Starting phenix.real_space_refine
on Wed Apr 30 22:46:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/04_2025/8yjl_39344.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 253 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      58      5.49       5
     S      63      5.16       5
     C    6023      2.51       5
     N    1652      2.21       5
     O    2057      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9853
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "J"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 344
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 574
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
    Chain: "F"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 227
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
    Chain: "C"
      Number of atoms: 1968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1968
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "D"
      Number of atoms: 2770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2770
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
  Time building chain proxies: 6.65, per 1000 atoms: 0.67
  Number of scatterers: 9853
  At special positions: 0
  Unit cell: (102.92, 98.77, 103.75, 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      63     16.00
     P      58     15.00
     O    2057      8.00
     N    1652      7.00
     C    6023      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " distance=2.03

  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: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      28.4% alpha, 27.2% beta
      14 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 4.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 9 through 20
    Processing helix  chain 'C' and resid 71 through 80
    Processing helix  chain 'C' and resid 141 through 155
      removed outlier: 4.014A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'B' and resid 8 through 19
      removed outlier: 4.173A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 80
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'A' and resid 9 through 20
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing helix  chain 'D' and resid 5 through 14
    Processing helix  chain 'D' and resid 35 through 43
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 112
      removed outlier: 3.860A  pdb=" N   GLY D  95 " --> pdb=" O   GLN D  91 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLU D  96 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA D  98 " --> pdb=" O   SER D  94 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLN D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 128
    Processing helix  chain 'D' and resid 134 through 149
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 180 through 186
      removed outlier: 3.751A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 230
    Processing helix  chain 'D' and resid 242 through 251
    Processing helix  chain 'D' and resid 256 through 263
      removed outlier: 3.698A  pdb=" N   LEU D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 302 through 311
    Processing helix  chain 'D' and resid 318 through 333
    Processing helix  chain 'D' and resid 339 through 344
      removed outlier: 4.036A  pdb=" N   PHE D 343 " --> pdb=" O   ARG D 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 62
      removed outlier: 4.397A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 70
      removed outlier: 6.591A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY C  34 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 122 through 125
      removed outlier: 3.792A  pdb=" N   GLY D 348 " --> pdb=" O   GLN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 203 through 208
      removed outlier: 5.344A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.644A  pdb=" N   THR D 336 " --> pdb=" O   ILE C 255 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.909A  pdb=" N   THR B  59 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   SER A 172 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ALA A 157 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   CYS A 162 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL A 203 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 71
      removed outlier: 7.228A  pdb=" N   GLU B  25 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71
      removed outlier: 7.129A  pdb=" N   GLU A  25 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   CYS A  27 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   GLN A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASP A  29 " --> pdb=" O   ASN A  36 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154
      removed outlier: 3.574A  pdb=" N   ALA D 174 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)

    461 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 3.47

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2396
        1.33 -     1.45: 2045
        1.45 -     1.57: 5464
        1.57 -     1.70: 113
        1.70 -     1.82: 102
  Bond restraints: 10120
  Sorted by residual:
  bond pdb=" CB  ASP B 243 "
