Starting phenix.real_space_refine
on Tue Mar 11 22:12:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x9s_38183/03_2025/8x9s_38183.cif"
  }
  resolution = 3.49
  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=   0.001 sd=   0.014
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      42      5.16       5
     C    4329      2.51       5
     N    1146      2.21       5
     O    1257      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6774
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2515
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 72
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 69
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 417
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "R"
      Number of atoms: 2039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2039
          Classifications: {'peptide': 268}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 261}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1782
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 8, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 73
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'DHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.73, per 1000 atoms: 0.70
  Number of scatterers: 6774
  At special positions: 0
  Unit cell: (76.36, 103.04, 124.2, 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      42     16.00
     O    1257      8.00
     N    1146      7.00
     C    4329      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 632 " - pdb=" SG  CYS R 704 " distance=2.02

  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1684

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      43.3% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.901A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'B' and resid 172 through 174
      No H-bonds generated for 'chain 'B' and resid 172 through 174'
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.168A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.556A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 566 through 591
    Processing helix  chain 'R' and resid 599 through 624
      removed outlier: 4.023A  pdb=" N   HIS R 603 " --> pdb=" O   ASN R 599 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG R 624 " --> pdb=" O   LEU R 620 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 629 through 662
      removed outlier: 3.562A  pdb=" N   GLN R 633 " --> pdb=" O   THR R 629 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 671 through 680
    Processing helix  chain 'R' and resid 681 through 694
      removed outlier: 4.048A  pdb=" N   PHE R 693 " --> pdb=" O   ILE R 689 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 713 through 743
      removed outlier: 3.747A  pdb=" N   ALA R 718 " --> pdb=" O   TRP R 714 " (cutoff:3.500A)
      Proline residue:  R 719  - end of helix
    Processing helix  chain 'R' and resid 754 through 770
      removed outlier: 4.026A  pdb=" N   THR R 758 " --> pdb=" O   ALA R 754 " (cutoff:3.500A)
      Proline residue:  R 767  - end of helix
      removed outlier: 3.707A  pdb=" N   GLY R 770 " --> pdb=" O   LEU R 766 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 774 through 781
      removed outlier: 3.865A  pdb=" N   LEU R 778 " --> pdb=" O   VAL R 774 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 787 through 795
      removed outlier: 3.786A  pdb=" N   ASN R 795 " --> pdb=" O   PHE R 791 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 797 through 807
    Processing helix  chain 'R' and resid 810 through 827
      removed outlier: 3.677A  pdb=" N   ARG R 814 " --> pdb=" O   ASN R 810 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA R 815 " --> pdb=" O   SER R 811 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR R 827 " --> pdb=" O   VAL R 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.676A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 59
      removed outlier: 4.147A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.592A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.738A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.308A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.073A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.697A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50
      removed outlier: 8.003A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.760A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.479A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.058A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.945A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 191
      removed outlier: 3.508A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232
      removed outlier: 4.487A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.612A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.849A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 221 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 210
      removed outlier: 3.849A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A 221 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.945A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    906 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: 1.82

  Time building geometry restraints manager: 2.22 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: 2195
        1.34 -     1.46: 1353
        1.46 -     1.58: 3310
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6917
  Sorted by residual:
  bond pdb=" CB  PRO R 767 "
       pdb=" CG  PRO R 767 "
    ideal  model  delta    sigma   weight residual
    1.492  1.642 -0.150 5.00e-02 4.00e+02 8.95e+00
  bond pdb=" CA  LEU R 794 "
       pdb=" C   LEU R 794 "
    ideal  model  delta    sigma   weight residual
    1.522  1.506  0.016 9.30e-03 1.16e+04 3.02e+00
  bond pdb=" CA  ALA R 565 "
       pdb=" C   ALA R 565 "
    ideal  model  delta    sigma   weight residual
    1.526  1.505  0.021 1.39e-02 5.18e+03 2.24e+00
  bond pdb=" CA  VAL R 564 "
       pdb=" C   VAL R 564 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.27e-02 6.20e+03 1.88e+00
  bond pdb=" C10 DHT R 901 "
       pdb=" C9  DHT R 901 "
    ideal  model  delta    sigma   weight residual
    1.551  1.524  0.027 2.00e-02 2.50e+03 1.87e+00
  ... (remaining 6912 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 9326
        2.39 -     4.79: 89
        4.79 -     7.18: 9
        7.18 -     9.57: 0
