlier: 3.597A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 111
    Processing helix  chain 'A' and resid 123 through 140
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.709A  pdb=" N   TYR A 148 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 3.887A  pdb=" N   ARG A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 302
      removed outlier: 3.955A  pdb=" N   VAL A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLY A 302 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 3.790A  pdb=" N   HIS A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 316 through 322
      removed outlier: 3.633A  pdb=" N   VAL A 320 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 330
      removed outlier: 3.512A  pdb=" N   GLU A 328 " --> pdb=" O   ASP A 324 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL A 329 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 364
      removed outlier: 3.705A  pdb=" N   ALA A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN A 353 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
      removed outlier: 3.556A  pdb=" N   ILE A 378 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR A 379 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 398
      removed outlier: 3.882A  pdb=" N   GLY A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 429
      removed outlier: 3.556A  pdb=" N   ALA A 417 " --> pdb=" O   PHE A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 444
      removed outlier: 3.664A  pdb=" N   LEU A 437 " --> pdb=" O   TYR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 467
    Processing helix  chain 'A' and resid 478 through 486
    Processing helix  chain 'A' and resid 499 through 506
    Processing helix  chain 'A' and resid 507 through 509
      No H-bonds generated for 'chain 'A' and resid 507 through 509'
    Processing helix  chain 'A' and resid 524 through 543
      removed outlier: 3.512A  pdb=" N   ASP A 528 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 75
      removed outlier: 3.619A  pdb=" N   CYS C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU C  75 " --> pdb=" O   GLU C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 111
    Processing helix  chain 'C' and resid 123 through 140
    Processing helix  chain 'C' and resid 144 through 148
      removed outlier: 3.711A  pdb=" N   TYR C 148 " --> pdb=" O   PRO C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 279
      removed outlier: 3.961A  pdb=" N   ARG C 270 " --> pdb=" O   GLU C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 302
      removed outlier: 3.897A  pdb=" N   VAL C 294 " --> pdb=" O   LYS C 290 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLY C 302 " --> pdb=" O   ARG C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 306
      removed outlier: 3.956A  pdb=" N   HIS C 306 " --> pdb=" O   PRO C 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 303 through 306'
    Processing helix  chain 'C' and resid 316 through 322
    Processing helix  chain 'C' and resid 322 through 330
      removed outlier: 3.506A  pdb=" N   ILE C 326 " --> pdb=" O   ARG C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 347
      No H-bonds generated for 'chain 'C' and resid 345 through 347'
    Processing helix  chain 'C' and resid 348 through 364
    Processing helix  chain 'C' and resid 374 through 379
    Processing helix  chain 'C' and resid 384 through 398
      removed outlier: 3.873A  pdb=" N   GLY C 398 " --> pdb=" O   ALA C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 3.912A  pdb=" N   ALA C 409 " --> pdb=" O   SER C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 431
      removed outlier: 3.581A  pdb=" N   ALA C 417 " --> pdb=" O   PHE C 413 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA C 430 " --> pdb=" O   ARG C 426 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA C 431 " --> pdb=" O   GLU C 427 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 444
      removed outlier: 3.713A  pdb=" N   LEU C 437 " --> pdb=" O   TYR C 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 467
    Processing helix  chain 'C' and resid 478 through 487
      removed outlier: 4.393A  pdb=" N   TYR C 487 " --> pdb=" O   LEU C 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 506
    Processing helix  chain 'C' and resid 507 through 509
      No H-bonds generated for 'chain 'C' and resid 507 through 509'
    Processing helix  chain 'C' and resid 524 through 543
      removed outlier: 3.612A  pdb=" N   ASP C 528 " --> pdb=" O   ILE C 524 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93
      removed outlier: 6.614A  pdb=" N   ILE A  90 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ARG A 116 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA A  92 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ASN A 118 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA A 115 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   ASP A 156 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU A 117 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE A 153 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE A 284 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   LEU A 155 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY A 332 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS A 401 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   MET A 403 " --> pdb=" O   CYS A 369 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   SER A  89 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   LEU A 404 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE A  91 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 516