       pdb=" CG  ASP B 243 "
    ideal  model  delta    sigma   weight residual
    1.516  1.573 -0.057 2.50e-02 1.60e+03 5.23e+00
  bond pdb=" CA  ASP B 243 "
       pdb=" CB  ASP B 243 "
    ideal  model  delta    sigma   weight residual
    1.530  1.562 -0.032 1.54e-02 4.22e+03 4.34e+00
  bond pdb=" C3'  DA J  12 "
       pdb=" O3'  DA J  12 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.38e+00
  bond pdb=" N   GLN D 315 "
       pdb=" CA  GLN D 315 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.026 1.42e-02 4.96e+03 3.28e+00
  bond pdb=" CB  GLU D 221 "
       pdb=" CG  GLU D 221 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 3.00e-02 1.11e+03 2.46e+00
  ... (remaining 10115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.03: 13604
        3.03 -     6.06: 245
        6.06 -     9.10: 44
        9.10 -    12.13: 8
       12.13 -    15.16: 2
  Bond angle restraints: 13903
  Sorted by residual:
  angle pdb=" CB  MET B 199 "
        pdb=" CG  MET B 199 "
        pdb=" SD  MET B 199 "
      ideal   model   delta    sigma   weight residual
     112.70  127.86  -15.16 3.00e+00 1.11e-01 2.55e+01
  angle pdb=" C   ASN B 187 "
        pdb=" N   VAL B 188 "
        pdb=" CA  VAL B 188 "
      ideal   model   delta    sigma   weight residual
     121.97  131.00   -9.03 1.80e+00 3.09e-01 2.51e+01
  angle pdb=" C   ALA B 242 "
        pdb=" N   ASP B 243 "
        pdb=" CA  ASP B 243 "
      ideal   model   delta    sigma   weight residual
     122.08  129.01   -6.93 1.47e+00 4.63e-01 2.22e+01
  angle pdb=" N   THR C 219 "
        pdb=" CA  THR C 219 "
        pdb=" C   THR C 219 "
      ideal   model   delta    sigma   weight residual
     109.81  119.73   -9.92 2.21e+00 2.05e-01 2.02e+01
  angle pdb=" CA  ASP B 243 "
        pdb=" CB  ASP B 243 "
        pdb=" CG  ASP B 243 "
      ideal   model   delta    sigma   weight residual
     112.60  116.91   -4.31 1.00e+00 1.00e+00 1.85e+01
  ... (remaining 13898 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.05: 5553
       28.05 -    56.10: 522
       56.10 -    84.16: 46
       84.16 -   112.21: 6
      112.21 -   140.26: 1
  Dihedral angle restraints: 6128
    sinusoidal: 2880
      harmonic: 3248
  Sorted by residual:
  dihedral pdb=" CB  CYS A 135 "
           pdb=" SG  CYS A 135 "
           pdb=" SG  CYS A 162 "
           pdb=" CB  CYS A 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.26   87.26     1      1.00e+01 1.00e-02 9.14e+01
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   MET B 199 "
           pdb=" CA  MET B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.73  -26.27     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  GLU A 198 "
           pdb=" C   GLU A 198 "
           pdb=" N   MET A 199 "
           pdb=" CA  MET A 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1335
       0.073 -    0.146: 225
       0.146 -    0.219: 34
       0.219 -    0.292: 6
       0.292 -    0.365: 1
  Chirality restraints: 1601
  Sorted by residual:
  chirality pdb=" CB  VAL B 203 "
            pdb=" CA  VAL B 203 "
            pdb=" CG1 VAL B 203 "
            pdb=" CG2 VAL B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CA  THR C 219 "
            pdb=" N   THR C 219 "
            pdb=" C   THR C 219 "
            pdb=" CB  THR C 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CB  ILE A  11 "
            pdb=" CA  ILE A  11 "
            pdb=" CG1 ILE A  11 "
            pdb=" CG2 ILE A  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1598 not shown)

  Planarity restraints: 1589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 219 "    0.055 5.00e-02 4.00e+02   8.12e-02 1.06e+01
        pdb=" N   PRO B 220 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO B 220 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 220 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO A 220 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 109 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.94e+00
        pdb=" C   LYS D 109 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LYS D 109 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN D 110 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1586 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3004
        2.85 -     3.36: 8360
        3.36 -     3.88: 17114
        3.88 -     4.39: 19512
        4.39 -     4.90: 32634
  Nonbonded interactions: 80624
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   GLU B 191 "
            pdb=" OG1 THR B 224 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ALA D  98 "
            pdb=" OG  SER D 101 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O   VAL D 123 "
            pdb=" OG1 THR D 127 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" OE1 GLU D 221 "
            pdb=" NE2 HIS D 280 "
     model   vdw
     2.372 3.120
  ... (remaining 80619 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'C' and resid 1 through 254)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.140
  Process input model:                     28.870
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10123  Z= 0.240
  Angle     :  0.998  15.161  13909  Z= 0.520
