Starting phenix.real_space_refine
on Mon May 12 09:48:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dso_47148/05_2025/9dso_47148.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      34      5.16       5
     C    5768      2.51       5
     N    1514      2.21       5
     O    1658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8975
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5805
          Classifications: {'peptide': 726}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 51, 'TRANS': 674}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 3046
          Classifications: {'peptide': 373}
          Link IDs: {'PTRANS': 11, 'TRANS': 361}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 123
          Classifications: {'peptide': 16}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.10, per 1000 atoms: 0.57
  Number of scatterers: 8975
  At special positions: 0
  Unit cell: (100.772, 89.208, 142.898, 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      34     16.00
     Mg      1     11.99
     O    1658      8.00
     N    1514      7.00
     C    5768      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: 2.30
  Conformation dependent library (CDL) restraints added in 994.4 milliseconds
  

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 8 sheets defined
      47.8% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 14
    Processing helix  chain 'A' and resid 54 through 63
      Proline residue:  A  60  - end of helix
    Processing helix  chain 'A' and resid 72 through 92
      removed outlier: 3.508A  pdb=" N   MET A  76 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 138
      removed outlier: 3.968A  pdb=" N   GLN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 3.614A  pdb=" N   ASP A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 189
      removed outlier: 3.716A  pdb=" N   LYS A 189 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 186 through 189'
    Processing helix  chain 'A' and resid 203 through 217
    Processing helix  chain 'A' and resid 235 through 243
    Processing helix  chain 'A' and resid 254 through 262
      removed outlier: 3.519A  pdb=" N   GLN A 258 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LYS A 262 " --> pdb=" O   GLN A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
    Processing helix  chain 'A' and resid 294 through 305
      removed outlier: 3.834A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 331
    Processing helix  chain 'A' and resid 347 through 359
      removed outlier: 3.649A  pdb=" N   VAL A 357 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 373 through 387
      removed outlier: 3.693A  pdb=" N   ARG A 387 " --> pdb=" O   HIS A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 410
    Processing helix  chain 'A' and resid 593 through 598
      removed outlier: 3.526A  pdb=" N   VAL A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 614
      removed outlier: 3.936A  pdb=" N   ARG A 607 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 618
      No H-bonds generated for 'chain 'A' and resid 616 through 618'
    Processing helix  chain 'A' and resid 619 through 644
    Processing helix  chain 'A' and resid 660 through 664
    Processing helix  chain 'A' and resid 681 through 688
    Processing helix  chain 'A' and resid 694 through 698
      removed outlier: 3.519A  pdb=" N   ALA A 697 " --> pdb=" O   SER A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 708
      removed outlier: 3.856A  pdb=" N   SER A 707 " --> pdb=" O   ARG A 703 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 703 through 708'
    Processing helix  chain 'A' and resid 713 through 717
    Processing helix  chain 'A' and resid 742 through 754
    Processing helix  chain 'A' and resid 755 through 757
      No H-bonds generated for 'chain 'A' and resid 755 through 757'
    Processing helix  chain 'A' and resid 758 through 765
    Processing helix  chain 'A' and resid 780 through 789
    Processing helix  chain 'A' and resid 791 through 796
      removed outlier: 3.510A  pdb=" N   ASN A 795 " --> pdb=" O   GLU A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 882
    Processing helix  chain 'A' and resid 894 through 901
      removed outlier: 3.923A  pdb=" N   LYS A 900 " --> pdb=" O   GLY A 896 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN A 901 " --> pdb=" O   ASN A 897 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 935
    Processing helix  chain 'B' and resid 49 through 55
      removed outlier: 3.681A  pdb=" N   ASP B  54 " --> pdb=" O   ALA B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 73
    Processing helix  chain 'B' and resid 79 through 94
    Processing helix  chain 'B' and resid 105 through 114
    Processing helix  chain 'B' and resid 159 through 175
      removed outlier: 3.865A  pdb=" N   GLY B 168 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR B 169 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 185 through 192
      removed outlier: 3.584A  pdb=" N   ILE B 189 " --> pdb=" O   PRO B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 195
      No H-bonds generated for 'chain 'B' and resid 193 through 195'
    Processing helix  chain 'B' and resid 235 through 237