        9.57 -    11.96: 2
  Bond angle restraints: 9426
  Sorted by residual:
  angle pdb=" CA  PRO R 767 "
        pdb=" N   PRO R 767 "
        pdb=" CD  PRO R 767 "
      ideal   model   delta    sigma   weight residual
     112.00  100.04   11.96 1.40e+00 5.10e-01 7.30e+01
  angle pdb=" N   LYS A 305 "
        pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
      ideal   model   delta    sigma   weight residual
     114.62  109.91    4.71 1.14e+00 7.69e-01 1.70e+01
  angle pdb=" CB  MET A 386 "
        pdb=" CG  MET A 386 "
        pdb=" SD  MET A 386 "
      ideal   model   delta    sigma   weight residual
     112.70  122.70  -10.00 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   PRO R 767 "
        pdb=" CD  PRO R 767 "
        pdb=" CG  PRO R 767 "
      ideal   model   delta    sigma   weight residual
     103.20   98.59    4.61 1.50e+00 4.44e-01 9.46e+00
  angle pdb=" CA  LYS A 305 "
        pdb=" C   LYS A 305 "
        pdb=" N   SER A 306 "
      ideal   model   delta    sigma   weight residual
     119.71  116.33    3.38 1.17e+00 7.31e-01 8.33e+00
  ... (remaining 9421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.51: 3538
       19.51 -    39.01: 419
       39.01 -    58.52: 118
       58.52 -    78.03: 9
       78.03 -    97.53: 12
  Dihedral angle restraints: 4096
    sinusoidal: 1500
      harmonic: 2596
  Sorted by residual:
  dihedral pdb=" CB  CYS R 632 "
           pdb=" SG  CYS R 632 "
           pdb=" SG  CYS R 704 "
           pdb=" CB  CYS R 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.26  -45.74     1      1.00e+01 1.00e-02 2.90e+01
  dihedral pdb=" CA  ILE B  81 "
           pdb=" C   ILE B  81 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.09  -18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  PRO R 767 "
           pdb=" C   PRO R 767 "
           pdb=" N   ILE R 768 "
           pdb=" CA  ILE R 768 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.56   17.44     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 4093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 943
       0.055 -    0.109: 147
       0.109 -    0.164: 17
       0.164 -    0.218: 2
       0.218 -    0.273: 1
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" C10 DHT R 901 "
            pdb=" C1  DHT R 901 "
            pdb=" C5  DHT R 901 "
            pdb=" C9  DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.97   -2.70   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C13 DHT R 901 "
            pdb=" C12 DHT R 901 "
            pdb=" C14 DHT R 901 "
            pdb=" C17 DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.87   -2.67   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C17 DHT R 901 "
            pdb=" C13 DHT R 901 "
            pdb=" C16 DHT R 901 "
            pdb=" O17 DHT R 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.63   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  DHT R 901 "    0.030 2.00e-02 2.50e+03   5.69e-02 3.24e+01
        pdb=" C3  DHT R 901 "   -0.098 2.00e-02 2.50e+03
        pdb=" C4  DHT R 901 "    0.030 2.00e-02 2.50e+03
        pdb=" O3  DHT R 901 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 766 "   -0.076 5.00e-02 4.00e+02   1.07e-01 1.82e+01
        pdb=" N   PRO R 767 "    0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO R 767 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO R 767 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "   -0.008 2.00e-02 2.50e+03   1.21e-02 3.63e+00
        pdb=" CG  TRP B  82 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1189 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1680
        2.79 -     3.32: 6488
        3.32 -     3.84: 10720
        3.84 -     4.37: 11031
        4.37 -     4.90: 19855
  Nonbonded interactions: 49774
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   CYS B  25 "
            pdb=" NZ  LYS G  29 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   THR B  34 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER R 593 "
            pdb=" NZ  LYS R 820 "
     model   vdw
     2.322 3.120
  ... (remaining 49769 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:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.090
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
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      :  0.003   0.150   6917  Z= 0.213
  Angle     :  0.569  11.964   9426  Z= 0.309
  Chirality :  0.039   0.273   1110
  Planarity :  0.004   0.107   1192
  Dihedral  : 18.163  97.531   2409
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 33.71 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.29), residues: 880
  helix:  1.92 (0.28), residues: 343
  sheet:  0.29 (0.46), residues: 141
  loop : -2.23 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 640 
 PHE   0.009   0.001   PHE B 222 
 TYR   0.007   0.001   TYR A 318 
 ARG   0.002   0.000   ARG A 389 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.9089 (t70) cc_final: 0.8886 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1789
  time to fit residues: 18.4614
Evaluate side-chains
  64 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.068308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.057961 restraints weight = 21756.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2603 rms_B_bonded: 3.04
r_work: 0.2513 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   6917  Z= 0.247
  Angle     :  0.539   6.082   9426  Z= 0.283
  Chirality :  0.040   0.131   1110
  Planarity :  0.003   0.041   1192
  Dihedral  :  3.874  15.292   1003
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.30 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.29), residues: 880
  helix:  1.74 (0.28), residues: 351
  sheet:  0.45 (0.47), residues: 139
  loop : -2.24 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 
 PHE   0.009   0.001   PHE A 340 
 TYR   0.011   0.001   TYR R 602 
 ARG   0.004   0.000   ARG A 373 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 63
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: R  601 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8581 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 89
  average time/residue: 0.1818
  time to fit residues: 22.1147
Evaluate side-chains
  81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 84 optimal weight:    0.0050
   chunk 85 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.7798