      removed outlier: 6.894A  pdb=" N   VAL A 493 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   LEU A 515 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ALA A 495 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 471 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   VAL A 496 " --> pdb=" O   ILE A 471 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL A 473 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ALA A 470 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE A 567 " --> pdb=" O   THR A 556 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 89 through 93
      removed outlier: 6.379A  pdb=" N   ALA C 115 " --> pdb=" O   ALA C 154 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ASP C 156 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU C 117 " --> pdb=" O   ASP C 156 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ILE C 153 " --> pdb=" O   ILE C 282 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   PHE C 284 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LEU C 155 " --> pdb=" O   PHE C 284 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY C 332 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   CYS C 401 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   MET C 403 " --> pdb=" O   CYS C 369 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   SER C  89 " --> pdb=" O   ILE C 402 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   LEU C 404 " --> pdb=" O   SER C  89 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ILE C  91 " --> pdb=" O   LEU C 404 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 512 through 516
      removed outlier: 6.909A  pdb=" N   VAL C 493 " --> pdb=" O   PHE C 513 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LEU C 515 " --> pdb=" O   VAL C 493 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ALA C 495 " --> pdb=" O   LEU C 515 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ILE C 471 " --> pdb=" O   ILE C 494 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   VAL C 496 " --> pdb=" O   ILE C 471 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL C 473 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ALA C 470 " --> pdb=" O   LEU C 551 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE C 567 " --> pdb=" O   THR C 556 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    870 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.07

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1090
        1.27 -     1.41: 1500
        1.41 -     1.55: 3891
        1.55 -     1.69: 3
        1.69 -     1.83: 58
  Bond restraints: 6542
  Sorted by residual:
  bond pdb=" C20 WV2 A 601 "
       pdb=" N3  WV2 A 601 "
    ideal  model  delta    sigma   weight residual
    1.451  1.134  0.317 2.00e-02 2.50e+03 2.51e+02
  bond pdb=" C20 WV2 A 602 "
       pdb=" N3  WV2 A 602 "
    ideal  model  delta    sigma   weight residual
    1.451  1.135  0.316 2.00e-02 2.50e+03 2.50e+02
  bond pdb=" C15 WV2 A 601 "
       pdb=" N3  WV2 A 601 "
    ideal  model  delta    sigma   weight residual
    1.450  1.141  0.309 2.00e-02 2.50e+03 2.39e+02
  bond pdb=" C15 WV2 A 602 "
       pdb=" N3  WV2 A 602 "
    ideal  model  delta    sigma   weight residual
    1.450  1.142  0.308 2.00e-02 2.50e+03 2.36e+02
  bond pdb=" C14 WV2 A 601 "
       pdb=" C15 WV2 A 601 "
    ideal  model  delta    sigma   weight residual
    1.521  1.370  0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 6537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.44: 8806
        3.44 -     6.89: 44
        6.89 -    10.33: 4
       10.33 -    13.78: 0
       13.78 -    17.22: 8
  Bond angle restraints: 8862
  Sorted by residual:
  angle pdb=" O   WV2 A 601 "
        pdb=" S   WV2 A 601 "
        pdb=" O2  WV2 A 601 "
      ideal   model   delta    sigma   weight residual
     118.67  101.45   17.22 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" O   WV2 A 602 "
        pdb=" S   WV2 A 602 "
        pdb=" O2  WV2 A 602 "
      ideal   model   delta    sigma   weight residual
     118.67  101.76   16.91 3.00e+00 1.11e-01 3.18e+01
  angle pdb=" C15 WV2 A 602 "
        pdb=" N3  WV2 A 602 "
        pdb=" C20 WV2 A 602 "
      ideal   model   delta    sigma   weight residual
     110.57  127.15  -16.58 3.00e+00 1.11e-01 3.05e+01
  angle pdb=" C15 WV2 A 601 "
        pdb=" N3  WV2 A 601 "
        pdb=" C20 WV2 A 601 "
      ideal   model   delta    sigma   weight residual
     110.57  127.09  -16.52 3.00e+00 1.11e-01 3.03e+01
  angle pdb=" C21 WV2 A 602 "
        pdb=" C20 WV2 A 602 "
        pdb=" N3  WV2 A 602 "
      ideal   model   delta    sigma   weight residual
     110.75  124.77  -14.02 3.00e+00 1.11e-01 2.18e+01
  ... (remaining 8857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.35: 3691
       30.35 -    60.70: 308
       60.70 -    91.05: 15
       91.05 -   121.40: 2
      121.40 -   151.75: 4
  Dihedral angle restraints: 4020
    sinusoidal: 1620
      harmonic: 2400
  Sorted by residual:
  dihedral pdb=" C15 WV2 A 601 "
           pdb=" C16 WV2 A 601 "