      No H-bonds generated for 'chain 'B' and resid 235 through 237'
    Processing helix  chain 'B' and resid 250 through 272
      removed outlier: 4.098A  pdb=" N   VAL B 271 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 306
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 311 through 331
    Processing helix  chain 'B' and resid 364 through 370
    Processing helix  chain 'B' and resid 376 through 386
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20
      removed outlier: 6.521A  pdb=" N   HIS A 227 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   LEU A 251 " --> pdb=" O   HIS A 227 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ILE A 229 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 8.577A  pdb=" N   GLU A 253 " --> pdb=" O   ILE A 229 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   CYS A 228 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ASN A  49 " --> pdb=" O   CYS A 228 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   TYR A 230 " --> pdb=" O   ASN A  49 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   TYR A  51 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   ASP A  48 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.574A  pdb=" N   VAL A  29 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591
    Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8
      removed outlier: 3.658A  pdb=" N   ARG B 342 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   PHE B 104 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU B 139 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   TYR B 203 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY B  25 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ARG B 208 " --> pdb=" O   GLU B  23 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   GLU B  23 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   GLY B 210 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8
      removed outlier: 3.658A  pdb=" N   ARG B 342 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   PHE B 104 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU B 139 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   TYR B 203 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY B  25 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   ARG B 208 " --> pdb=" O   GLU B  23 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   GLU B  23 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   GLY B 210 " --> pdb=" O   PRO B  21 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   LEU B  18 " --> pdb=" O   GLU C 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 177
      removed outlier: 3.752A  pdb=" N   CYS B 224 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   TYR B 239 " --> pdb=" O   ARG B 275 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   ILE B 277 " --> pdb=" O   TYR B 239 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   GLU B 241 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   GLY B 279 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LYS B 243 " --> pdb=" O   GLY B 279 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   LYS B 281 " --> pdb=" O   LYS B 243 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   THR B 245 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 68
      removed outlier: 6.643A  pdb=" N   LYS B  67 " --> pdb=" O   HIS B 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    456 hydrogen bonds defined for protein.
    1275 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: 2.84

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2914
        1.34 -     1.45: 1306
        1.45 -     1.57: 4925
        1.57 -     1.69: 0
        1.69 -     1.80: 52
  Bond restraints: 9197
  Sorted by residual:
  bond pdb=" N   TYR A 789 "
       pdb=" CA  TYR A 789 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 7.03e+00
  bond pdb=" N   THR B 176 "
       pdb=" CA  THR B 176 "
    ideal  model  delta    sigma   weight residual
    1.454  1.478 -0.024 1.29e-02 6.01e+03 3.49e+00
  bond pdb=" C   THR B 176 "
       pdb=" O   THR B 176 "
    ideal  model  delta    sigma   weight residual
    1.234  1.250 -0.016 1.26e-02 6.30e+03 1.65e+00
  bond pdb=" CA  THR B 176 "
       pdb=" C   THR B 176 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.015 1.23e-02 6.61e+03 1.54e+00
  bond pdb=" C   TYR A 789 "
       pdb=" O   TYR A 789 "
    ideal  model  delta    sigma   weight residual
    1.233  1.250 -0.017 1.49e-02 4.50e+03 1.32e+00
  ... (remaining 9192 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 11917
        1.14 -     2.29: 424
        2.29 -     3.43: 84
        3.43 -     4.57: 28
        4.57 -     5.71: 8
  Bond angle restraints: 12461
  Sorted by residual:
  angle pdb=" N   ILE A 911 "
        pdb=" CA  ILE A 911 "
        pdb=" C   ILE A 911 "
      ideal   model   delta    sigma   weight residual
     113.53  109.33    4.20 9.80e-01 1.04e+00 1.83e+01
  angle pdb=" CA  THR B 176 "
        pdb=" CB  THR B 176 "
        pdb=" OG1 THR B 176 "
      ideal   model   delta    sigma   weight residual
     109.60  105.00    4.60 1.50e+00 4.44e-01 9.41e+00
  angle pdb=" C   GLU A 345 "
        pdb=" N   ASN A 346 "