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS
A 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.068469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.058078 restraints weight = 21912.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2605 rms_B_bonded: 3.07
r_work: 0.2516 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6917  Z= 0.207
  Angle     :  0.517   6.621   9426  Z= 0.271
  Chirality :  0.039   0.129   1110
  Planarity :  0.003   0.038   1192
  Dihedral  :  3.684  15.763   1003
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.73 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.29), residues: 880
  helix:  1.71 (0.28), residues: 351
  sheet:  0.40 (0.47), residues: 139
  loop : -2.21 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 
 PHE   0.008   0.001   PHE B 222 
 TYR   0.008   0.001   TYR R 602 
 ARG   0.003   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: R  601 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8423 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8248 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 84
  average time/residue: 0.1697
  time to fit residues: 20.2395
Evaluate side-chains
  81 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0170
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0050
   overall best weight:    1.0038

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 640 HIS
A 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.069786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.059379 restraints weight = 21913.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.2636 rms_B_bonded: 3.14
r_work: 0.2545 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6917  Z= 0.153
  Angle     :  0.494   7.407   9426  Z= 0.257
  Chirality :  0.038   0.128   1110
  Planarity :  0.003   0.037   1192
  Dihedral  :  3.554  15.087   1003
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.73 %
    Favored  : 65.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.29), residues: 880
  helix:  1.81 (0.28), residues: 352
  sheet:  0.46 (0.47), residues: 137
  loop : -2.18 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 640 
 PHE   0.009   0.001   PHE A 340 
 TYR   0.008   0.001   TYR A 358 
 ARG   0.003   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 0.778 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8669 (mtm-85)
  outliers start: 31
  outliers final: 23
  residues processed: 94
  average time/residue: 0.1798
  time to fit residues: 24.0033
Evaluate side-chains
  88 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  618 LEU
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  688 ILE
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0670
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.9924

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
R 640 HIS
R 806 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.068514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.058004 restraints weight = 21843.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2598 rms_B_bonded: 3.13
r_work: 0.2506 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6917  Z= 0.224
  Angle     :  0.523   8.182   9426  Z= 0.272
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.036   1192
  Dihedral  :  3.666  15.658   1003
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 29.73 %
    Favored  : 64.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.29), residues: 880
  helix:  1.78 (0.28), residues: 352
  sheet:  0.47 (0.47), residues: 139
  loop : -2.20 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.009   0.001   PHE A 340 
 TYR   0.009   0.001   TYR R 602 
 ARG   0.002   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 60
  time to evaluate  : 0.776 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8752 (mtm-85)
  outliers start: 39
  outliers final: 29
  residues processed: 94
  average time/residue: 0.1882
  time to fit residues: 25.1091
Evaluate side-chains
  89 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  688 ILE
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.067473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.056989 restraints weight = 22050.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2570 rms_B_bonded: 3.13
r_work: 0.2478 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6917  Z= 0.270
  Angle     :  0.546   8.820   9426  Z= 0.283
  Chirality :  0.040   0.126   1110
  Planarity :  0.003   0.036   1192
  Dihedral  :  3.780  16.029   1003
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 30.58 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.29), residues: 880
  helix:  1.70 (0.28), residues: 352
  sheet:  0.31 (0.44), residues: 150
  loop : -2.19 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 235 
 TYR   0.010   0.001   TYR R 602 
 ARG   0.002   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 61
  time to evaluate  : 0.757 
Fit side-chains
REVERT: B   61 MET cc_start: 0.9512 (ppp) cc_final: 0.9250 (ppp)
REVERT: R  601 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8882 (mtm-85)
  outliers start: 38
  outliers final: 34
  residues processed: 94
  average time/residue: 0.1583
  time to fit residues: 20.9787
Evaluate side-chains
  95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 60
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  688 ILE
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  714 TRP
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.068279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.057805 restraints weight = 21806.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 3.13
r_work: 0.2496 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6917  Z= 0.208
  Angle     :  0.525   9.681   9426  Z= 0.271
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.715  15.941   1003
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.01 %
    Favored  : 64.30 %
  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: -0.14 (0.29), residues: 880
  helix:  1.76 (0.28), residues: 352
  sheet:  0.35 (0.44), residues: 149
  loop : -2.19 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 806 
 PHE   0.009   0.001   PHE A 340 
 TYR   0.008   0.001   TYR R 602 
 ARG   0.002   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 63
  time to evaluate  : 0.812 
Fit side-chains
REVERT: B   61 MET cc_start: 0.9515 (ppp) cc_final: 0.9251 (ppp)