           pdb=" N3  WV2 A 601 "
           pdb=" C17 WV2 A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.11  -86.64  151.75     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C16 WV2 A 602 "
           pdb=" C17 WV2 A 602 "
           pdb=" C18 WV2 A 602 "
           pdb=" C19 WV2 A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     248.73  103.98  144.75     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" C16 WV2 A 601 "
           pdb=" C17 WV2 A 601 "
           pdb=" C18 WV2 A 601 "
           pdb=" C19 WV2 A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     248.73  105.07  143.66     1      3.00e+01 1.11e-03 1.93e+01
  ... (remaining 4017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 905
       0.069 -    0.139: 105
       0.139 -    0.208: 4
       0.208 -    0.277: 0
       0.277 -    0.346: 2
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" C17 WV2 A 601 "
            pdb=" C16 WV2 A 601 "
            pdb=" C18 WV2 A 601 "
            pdb=" C19 WV2 A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.39   -2.74   -0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" C17 WV2 A 602 "
            pdb=" C16 WV2 A 602 "
            pdb=" C18 WV2 A 602 "
            pdb=" C19 WV2 A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.39   -2.73   -0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" CA  ASN C 566 "
            pdb=" N   ASN C 566 "
            pdb=" C   ASN C 566 "
            pdb=" CB  ASN C 566 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.64e-01
  ... (remaining 1013 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 344 "   -0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO C 345 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 345 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 345 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 519 "   -0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO A 520 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 520 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 520 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 344 "   -0.030 5.00e-02 4.00e+02   4.64e-02 3.45e+00
        pdb=" N   PRO A 345 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 345 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 345 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1516
        2.80 -     3.33: 5451
        3.33 -     3.85: 10048
        3.85 -     4.38: 11268
        4.38 -     4.90: 20294
  Nonbonded interactions: 48577
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 100 "
            pdb=" OE1 GLU C 102 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O1  WV2 A 602 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O1  WV2 A 601 "
            pdb=" O   HOH A 702 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER A 144 "
            pdb=" OG  SER A 147 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   SER A 144 "
            pdb=" OG  SER A 144 "
     model   vdw
     2.393 3.040
  ... (remaining 48572 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 66 through 574)
  selection = chain 'C'
}

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:             1.710
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.300
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
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      :  0.010   0.317   6542  Z= 0.489
  Angle     :  0.777  17.221   8862  Z= 0.343
  Chirality :  0.047   0.346   1016
  Planarity :  0.005   0.056   1156
  Dihedral  : 20.428 151.752   2468
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 31.14 %
    Favored  : 68.86 %
  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:  0.58 (0.28), residues: 832
  helix:  0.97 (0.24), residues: 384
  sheet:  1.34 (0.41), residues: 164
  loop : -0.96 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 382 
 TYR   0.009   0.001   TYR A 126 
 PHE   0.012   0.001   PHE A 274 
 TRP   0.006   0.001   TRP A 558 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00985 /  0.49 ( 6542)
  covalent geometry    : angle       0.77740 /  0.34 ( 8862)
  hydrogen bonds       : bond        0.18697 / 11.89 (  297)
  hydrogen bonds       : angle       4.99668 /  3.53 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  266 GLU cc_start: 0.6856 (tp30) cc_final: 0.6465 (tp30)
REVERT: A  270 ARG cc_start: 0.5945 (mpp80) cc_final: 0.5483 (mtt180)
REVERT: A  273 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.6310 (ttp80)
REVERT: C  436 GLN cc_start: 0.8081 (tp40) cc_final: 0.7795 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.7569
  time to fit residues: 66.7157
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0470
   overall best weight:    0.7078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 306 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.182998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143713 restraints weight = 6886.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.23
r_work: 0.3309 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6542  Z= 0.100
  Angle     :  0.464   5.454   8862  Z= 0.237
  Chirality :  0.042   0.141   1016
  Planarity :  0.004   0.044   1156
  Dihedral  : 12.172 137.869    974
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 27.69 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.29), residues: 832