        pdb=" CA  ASN A 346 "
      ideal   model   delta    sigma   weight residual
     121.54  127.17   -5.63 1.91e+00 2.74e-01 8.70e+00
  angle pdb=" N   HIS B 373 "
        pdb=" CA  HIS B 373 "
        pdb=" C   HIS B 373 "
      ideal   model   delta    sigma   weight residual
     112.68  108.92    3.76 1.33e+00 5.65e-01 8.00e+00
  angle pdb=" C   GLN A 192 "
        pdb=" CA  GLN A 192 "
        pdb=" CB  GLN A 192 "
      ideal   model   delta    sigma   weight residual
     110.34  114.10   -3.76 1.40e+00 5.10e-01 7.23e+00
  ... (remaining 12456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 4976
       16.68 -    33.37: 442
       33.37 -    50.05: 84
       50.05 -    66.74: 15
       66.74 -    83.42: 5
  Dihedral angle restraints: 5522
    sinusoidal: 2258
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" CA  GLN A 803 "
           pdb=" C   GLN A 803 "
           pdb=" N   HIS A 804 "
           pdb=" CA  HIS A 804 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.45  -22.55     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  GLN A 192 "
           pdb=" C   GLN A 192 "
           pdb=" N   VAL A 193 "
           pdb=" CA  VAL A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.57  -21.43     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  SER A 347 "
           pdb=" C   SER A 347 "
           pdb=" N   ILE A 348 "
           pdb=" CA  ILE A 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 5519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 855
       0.035 -    0.070: 355
       0.070 -    0.106: 100
       0.106 -    0.141: 32
       0.141 -    0.176: 3
  Chirality restraints: 1345
  Sorted by residual:
  chirality pdb=" CB  ILE B 374 "
            pdb=" CA  ILE B 374 "
            pdb=" CG1 ILE B 374 "
            pdb=" CG2 ILE B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.76e-01
  chirality pdb=" CA  TYR A 754 "
            pdb=" N   TYR A 754 "
            pdb=" C   TYR A 754 "
            pdb=" CB  TYR A 754 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" CA  ILE A 843 "
            pdb=" N   ILE A 843 "
            pdb=" C   ILE A 843 "
            pdb=" CB  ILE A 843 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1342 not shown)

  Planarity restraints: 1617
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 616 "    0.027 5.00e-02 4.00e+02   4.14e-02 2.75e+00
        pdb=" N   PRO A 617 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 617 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 617 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 754 "    0.014 2.00e-02 2.50e+03   1.11e-02 2.48e+00
        pdb=" CG  TYR A 754 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 754 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 754 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 754 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 754 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 754 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 754 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 192 "    0.007 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" CD  GLN A 192 "   -0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 192 "    0.010 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 192 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1614 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 971
        2.75 -     3.29: 8615
        3.29 -     3.82: 14994
        3.82 -     4.36: 18342
        4.36 -     4.90: 31459
  Nonbonded interactions: 74381
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 922 "
            pdb=" OE2 GLU B 297 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH1 ARG A 922 "
            pdb=" O   GLU B 292 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   ASN A 346 "
            pdb=" OG  SER A 347 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   VAL B   9 "
            pdb=" NH2 ARG B  12 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OE1 GLU A 378 "
            pdb=" OG  SER A 668 "
     model   vdw
     2.304 3.040
  ... (remaining 74376 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:             0.880
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.220
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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      :  0.004   0.039   9197  Z= 0.176
  Angle     :  0.543   5.714  12461  Z= 0.292
  Chirality :  0.043   0.176   1345
  Planarity :  0.004   0.041   1617
  Dihedral  : 13.115  83.422   3412
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1099
  helix:  1.21 (0.25), residues: 431
  sheet:  0.77 (0.43), residues: 132
  loop :  0.99 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 355 
 HIS   0.005   0.001   HIS A 227 
 PHE   0.016   0.002   PHE B 257 
 TYR   0.026   0.002   TYR A 754 
 ARG   0.004   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15082 (  415)
  hydrogen bonds       : angle       6.35755 ( 1275)
  covalent geometry    : bond        0.00422 ( 9197)
  covalent geometry    : angle       0.54332 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.085 
Fit side-chains
REVERT: A  178 THR cc_start: 0.8738 (m) cc_final: 0.8501 (m)