  Chirality :  0.058   0.365   1601
  Planarity :  0.007   0.081   1589
  Dihedral  : 19.381 140.260   4011
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -2.81 (0.21), residues: 1107
  helix: -2.30 (0.22), residues: 315
  sheet: -0.90 (0.26), residues: 357
  loop : -2.18 (0.24), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  28 
 HIS   0.003   0.001   HIS A 246 
 PHE   0.021   0.003   PHE D 283 
 TYR   0.024   0.003   TYR C 133 
 ARG   0.015   0.001   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13451 (  489)
  hydrogen bonds       : angle       7.71590 ( 1349)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       0.97859 (    6)
  covalent geometry    : bond        0.00533 (10120)
  covalent geometry    : angle       0.99810 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  199 MET cc_start: 0.5430 (tpt) cc_final: 0.5024 (tpp)
REVERT: A  244 MET cc_start: 0.7863 (tmm) cc_final: 0.7251 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2031
  time to fit residues: 44.4937
Evaluate side-chains
  111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
C  49 GLN
B  71 ASN
B 204 GLN
D 137 HIS
D 143 HIS
D 253 HIS
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.150560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114522 restraints weight = 12481.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.118478 restraints weight = 9118.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.119688 restraints weight = 5739.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10123  Z= 0.231
  Angle     :  0.658   8.260  13909  Z= 0.352
  Chirality :  0.046   0.251   1601
  Planarity :  0.004   0.053   1589
  Dihedral  : 20.614 148.735   1871
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  8.99 %
    Favored  : 89.46 %
  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: -2.08 (0.23), residues: 1107
  helix: -0.89 (0.26), residues: 318
  sheet: -1.08 (0.26), residues: 363
  loop : -1.86 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.004   0.001   HIS D 253 
 PHE   0.014   0.002   PHE D 316 
 TYR   0.017   0.002   TYR B 211 
 ARG   0.005   0.001   ARG D 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  489)
  hydrogen bonds       : angle       6.12495 ( 1349)
  SS BOND              : bond        0.01001 (    3)
  SS BOND              : angle       1.39363 (    6)
  covalent geometry    : bond        0.00523 (10120)
  covalent geometry    : angle       0.65800 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.122 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7096 (pm20) cc_final: 0.6697 (pm20)
REVERT: B   27 CYS cc_start: 0.7380 (t) cc_final: 0.7080 (p)
REVERT: A  244 MET cc_start: 0.8268 (tmm) cc_final: 0.7646 (ttm)
  outliers start: 15
  outliers final: 10
  residues processed: 139
  average time/residue: 0.2257
  time to fit residues: 45.1991
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue   94 ASP
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0770
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0010
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3944

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
D  48 GLN
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.154495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.118768 restraints weight = 12545.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.122455 restraints weight = 9193.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123927 restraints weight = 5924.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10123  Z= 0.127
  Angle     :  0.557   7.546  13909  Z= 0.301
  Chirality :  0.042   0.161   1601
  Planarity :  0.003   0.043   1589
  Dihedral  : 20.293 139.356   1871
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.81 %
    Favored  : 85.54 %
  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: -1.56 (0.24), residues: 1107
  helix: -0.07 (0.29), residues: 317
  sheet: -0.99 (0.26), residues: 363
  loop : -1.66 (0.26), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 143 
 PHE   0.009   0.001   PHE D 316 
 TYR   0.012   0.001   TYR B 211 
 ARG   0.004   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  489)
  hydrogen bonds       : angle       5.59494 ( 1349)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       0.84633 (    6)
  covalent geometry    : bond        0.00283 (10120)
  covalent geometry    : angle       0.55640 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.038 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7073 (pm20) cc_final: 0.6697 (pm20)
REVERT: B   27 CYS cc_start: 0.7317 (t) cc_final: 0.7044 (p)
REVERT: B   68 MET cc_start: 0.7936 (mmt) cc_final: 0.7107 (mmt)
REVERT: B  224 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8702 (p)
REVERT: A  199 MET cc_start: 0.7204 (tpp) cc_final: 0.6761 (tpt)
REVERT: A  244 MET cc_start: 0.8266 (tmm) cc_final: 0.7636 (ttm)
  outliers start: 16
  outliers final: 9
  residues processed: 138
  average time/residue: 0.2019
  time to fit residues: 40.1056
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    0.0470
   chunk 11 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0010