  helix:  2.06 (0.26), residues: 390
  sheet:  0.95 (0.40), residues: 168
  loop : -0.87 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 382 
 TYR   0.009   0.001   TYR A 517 
 PHE   0.012   0.001   PHE C 274 
 TRP   0.004   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 6542)
  covalent geometry    : angle       0.46402 /  0.24 ( 8862)
  hydrogen bonds       : bond        0.04306 /  2.89 (  297)
  hydrogen bonds       : angle       3.49788 /  2.43 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  139 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.5949 (mp0)
REVERT: A  273 ARG cc_start: 0.6967 (ttm-80) cc_final: 0.6431 (ttp-110)
REVERT: A  287 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7641 (t80)
  outliers start: 21
  outliers final: 5
  residues processed: 85
  average time/residue: 0.6836
  time to fit residues: 60.3962
Evaluate side-chains
  75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [48, 5, 34, 60, 73, 75, 1, 11, 4, 19, 78]
   chunk 48 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0470
   chunk 11 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0570
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.0200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 306 HIS
C 306 HIS
C 436 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.176689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136108 restraints weight = 6907.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.28
r_work: 0.3363 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6542  Z= 0.108
  Angle     :  0.453   4.575   8862  Z= 0.232
  Chirality :  0.042   0.144   1016
  Planarity :  0.004   0.042   1156
  Dihedral  : 12.272 137.050    974
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 26.35 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.30), residues: 832
  helix:  2.40 (0.26), residues: 390
  sheet:  0.73 (0.40), residues: 168
  loop : -0.76 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 382 
 TYR   0.008   0.001   TYR A 126 
 PHE   0.012   0.001   PHE C 274 
 TRP   0.004   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 6542)
  covalent geometry    : angle       0.45260 /  0.23 ( 8862)
  hydrogen bonds       : bond        0.04302 /  2.91 (  297)
  hydrogen bonds       : angle       3.34088 /  2.35 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  139 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.5982 (mp0)
REVERT: A  273 ARG cc_start: 0.6960 (ttm-80) cc_final: 0.6518 (ttp-110)
REVERT: A  287 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7588 (t80)
REVERT: A  464 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7191 (t80)
REVERT: C  102 GLU cc_start: 0.6882 (mp0) cc_final: 0.6512 (pm20)
REVERT: C  373 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7579 (mtt)
  outliers start: 18
  outliers final: 7
  residues processed: 84
  average time/residue: 0.6469
  time to fit residues: 56.6252
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [70, 50, 53, 45, 15, 0, 16, 44, 12, 11, 27]
   chunk 70 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0050
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0670
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 306 HIS
C 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.179147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.139107 restraints weight = 6913.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.27
r_work: 0.3243 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6542  Z= 0.106
  Angle     :  0.441   4.607   8862  Z= 0.226
  Chirality :  0.042   0.140   1016
  Planarity :  0.003   0.040   1156
  Dihedral  : 12.391 136.897    974
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 25.00 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.30), residues: 832
  helix:  2.59 (0.26), residues: 388
  sheet:  0.58 (0.40), residues: 168
  loop : -0.69 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 382 
 TYR   0.008   0.001   TYR A 126 
 PHE   0.013   0.001   PHE C 274 
 TRP   0.004   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 6542)
  covalent geometry    : angle       0.44139 /  0.23 ( 8862)
  hydrogen bonds       : bond        0.03976 /  2.69 (  297)
  hydrogen bonds       : angle       3.29626 /  2.32 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  139 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6048 (mp0)
REVERT: A  273 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.6437 (ttp-110)
REVERT: A  287 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7536 (t80)
REVERT: A  359 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (mtt-85)
REVERT: C  359 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7677 (mtt180)
REVERT: C  479 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7137 (ttm170)
  outliers start: 19
  outliers final: 7
  residues processed: 86
  average time/residue: 0.6709
  time to fit residues: 60.0986
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  359 ARG
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  359 ARG
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  479 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [30, 54, 22, 44, 32, 70, 73, 78, 65, 20, 31]
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 306 HIS
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.173859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.133433 restraints weight = 6927.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.28