REVERT: A  640 MET cc_start: 0.8253 (tpp) cc_final: 0.8012 (tpt)
REVERT: A  673 LYS cc_start: 0.7537 (mmtp) cc_final: 0.7325 (tppt)
REVERT: A  786 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7526 (ttpp)
REVERT: B   34 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7159 (mt-10)
REVERT: B   95 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7857 (ttpp)
REVERT: B  351 ASN cc_start: 0.7789 (t0) cc_final: 0.7507 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 1.3918
  time to fit residues: 215.2726
Evaluate side-chains
  104 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
B 250 ASN
B 267 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.156159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.117560 restraints weight = 9454.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.64
r_work: 0.3142 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9197  Z= 0.123
  Angle     :  0.498   6.876  12461  Z= 0.259
  Chirality :  0.043   0.145   1345
  Planarity :  0.004   0.047   1617
  Dihedral  :  3.987  21.545   1211
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  7.95 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.25), residues: 1099
  helix:  1.63 (0.25), residues: 431
  sheet:  0.61 (0.41), residues: 145
  loop :  1.04 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.012   0.001   PHE B 257 
 TYR   0.011   0.001   TYR A 921 
 ARG   0.003   0.000   ARG A 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04535 (  415)
  hydrogen bonds       : angle       4.65732 ( 1275)
  covalent geometry    : bond        0.00282 ( 9197)
  covalent geometry    : angle       0.49779 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A    8 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7190 (mtm110)
REVERT: A  395 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.6175 (ttm170)
REVERT: A  606 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6294 (tm-30)
REVERT: B    3 VAL cc_start: 0.7068 (p) cc_final: 0.6678 (m)
REVERT: B   10 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7287 (mttt)
REVERT: B   34 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7276 (mt-10)
REVERT: B  351 ASN cc_start: 0.7871 (t0) cc_final: 0.7483 (t0)
  outliers start: 16
  outliers final: 5
  residues processed: 114
  average time/residue: 1.4024
  time to fit residues: 170.1674
Evaluate side-chains
  101 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  849 ARG
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 38 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0040
   chunk 25 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 93 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B 250 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.157241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.119315 restraints weight = 9561.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.64
r_work: 0.3074 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9197  Z= 0.100
  Angle     :  0.454   5.985  12461  Z= 0.237
  Chirality :  0.041   0.140   1345
  Planarity :  0.004   0.047   1617
  Dihedral  :  3.822  20.226   1211
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.74 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.25), residues: 1099
  helix:  1.84 (0.25), residues: 438
  sheet:  0.73 (0.42), residues: 141
  loop :  1.14 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.009   0.001   PHE B 257 
 TYR   0.011   0.001   TYR A 921 
 ARG   0.002   0.000   ARG A 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  415)
  hydrogen bonds       : angle       4.39093 ( 1275)
  covalent geometry    : bond        0.00222 ( 9197)
  covalent geometry    : angle       0.45437 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A  119 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6962 (mmm160)
REVERT: A  395 ARG cc_start: 0.6591 (ttm-80) cc_final: 0.6107 (ttm170)
REVERT: A  606 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6250 (tm-30)
REVERT: B   10 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7125 (mttt)
REVERT: B   34 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7154 (mt-10)
REVERT: B  351 ASN cc_start: 0.7881 (t0) cc_final: 0.7407 (t0)
REVERT: B  372 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7577 (mm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 108
  average time/residue: 1.3711
  time to fit residues: 157.5576
Evaluate side-chains
  97 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ARG
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0030
   chunk 102 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 68 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0670
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.7130

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B  64 GLN
B 134 GLN
B 250 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.157370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.119840 restraints weight = 9528.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.65
r_work: 0.3065 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9197  Z= 0.106
  Angle     :  0.454   6.082  12461  Z= 0.236
  Chirality :  0.041   0.138   1345
  Planarity :  0.004   0.047   1617
  Dihedral  :  3.789  20.075   1211