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.3684

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
A  49 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.154127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.118455 restraints weight = 12433.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.122179 restraints weight = 8863.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.123970 restraints weight = 5681.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10123  Z= 0.124
  Angle     :  0.546   6.491  13909  Z= 0.295
  Chirality :  0.042   0.157   1601
  Planarity :  0.003   0.031   1589
  Dihedral  : 20.261 137.807   1871
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.36 %
    Favored  : 83.47 %
  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: -1.26 (0.24), residues: 1107
  helix:  0.33 (0.30), residues: 318
  sheet: -0.88 (0.27), residues: 352
  loop : -1.56 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.009   0.001   PHE D 316 
 TYR   0.011   0.001   TYR B 211 
 ARG   0.004   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  489)
  hydrogen bonds       : angle       5.40113 ( 1349)
  SS BOND              : bond        0.00213 (    3)
  SS BOND              : angle       0.74868 (    6)
  covalent geometry    : bond        0.00273 (10120)
  covalent geometry    : angle       0.54566 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.730 
Fit side-chains
REVERT: B   27 CYS cc_start: 0.7299 (t) cc_final: 0.7043 (p)
REVERT: B   68 MET cc_start: 0.7921 (mmt) cc_final: 0.7057 (mmt)
REVERT: A   17 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7290 (mp0)
REVERT: A  244 MET cc_start: 0.8199 (tmm) cc_final: 0.7657 (ttm)
REVERT: D   40 TYR cc_start: 0.8880 (m-80) cc_final: 0.8448 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2232
  time to fit residues: 45.6902
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0980
   chunk 109 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
A  49 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.147993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.114216 restraints weight = 12704.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.117160 restraints weight = 8917.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.118918 restraints weight = 5943.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10123  Z= 0.165
  Angle     :  0.580   7.936  13909  Z= 0.310
  Chirality :  0.043   0.169   1601
  Planarity :  0.003   0.032   1589
  Dihedral  : 20.365 133.994   1871
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.05 %
    Favored  : 80.48 %
  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: -1.15 (0.24), residues: 1107
  helix:  0.44 (0.30), residues: 315
  sheet: -0.87 (0.27), residues: 352
  loop : -1.45 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 143 
 PHE   0.009   0.001   PHE D 316 
 TYR   0.013   0.001   TYR B 211 
 ARG   0.002   0.000   ARG D 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  489)
  hydrogen bonds       : angle       5.53964 ( 1349)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       0.86483 (    6)
  covalent geometry    : bond        0.00374 (10120)
  covalent geometry    : angle       0.58005 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7519 (t)
REVERT: B   27 CYS cc_start: 0.7383 (t) cc_final: 0.7115 (p)
REVERT: B   86 ASP cc_start: 0.6880 (m-30) cc_final: 0.6655 (m-30)
REVERT: A   17 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: A  199 MET cc_start: 0.6986 (tpp) cc_final: 0.6670 (mmm)
REVERT: A  244 MET cc_start: 0.8174 (tmm) cc_final: 0.7716 (ttm)
REVERT: D   40 TYR cc_start: 0.8898 (m-80) cc_final: 0.8538 (m-10)
  outliers start: 24
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2641
  time to fit residues: 52.5700
Evaluate side-chains
  132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 2.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0270
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
B 184 GLN
A  38 GLN
A  49 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.148230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.114497 restraints weight = 12792.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117464 restraints weight = 9155.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118722 restraints weight = 6079.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10123  Z= 0.150
  Angle     :  0.576   8.682  13909  Z= 0.305
  Chirality :  0.043   0.191   1601
  Planarity :  0.003   0.032   1589
  Dihedral  : 20.354 131.207   1871
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.49 %
    Favored  : 79.24 %
  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: -1.06 (0.24), residues: 1107
  helix:  0.53 (0.30), residues: 315
  sheet: -0.86 (0.27), residues: 352
  loop : -1.36 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 143 
 PHE   0.010   0.001   PHE D 316 
 TYR   0.014   0.001   TYR B 211 
 ARG   0.006   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  489)
  hydrogen bonds       : angle       5.48653 ( 1349)
  SS BOND              : bond        0.00166 (    3)
  SS BOND              : angle       0.89405 (    6)