REVERT: R  601 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8783 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8312 (t80)
  outliers start: 40
  outliers final: 32
  residues processed: 97
  average time/residue: 0.1702
  time to fit residues: 23.3840
Evaluate side-chains
  96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 62
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  644 LEU
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  688 ILE
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  714 TRP
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain R residue  808 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 640 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.069076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.058627 restraints weight = 21876.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.2607 rms_B_bonded: 3.15
r_work: 0.2515 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6917  Z= 0.172
  Angle     :  0.517   8.267   9426  Z= 0.265
  Chirality :  0.039   0.127   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.630  15.477   1003
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 29.87 %
    Favored  : 64.30 %
  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: -0.07 (0.29), residues: 880
  helix:  1.83 (0.28), residues: 352
  sheet:  0.55 (0.46), residues: 139
  loop : -2.17 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 806 
 PHE   0.008   0.001   PHE A 340 
 TYR   0.008   0.001   TYR A 358 
 ARG   0.002   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 67
  time to evaluate  : 0.752 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8714 (m-10) cc_final: 0.8437 (m-10)
REVERT: R  601 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8750 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8196 (t80)
  outliers start: 41
  outliers final: 30
  residues processed: 101
  average time/residue: 0.1606
  time to fit residues: 22.7873
Evaluate side-chains
  97 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  645 SER
Chi-restraints excluded: chain R residue  692 SER
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain R residue  714 TRP
Chi-restraints excluded: chain R residue  717 VAL
Chi-restraints excluded: chain R residue  727 ASN
Chi-restraints excluded: chain R residue  741 ILE
Chi-restraints excluded: chain R residue  808 LEU
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.0000
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0010
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** R 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.071604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.061152 restraints weight = 21574.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 3.11
r_work: 0.2577 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6917  Z= 0.133
  Angle     :  0.511  10.818   9426  Z= 0.259
  Chirality :  0.038   0.128   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.451  14.665   1003
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 32.01 %
    Favored  : 64.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.29), residues: 880
  helix:  1.91 (0.29), residues: 353
  sheet:  0.70 (0.47), residues: 134
  loop : -2.18 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 640 
 PHE   0.010   0.001   PHE A 290 
 TYR   0.009   0.001   TYR R 641 
 ARG   0.002   0.000   ARG B 251 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.854 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8633 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8008 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 89
  average time/residue: 0.1691
  time to fit residues: 21.0938
Evaluate side-chains
  85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0170
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
R 640 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.072609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.062302 restraints weight = 21606.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.2691 rms_B_bonded: 3.11
r_work: 0.2601 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   6917  Z= 0.137
  Angle     :  0.515  10.585   9426  Z= 0.259
  Chirality :  0.038   0.128   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.409  18.628   1003
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 32.72 %
    Favored  : 64.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.29), residues: 880
  helix:  1.97 (0.28), residues: 353
  sheet:  0.71 (0.47), residues: 134
  loop : -2.15 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 640 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.007   0.001   TYR A 358 
 ARG   0.002   0.000   ARG B  49 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.785 
Fit side-chains
REVERT: R  601 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8586 (mtm-85)
REVERT: A  391 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7904 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 86
  average time/residue: 0.1852
  time to fit residues: 21.9652
Evaluate side-chains
  85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  601 ARG
Chi-restraints excluded: chain R residue  632 CYS
Chi-restraints excluded: chain R residue  640 HIS
Chi-restraints excluded: chain R residue  700 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0070
   chunk 73 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.5602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.070124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.059665 restraints weight = 21835.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2634 rms_B_bonded: 3.21
r_work: 0.2541 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6917  Z= 0.188
  Angle     :  0.533  10.175   9426  Z= 0.268
  Chirality :  0.039   0.130   1110
  Planarity :  0.003   0.035   1192
  Dihedral  :  3.523  15.876   1003
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 32.01 %
    Favored  : 64.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.29), residues: 880
  helix:  1.90 (0.28), residues: 353
  sheet:  0.71 (0.46), residues: 134
  loop : -2.15 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B  82 
 HIS   0.013   0.001   HIS R 640 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.007   0.001   TYR R 602 
 ARG   0.002   0.000   ARG B  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2801.19 seconds
wall clock time: 49 minutes 8.61 seconds (2948.61 seconds total)