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.29 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1099
  helix:  1.98 (0.25), residues: 438
  sheet:  0.69 (0.42), residues: 141
  loop :  1.18 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.009   0.001   PHE B 257 
 TYR   0.012   0.001   TYR A 641 
 ARG   0.002   0.000   ARG A 607 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  415)
  hydrogen bonds       : angle       4.27697 ( 1275)
  covalent geometry    : bond        0.00243 ( 9197)
  covalent geometry    : angle       0.45395 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  119 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.7004 (mmm160)
REVERT: A  395 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.6193 (ttm170)
REVERT: A  606 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6134 (tm-30)
REVERT: B   34 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7138 (mt-10)
REVERT: B  351 ASN cc_start: 0.7826 (t0) cc_final: 0.7386 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 103
  average time/residue: 1.4319
  time to fit residues: 156.6628
Evaluate side-chains
  104 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ARG
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  880 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 109 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 65 optimal weight:    0.1980
   chunk 58 optimal weight:    0.6980
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B 250 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.154747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117228 restraints weight = 9543.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.65
r_work: 0.3036 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9197  Z= 0.150
  Angle     :  0.492   6.570  12461  Z= 0.254
  Chirality :  0.043   0.142   1345
  Planarity :  0.004   0.049   1617
  Dihedral  :  3.908  21.272   1211
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.81 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.25), residues: 1099
  helix:  1.92 (0.25), residues: 432
  sheet:  0.62 (0.41), residues: 141
  loop :  1.13 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 355 
 HIS   0.005   0.001   HIS A 337 
 PHE   0.012   0.001   PHE B  66 
 TYR   0.014   0.002   TYR A 641 
 ARG   0.005   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  415)
  hydrogen bonds       : angle       4.33652 ( 1275)
  covalent geometry    : bond        0.00368 ( 9197)
  covalent geometry    : angle       0.49206 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 1.291 
Fit side-chains
REVERT: A  119 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.7002 (mmm160)
REVERT: A  366 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7574 (mtt)
REVERT: A  395 ARG cc_start: 0.6616 (ttm-80) cc_final: 0.6139 (ttm170)
REVERT: A  606 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6152 (tm-30)
REVERT: A  673 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7136 (ptmm)
REVERT: B    3 VAL cc_start: 0.6877 (p) cc_final: 0.6533 (m)
REVERT: B   34 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7126 (mt-10)
REVERT: B  351 ASN cc_start: 0.7846 (t0) cc_final: 0.7402 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 110
  average time/residue: 1.3406
  time to fit residues: 157.3515
Evaluate side-chains
  114 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ARG
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain A residue  880 ILE
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 68 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B  64 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.153670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.116264 restraints weight = 9587.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.64
r_work: 0.3023 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9197  Z= 0.152
  Angle     :  0.504   7.425  12461  Z= 0.259
  Chirality :  0.043   0.144   1345
  Planarity :  0.004   0.049   1617
  Dihedral  :  3.993  22.137   1211
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.22 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.25), residues: 1099
  helix:  1.78 (0.25), residues: 438
  sheet:  0.66 (0.42), residues: 140
  loop :  1.08 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.014   0.001   PHE B  66 
 TYR   0.013   0.002   TYR A 641 
 ARG   0.006   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  415)
  hydrogen bonds       : angle       4.37542 ( 1275)
  covalent geometry    : bond        0.00374 ( 9197)
  covalent geometry    : angle       0.50387 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  395 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.6174 (ttm170)
REVERT: A  606 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6151 (tm-30)
REVERT: A  673 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7170 (pptt)
REVERT: B    3 VAL cc_start: 0.7003 (p) cc_final: 0.6635 (m)
REVERT: B   34 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7371 (mt-10)
REVERT: B  303 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7359 (mtpm)
REVERT: B  351 ASN cc_start: 0.7807 (t0) cc_final: 0.7355 (t0)
REVERT: B  372 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7731 (mt-10)