  covalent geometry    : bond        0.00340 (10120)
  covalent geometry    : angle       0.57571 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7525 (t)
REVERT: B   27 CYS cc_start: 0.7334 (t) cc_final: 0.7093 (p)
REVERT: A   17 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7369 (mp0)
REVERT: A  199 MET cc_start: 0.6966 (tpp) cc_final: 0.6712 (mmm)
REVERT: A  244 MET cc_start: 0.8160 (tmm) cc_final: 0.7757 (ttm)
REVERT: D   40 TYR cc_start: 0.8907 (m-80) cc_final: 0.8584 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2459
  time to fit residues: 49.6199
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 98 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D  48 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.148834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.114831 restraints weight = 12927.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117992 restraints weight = 8977.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.119853 restraints weight = 5855.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10123  Z= 0.142
  Angle     :  0.575   8.593  13909  Z= 0.303
  Chirality :  0.043   0.207   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.304 127.182   1871
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.18 %
    Favored  : 79.13 %
  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: -0.93 (0.25), residues: 1107
  helix:  0.66 (0.30), residues: 315
  sheet: -0.76 (0.27), residues: 372
  loop : -1.33 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 143 
 PHE   0.010   0.001   PHE D 316 
 TYR   0.013   0.001   TYR B 211 
 ARG   0.006   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  489)
  hydrogen bonds       : angle       5.44747 ( 1349)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       0.85470 (    6)
  covalent geometry    : bond        0.00324 (10120)
  covalent geometry    : angle       0.57488 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7496 (t)
REVERT: B   27 CYS cc_start: 0.7365 (t) cc_final: 0.7097 (p)
REVERT: A    8 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7859 (pt0)
REVERT: A   17 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: A  199 MET cc_start: 0.6721 (tpp) cc_final: 0.6449 (mmm)
REVERT: A  244 MET cc_start: 0.8169 (tmm) cc_final: 0.7778 (ttm)
REVERT: D   40 TYR cc_start: 0.8919 (m-80) cc_final: 0.8591 (m-10)
  outliers start: 26
  outliers final: 13
  residues processed: 138
  average time/residue: 0.2043
  time to fit residues: 41.1246
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   27 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 71 optimal weight:    0.3980
   chunk 110 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.147518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.113869 restraints weight = 12892.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117098 restraints weight = 9051.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.118432 restraints weight = 5913.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10123  Z= 0.163
  Angle     :  0.600   8.375  13909  Z= 0.314
  Chirality :  0.044   0.293   1601
  Planarity :  0.003   0.032   1589
  Dihedral  : 20.298 122.374   1871
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.90 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.97 (0.25), residues: 1107
  helix:  0.64 (0.30), residues: 316
  sheet: -0.85 (0.27), residues: 372
  loop : -1.29 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 143 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.014   0.002   TYR B 211 
 ARG   0.007   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03183 (  489)
  hydrogen bonds       : angle       5.52341 ( 1349)
  SS BOND              : bond        0.00168 (    3)
  SS BOND              : angle       0.94229 (    6)
  covalent geometry    : bond        0.00374 (10120)
  covalent geometry    : angle       0.59975 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7516 (t)
REVERT: B    3 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7250 (tp30)
REVERT: B   27 CYS cc_start: 0.7431 (t) cc_final: 0.7133 (p)
REVERT: B   86 ASP cc_start: 0.6928 (m-30) cc_final: 0.6672 (m-30)
REVERT: A    8 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7933 (pt0)
REVERT: A   17 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7400 (mp0)
REVERT: D   40 TYR cc_start: 0.8921 (m-80) cc_final: 0.8522 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2077
  time to fit residues: 41.7439
Evaluate side-chains
  138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   27 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    0.0370
   chunk 70 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.147849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114480 restraints weight = 12852.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117646 restraints weight = 9037.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118984 restraints weight = 5931.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10123  Z= 0.152
  Angle     :  0.596   8.473  13909  Z= 0.312
  Chirality :  0.044   0.251   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.279 120.422   1871