r_work: 0.3297 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6542  Z= 0.158
  Angle     :  0.506   5.654   8862  Z= 0.260
  Chirality :  0.044   0.154   1016
  Planarity :  0.004   0.040   1156
  Dihedral  : 13.031 140.364    974
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.85 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.29), residues: 832
  helix:  2.37 (0.26), residues: 388
  sheet:  0.18 (0.39), residues: 168
  loop : -0.76 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 382 
 TYR   0.010   0.001   TYR C 126 
 PHE   0.015   0.002   PHE C 274 
 TRP   0.005   0.001   TRP C 558 
 HIS   0.004   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.16 ( 6542)
  covalent geometry    : angle       0.50592 /  0.26 ( 8862)
  hydrogen bonds       : bond        0.05288 /  3.60 (  297)
  hydrogen bonds       : angle       3.40493 /  2.41 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6296 (tp30) cc_final: 0.5235 (pp20)
REVERT: A  139 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6122 (mp0)
REVERT: A  266 GLU cc_start: 0.6912 (tp30) cc_final: 0.6347 (tp30)
REVERT: A  270 ARG cc_start: 0.6301 (mpp80) cc_final: 0.5837 (mpp80)
REVERT: A  273 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6600 (ttp-110)
REVERT: A  287 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7590 (t80)
REVERT: A  359 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7941 (mtt-85)
REVERT: C  102 GLU cc_start: 0.6926 (mp0) cc_final: 0.6549 (pt0)
REVERT: C  103 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6347 (mpt-90)
REVERT: C  373 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7726 (mtt)
REVERT: C  436 GLN cc_start: 0.8239 (tp40) cc_final: 0.7814 (tm-30)
REVERT: C  479 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7075 (ttm170)
  outliers start: 24
  outliers final: 10
  residues processed: 96
  average time/residue: 0.6705
  time to fit residues: 67.1033
Evaluate side-chains
  89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  359 ARG
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Chi-restraints excluded: chain C residue  479 ARG
Chi-restraints excluded: chain C residue  497 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [27, 74, 79, 29, 10, 22, 35, 9, 72, 14, 37]
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   overall best weight:    0.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 316 ASN
C 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.177657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.133902 restraints weight = 6875.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.48
r_work: 0.3319 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6542  Z= 0.103
  Angle     :  0.442   4.882   8862  Z= 0.227
  Chirality :  0.042   0.137   1016
  Planarity :  0.003   0.038   1156
  Dihedral  : 12.877 137.343    974
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 25.75 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.30), residues: 832
  helix:  2.57 (0.26), residues: 388
  sheet:  0.21 (0.39), residues: 168
  loop : -0.69 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 382 
 TYR   0.009   0.001   TYR A 126 
 PHE   0.013   0.001   PHE C 274 
 TRP   0.005   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.10 ( 6542)
  covalent geometry    : angle       0.44224 /  0.23 ( 8862)
  hydrogen bonds       : bond        0.03860 /  2.61 (  297)
  hydrogen bonds       : angle       3.28348 /  2.32 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6248 (tp30) cc_final: 0.5167 (pp20)
REVERT: A  139 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.5976 (mp0)
REVERT: A  270 ARG cc_start: 0.6217 (mpp80) cc_final: 0.5806 (mpp80)
REVERT: A  273 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6554 (ttp-110)
REVERT: A  287 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: A  359 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7924 (mtm-85)
REVERT: C  102 GLU cc_start: 0.6852 (mp0) cc_final: 0.6459 (pt0)
REVERT: C  103 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6184 (mpt-90)
REVERT: C  373 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7572 (mtt)
REVERT: C  436 GLN cc_start: 0.8164 (tp40) cc_final: 0.7799 (tm-30)
REVERT: C  479 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6988 (ttm170)
  outliers start: 17
  outliers final: 8
  residues processed: 86
  average time/residue: 0.6654
  time to fit residues: 59.6094
Evaluate side-chains
  84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  359 ARG
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Chi-restraints excluded: chain C residue  479 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [59, 64, 20, 49, 28, 13, 17, 51, 1, 48, 50]
   chunk 59 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.164682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.121832 restraints weight = 6957.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 2.41
r_work: 0.3259 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6542  Z= 0.231
  Angle     :  0.579   6.275   8862  Z= 0.298
  Chirality :  0.047   0.165   1016
  Planarity :  0.004   0.038   1156
  Dihedral  : 13.514 146.234    974
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.55 %
    Favored  : 71.86 %