  outliers start: 24
  outliers final: 12
  residues processed: 109
  average time/residue: 1.2981
  time to fit residues: 151.1645
Evaluate side-chains
  110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  800 VAL
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  372 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B 250 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.155756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.118158 restraints weight = 9614.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.70
r_work: 0.3122 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9197  Z= 0.111
  Angle     :  0.469   7.650  12461  Z= 0.242
  Chirality :  0.041   0.140   1345
  Planarity :  0.004   0.048   1617
  Dihedral  :  3.861  21.224   1211
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.84 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.25), residues: 1099
  helix:  1.85 (0.25), residues: 441
  sheet:  0.72 (0.42), residues: 140
  loop :  1.12 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.010   0.001   PHE A   7 
 TYR   0.011   0.001   TYR A 921 
 ARG   0.011   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 (  415)
  hydrogen bonds       : angle       4.27211 ( 1275)
  covalent geometry    : bond        0.00258 ( 9197)
  covalent geometry    : angle       0.46900 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  395 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.6213 (ttm170)
REVERT: A  606 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6266 (tm-30)
REVERT: A  673 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7254 (pptt)
REVERT: B    3 VAL cc_start: 0.7098 (p) cc_final: 0.6739 (m)
REVERT: B   34 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7390 (mt-10)
REVERT: B  172 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (mt-10)
REVERT: B  254 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7487 (p)
REVERT: B  303 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7529 (ttpp)
REVERT: B  351 ASN cc_start: 0.7856 (t0) cc_final: 0.7440 (t0)
REVERT: B  372 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7652 (mt-10)
  outliers start: 23
  outliers final: 10
  residues processed: 114
  average time/residue: 1.3489
  time to fit residues: 163.6908
Evaluate side-chains
  111 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  372 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
A 373 ASN
B  64 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.155926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119041 restraints weight = 9641.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.62
r_work: 0.3053 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9197  Z= 0.113
  Angle     :  0.474   8.257  12461  Z= 0.244
  Chirality :  0.042   0.140   1345
  Planarity :  0.004   0.048   1617
  Dihedral  :  3.807  20.725   1211
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.46 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1099
  helix:  1.96 (0.25), residues: 439
  sheet:  0.74 (0.42), residues: 140
  loop :  1.18 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 355 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.010   0.001   PHE B 257 
 TYR   0.011   0.001   TYR A 921 
 ARG   0.011   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  415)
  hydrogen bonds       : angle       4.23849 ( 1275)
  covalent geometry    : bond        0.00267 ( 9197)
  covalent geometry    : angle       0.47406 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 1.052 
Fit side-chains
REVERT: A  395 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6076 (ttm170)
REVERT: A  606 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6190 (tm-30)
REVERT: A  673 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7338 (pptt)
REVERT: B    3 VAL cc_start: 0.7029 (p) cc_final: 0.6667 (m)
REVERT: B   34 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: B  172 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7483 (mt-10)
REVERT: B  254 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7437 (p)
REVERT: B  303 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7438 (ttpp)
REVERT: B  351 ASN cc_start: 0.7786 (t0) cc_final: 0.7351 (t0)
REVERT: B  372 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7624 (mt-10)
  outliers start: 19
  outliers final: 12
  residues processed: 108
  average time/residue: 1.3224
  time to fit residues: 152.3767
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  849 ARG
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  372 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.2980
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.157752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.120836 restraints weight = 9581.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.65
r_work: 0.3078 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9197  Z= 0.093
  Angle     :  0.452   8.254  12461  Z= 0.232
  Chirality :  0.041   0.136   1345
  Planarity :  0.004   0.055   1617
  Dihedral  :  3.681  19.507   1211
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.57 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.25), residues: 1099