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.42 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.25), residues: 1107
  helix:  0.71 (0.30), residues: 316
  sheet: -0.82 (0.27), residues: 372
  loop : -1.26 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D 143 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.015   0.001   TYR B 211 
 ARG   0.003   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03133 (  489)
  hydrogen bonds       : angle       5.48121 ( 1349)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.91448 (    6)
  covalent geometry    : bond        0.00352 (10120)
  covalent geometry    : angle       0.59566 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7502 (t)
REVERT: B    3 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7242 (tp30)
REVERT: B   27 CYS cc_start: 0.7407 (t) cc_final: 0.7133 (p)
REVERT: B   86 ASP cc_start: 0.6889 (m-30) cc_final: 0.6641 (m-30)
REVERT: B  139 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6974 (ppp)
REVERT: A    8 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7930 (pt0)
REVERT: A   17 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: D   40 TYR cc_start: 0.8918 (m-80) cc_final: 0.8581 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 139
  average time/residue: 0.2354
  time to fit residues: 48.5208
Evaluate side-chains
  141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   27 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0870
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.3364

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110351 restraints weight = 12779.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114015 restraints weight = 9067.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.115186 restraints weight = 5756.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10123  Z= 0.255
  Angle     :  0.693   8.212  13909  Z= 0.357
  Chirality :  0.048   0.422   1601
  Planarity :  0.003   0.032   1589
  Dihedral  : 20.515 114.561   1871
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.21 %
    Favored  : 78.31 %
  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: -1.23 (0.25), residues: 1107
  helix:  0.40 (0.29), residues: 316
  sheet: -1.06 (0.27), residues: 372
  loop : -1.37 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 274 
 HIS   0.007   0.001   HIS D 280 
 PHE   0.015   0.002   PHE B   2 
 TYR   0.018   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  489)
  hydrogen bonds       : angle       5.89970 ( 1349)
  SS BOND              : bond        0.00305 (    3)
  SS BOND              : angle       1.36094 (    6)
  covalent geometry    : bond        0.00591 (10120)
  covalent geometry    : angle       0.69264 (13903)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7528 (t)
REVERT: B    3 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7179 (tp30)
REVERT: B   27 CYS cc_start: 0.7491 (t) cc_final: 0.7225 (p)
REVERT: B   86 ASP cc_start: 0.7154 (m-30) cc_final: 0.6900 (m-30)
REVERT: B  139 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7073 (ppp)
REVERT: A    1 MET cc_start: 0.7196 (ppp) cc_final: 0.6491 (ppp)
REVERT: A   17 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6947 (mp0)
REVERT: D   40 TYR cc_start: 0.8949 (m-80) cc_final: 0.8497 (m-10)
REVERT: D   67 MET cc_start: 0.7345 (mtm) cc_final: 0.6979 (mtm)
  outliers start: 24
  outliers final: 16
  residues processed: 136
  average time/residue: 0.1992
  time to fit residues: 39.2475
Evaluate side-chains
  133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   27 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  187 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 97 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0170
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.149567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114573 restraints weight = 12644.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.118042 restraints weight = 8829.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.119788 restraints weight = 5743.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10123  Z= 0.149
  Angle     :  0.627   8.960  13909  Z= 0.326
  Chirality :  0.044   0.288   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.388 114.751   1871
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.25 %
    Favored  : 77.69 %
  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: -1.11 (0.25), residues: 1107
  helix:  0.53 (0.29), residues: 316
  sheet: -1.01 (0.26), residues: 372
  loop : -1.30 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 280 
 PHE   0.009   0.001   PHE C   2 
 TYR   0.016   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03193 (  489)
  hydrogen bonds       : angle       5.60022 ( 1349)
  SS BOND              : bond        0.00172 (    3)
  SS BOND              : angle       0.94243 (    6)
  covalent geometry    : bond        0.00343 (10120)
  covalent geometry    : angle       0.62709 (13903)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3129.86 seconds
wall clock time: 55 minutes 56.86 seconds (3356.86 seconds total)