  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:  0.96 (0.29), residues: 832
  helix:  2.09 (0.26), residues: 388
  sheet: -0.19 (0.38), residues: 168
  loop : -0.90 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 337 
 TYR   0.011   0.002   TYR A 126 
 PHE   0.015   0.002   PHE C 274 
 TRP   0.007   0.001   TRP C 558 
 HIS   0.005   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00592 /  0.23 ( 6542)
  covalent geometry    : angle       0.57853 /  0.30 ( 8862)
  hydrogen bonds       : bond        0.06401 /  4.38 (  297)
  hydrogen bonds       : angle       3.52444 /  2.50 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6221 (tp30) cc_final: 0.5128 (pp20)
REVERT: A  139 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6089 (mp0)
REVERT: A  273 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6537 (ttp-110)
REVERT: A  287 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7591 (t80)
REVERT: A  359 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7860 (mtt-85)
REVERT: C  102 GLU cc_start: 0.6851 (mp0) cc_final: 0.6537 (pt0)
REVERT: C  103 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6364 (mpt-90)
REVERT: C  373 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7733 (mtt)
REVERT: C  457 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6192 (mt)
REVERT: C  479 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7099 (ttm170)
REVERT: C  547 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6524 (mtt-85)
  outliers start: 24
  outliers final: 10
  residues processed: 98
  average time/residue: 0.7073
  time to fit residues: 72.0978
Evaluate side-chains
  97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  359 ARG
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  457 ILE
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Chi-restraints excluded: chain C residue  479 ARG
Chi-restraints excluded: chain C residue  497 THR
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [18, 72, 24, 44, 32, 40, 83, 45, 20, 54, 17]
   chunk 18 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 316 ASN
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.176908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.133126 restraints weight = 6862.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.48
r_work: 0.3274 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6542  Z= 0.096
  Angle     :  0.444   5.552   8862  Z= 0.229
  Chirality :  0.042   0.132   1016
  Planarity :  0.003   0.037   1156
  Dihedral  : 13.084 140.211    974
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 26.20 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.30), residues: 832
  helix:  2.48 (0.26), residues: 388
  sheet: -0.04 (0.39), residues: 168
  loop : -0.78 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 382 
 TYR   0.010   0.001   TYR A 126 
 PHE   0.013   0.001   PHE C 274 
 TRP   0.006   0.001   TRP C 525 
 HIS   0.003   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 6542)
  covalent geometry    : angle       0.44365 /  0.23 ( 8862)
  hydrogen bonds       : bond        0.03815 /  2.59 (  297)
  hydrogen bonds       : angle       3.34942 /  2.36 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6298 (tp30) cc_final: 0.5059 (pp20)
REVERT: A  139 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.5994 (mp0)
REVERT: A  273 ARG cc_start: 0.7038 (ttm-80) cc_final: 0.6539 (ttp-110)
REVERT: A  287 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7555 (t80)
REVERT: A  359 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7887 (mtm-85)
REVERT: C  102 GLU cc_start: 0.6851 (mp0) cc_final: 0.6475 (pt0)
REVERT: C  103 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6184 (mpt-90)
REVERT: C  373 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7559 (mtt)
REVERT: C  436 GLN cc_start: 0.8279 (tt0) cc_final: 0.7921 (tm-30)
REVERT: C  464 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.6986 (t80)
REVERT: C  479 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6944 (ttm170)
REVERT: C  547 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6474 (mtt-85)
  outliers start: 20
  outliers final: 8
  residues processed: 88
  average time/residue: 0.6593
  time to fit residues: 60.5557
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  359 ARG
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain C residue  103 ARG
Chi-restraints excluded: chain C residue  144 SER
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Chi-restraints excluded: chain C residue  479 ARG
Chi-restraints excluded: chain C residue  547 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [25, 56, 27, 35, 47, 29, 3, 81, 1, 21, 52]
   chunk 25 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0020
   chunk 47 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0970
   chunk 21 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0470
   overall best weight:    0.3484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 316 ASN
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.180113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.135508 restraints weight = 6927.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.59
r_work: 0.3342 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6542  Z= 0.075
  Angle     :  0.412   6.140   8862  Z= 0.210
  Chirality :  0.041   0.133   1016
  Planarity :  0.003   0.037   1156
  Dihedral  : 12.663 139.168    974