  helix:  2.12 (0.25), residues: 435
  sheet:  0.80 (0.43), residues: 140
  loop :  1.22 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 291 
 HIS   0.005   0.001   HIS A 337 
 PHE   0.010   0.001   PHE B 257 
 TYR   0.010   0.001   TYR A 921 
 ARG   0.014   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (  415)
  hydrogen bonds       : angle       4.12235 ( 1275)
  covalent geometry    : bond        0.00211 ( 9197)
  covalent geometry    : angle       0.45196 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  373 ASN cc_start: 0.8018 (t0) cc_final: 0.7664 (t0)
REVERT: A  395 ARG cc_start: 0.6626 (ttm-80) cc_final: 0.6064 (ttm170)
REVERT: A  606 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6218 (tm-30)
REVERT: A  673 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7209 (pptt)
REVERT: B    3 VAL cc_start: 0.6888 (p) cc_final: 0.6503 (m)
REVERT: B   34 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7208 (mt-10)
REVERT: B  202 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6264 (mm-30)
REVERT: B  303 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7372 (ttpp)
REVERT: B  372 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7487 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 109
  average time/residue: 1.3487
  time to fit residues: 156.4102
Evaluate side-chains
  108 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  849 ARG
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0870
   chunk 90 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
B  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.155615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.118810 restraints weight = 9658.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.62
r_work: 0.3055 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9197  Z= 0.119
  Angle     :  0.477   8.317  12461  Z= 0.244
  Chirality :  0.042   0.140   1345
  Planarity :  0.004   0.057   1617
  Dihedral  :  3.757  20.321   1211
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.98 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.25), residues: 1099
  helix:  2.06 (0.25), residues: 435
  sheet:  0.75 (0.42), residues: 140
  loop :  1.20 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 355 
 HIS   0.005   0.001   HIS A 337 
 PHE   0.010   0.001   PHE B  66 
 TYR   0.011   0.001   TYR A 641 
 ARG   0.014   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  415)
  hydrogen bonds       : angle       4.19180 ( 1275)
  covalent geometry    : bond        0.00285 ( 9197)
  covalent geometry    : angle       0.47687 (12461)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  373 ASN cc_start: 0.8038 (t0) cc_final: 0.7703 (t0)
REVERT: A  395 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.6101 (ttm170)
REVERT: A  606 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6175 (tm-30)
REVERT: A  673 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7286 (pptt)
REVERT: B    3 VAL cc_start: 0.6902 (p) cc_final: 0.6522 (m)
REVERT: B   34 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7229 (mt-10)
REVERT: B  202 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6309 (mm-30)
REVERT: B  303 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7420 (ttpp)
REVERT: B  372 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7608 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 1.3410
  time to fit residues: 148.6479
Evaluate side-chains
  105 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  673 LYS
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  701 ILE
Chi-restraints excluded: chain A residue  703 ARG
Chi-restraints excluded: chain A residue  776 ASN
Chi-restraints excluded: chain A residue  849 ARG
Chi-restraints excluded: chain A residue  868 SER
Chi-restraints excluded: chain B residue   14 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  303 LYS
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  372 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0370
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS
B 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.156946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.119889 restraints weight = 9572.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.63
r_work: 0.3065 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9197  Z= 0.103
  Angle     :  0.461   8.352  12461  Z= 0.237
  Chirality :  0.041   0.139   1345
  Planarity :  0.004   0.058   1617
  Dihedral  :  3.703  19.991   1211
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.88 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.25), residues: 1099
  helix:  2.12 (0.25), residues: 435
  sheet:  0.83 (0.43), residues: 137
  loop :  1.21 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 355 
 HIS   0.005   0.001   HIS A 337 
 PHE   0.010   0.001   PHE B 257 
 TYR   0.010   0.001   TYR A 921 
 ARG   0.014   0.000   ARG A   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  415)
  hydrogen bonds       : angle       4.14887 ( 1275)
  covalent geometry    : bond        0.00239 ( 9197)
  covalent geometry    : angle       0.46130 (12461)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7047.91 seconds
wall clock time: 122 minutes 2.90 seconds (7322.90 seconds total)