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 27.10 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.30), residues: 832
  helix:  2.70 (0.27), residues: 390
  sheet:  0.23 (0.40), residues: 168
  loop : -0.64 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 382 
 TYR   0.008   0.001   TYR A 126 
 PHE   0.012   0.001   PHE C 274 
 TRP   0.009   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00170 /  0.07 ( 6542)
  covalent geometry    : angle       0.41225 /  0.21 ( 8862)
  hydrogen bonds       : bond        0.02826 /  1.89 (  297)
  hydrogen bonds       : angle       3.20920 /  2.26 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6323 (tp30) cc_final: 0.5098 (pp20)
REVERT: A  139 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5925 (mp0)
REVERT: A  273 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6522 (ttp-110)
REVERT: A  287 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7584 (t80)
REVERT: A  464 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7023 (t80)
REVERT: C  102 GLU cc_start: 0.6864 (mp0) cc_final: 0.6494 (pt0)
REVERT: C  373 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7384 (mtt)
REVERT: C  464 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6991 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 79
  average time/residue: 0.6681
  time to fit residues: 55.1224
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  287 PHE
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Chi-restraints excluded: chain C residue  497 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [64, 77, 1, 13, 6, 48, 29, 60, 10, 0, 33]
   chunk 64 optimal weight:   10.0000
   chunk 77 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0370
   chunk 60 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0050
   overall best weight:    0.9272

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.178250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.133666 restraints weight = 6798.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.56
r_work: 0.3321 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6542  Z= 0.099
  Angle     :  0.435   6.044   8862  Z= 0.222
  Chirality :  0.042   0.135   1016
  Planarity :  0.003   0.045   1156
  Dihedral  : 12.764 138.624    974
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 27.69 %
    Favored  : 70.51 %
  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:  1.66 (0.30), residues: 832
  helix:  2.67 (0.26), residues: 390
  sheet:  0.22 (0.40), residues: 168
  loop : -0.65 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 382 
 TYR   0.009   0.001   TYR A 126 
 PHE   0.013   0.001   PHE C 274 
 TRP   0.007   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.10 ( 6542)
  covalent geometry    : angle       0.43490 /  0.22 ( 8862)
  hydrogen bonds       : bond        0.03655 /  2.48 (  297)
  hydrogen bonds       : angle       3.22017 /  2.27 (  870)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   81 GLU cc_start: 0.6304 (tp30) cc_final: 0.5067 (pp20)
REVERT: A  139 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5936 (mp0)
REVERT: A  273 ARG cc_start: 0.7021 (ttm-80) cc_final: 0.6512 (ttp-110)
REVERT: C  102 GLU cc_start: 0.6876 (mp0) cc_final: 0.6505 (pt0)
REVERT: C  304 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6645 (pm20)
REVERT: C  373 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7503 (mtt)
REVERT: C  436 GLN cc_start: 0.8291 (tt0) cc_final: 0.7948 (tm-30)
REVERT: C  464 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7009 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 80
  average time/residue: 0.6278
  time to fit residues: 52.4005
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 GLU
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  270 ARG
Chi-restraints excluded: chain C residue  304 GLU
Chi-restraints excluded: chain C residue  373 MET
Chi-restraints excluded: chain C residue  464 PHE
Chi-restraints excluded: chain C residue  473 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks: [28, 40, 12, 11, 68, 57, 42, 74, 39, 30, 13]
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 316 ASN
A 372 GLN
C 306 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.175249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.131517 restraints weight = 6884.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.48
r_work: 0.3284 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6542  Z= 0.155
  Angle     :  0.504   6.028   8862  Z= 0.258
  Chirality :  0.044   0.150   1016
  Planarity :  0.004   0.049   1156
  Dihedral  : 13.159 137.810    974
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 27.99 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.30), residues: 832
  helix:  2.45 (0.26), residues: 388
  sheet:  0.02 (0.39), residues: 168
  loop : -0.79 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 382 
 TYR   0.010   0.001   TYR A 126 
 PHE   0.014   0.002   PHE C 274 
 TRP   0.004   0.001   TRP C 525 
 HIS   0.004   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.15 ( 6542)
  covalent geometry    : angle       0.50350 /  0.26 ( 8862)
  hydrogen bonds       : bond        0.05019 /  3.43 (  297)
  hydrogen bonds       : angle       3.36766 /  2.38 (  870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2207.66 seconds
wall clock time: 38 minutes 18.96 seconds (2298.96 seconds total)