Starting phenix.real_space_refine
on Thu Jan 16 21:23:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/01_2025/8yjl_39344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/01_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_39344/01_2025/8yjl_39344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/01_2025/8yjl_39344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/01_2025/8yjl_39344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/01_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-5571/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: 6.47, per 1000 atoms: 0.66
  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 1.0 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: 3.61
  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: 3.88

  Time building geometry restraints manager: 2.76 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:             3.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.820
  Find NCS groups from input model:        0.310
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.400
-------------------------------------------------------------------------------
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  10120  Z= 0.336
  Angle     :  0.998  15.161  13903  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 

*********************** 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  : 0.964 
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: 0.2133
  time to fit residues: 46.3160
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  : 1.076 
-------------------------------------------------------------------------------
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 = 12481.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.118461 restraints weight = 9118.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119673 restraints weight = 5745.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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  10120  Z= 0.329
  Angle     :  0.658   8.260  13903  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 

*********************** 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  : 1.038 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7096 (pm20) cc_final: 0.6695 (pm20)
REVERT: B   27 CYS cc_start: 0.7381 (t) cc_final: 0.7079 (p)
REVERT: A  244 MET cc_start: 0.8267 (tmm) cc_final: 0.7644 (ttm)
  outliers start: 15
  outliers final: 10
  residues processed: 139
  average time/residue: 0.2175
  time to fit residues: 43.1201
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  : 1.113 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 72 optimal weight:    2.9990
   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:    1.9990
   chunk 84 optimal weight:    0.0010
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6388

-------------------------------------------------------------------------------
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
D 302 ASN
** 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 = 0.3869 r_free = 0.3869 target = 0.151799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116165 restraints weight = 12597.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.119689 restraints weight = 8910.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.121414 restraints weight = 5753.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10120  Z= 0.221
  Angle     :  0.578   7.265  13903  Z= 0.311
  Chirality :  0.043   0.174   1601
  Planarity :  0.004   0.045   1589
  Dihedral  : 20.314 137.226   1871
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.22 %
    Favored  : 84.92 %
  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: -1.63 (0.24), residues: 1107
  helix: -0.13 (0.28), residues: 317
  sheet: -1.06 (0.26), residues: 363
  loop : -1.68 (0.26), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 143 
 PHE   0.010   0.001   PHE D 316 
 TYR   0.013   0.001   TYR B 211 
 ARG   0.003   0.000   ARG D 261 

*********************** 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
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.039 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7120 (pm20) cc_final: 0.6681 (pm20)
REVERT: B   27 CYS cc_start: 0.7340 (t) cc_final: 0.7076 (p)
REVERT: B   68 MET cc_start: 0.7941 (mmt) cc_final: 0.7094 (mmt)
REVERT: B  224 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (p)
REVERT: A  199 MET cc_start: 0.7133 (tpp) cc_final: 0.6888 (mmm)
REVERT: A  244 MET cc_start: 0.8241 (tmm) cc_final: 0.7698 (ttm)
  outliers start: 18
  outliers final: 11
  residues processed: 137
  average time/residue: 0.2160
  time to fit residues: 42.6818
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 ASP
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  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 A residue  139 MET
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:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0870
   chunk 104 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.148377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.114606 restraints weight = 12673.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117598 restraints weight = 9108.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.118977 restraints weight = 6017.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10120  Z= 0.210
  Angle     :  0.570   7.535  13903  Z= 0.306
  Chirality :  0.043   0.148   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.368 136.082   1871
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.91 %
    Favored  : 81.92 %
  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: -1.35 (0.24), residues: 1107
  helix:  0.24 (0.29), residues: 318
  sheet: -0.91 (0.27), residues: 348
  loop : -1.61 (0.26), residues: 441

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   0.013   0.001   TYR B 211 
 ARG   0.004   0.000   ARG D 261 

*********************** 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
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.032 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7135 (pm20) cc_final: 0.6541 (pm20)
REVERT: B   27 CYS cc_start: 0.7367 (t) cc_final: 0.7117 (p)
REVERT: B   68 MET cc_start: 0.7903 (mmt) cc_final: 0.7070 (mmt)
REVERT: A   17 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7376 (mp0)
REVERT: A  244 MET cc_start: 0.8224 (tmm) cc_final: 0.7732 (ttm)
REVERT: D   40 TYR cc_start: 0.8913 (m-80) cc_final: 0.8492 (m-10)
REVERT: D   75 MET cc_start: 0.8364 (mmm) cc_final: 0.8145 (mmm)
  outliers start: 21
  outliers final: 14
  residues processed: 137
  average time/residue: 0.2092
  time to fit residues: 41.5167
Evaluate side-chains
  129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  167 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  229 MET
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 A residue  139 MET
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:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 184 GLN
A  38 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3779 r_free = 0.3779 target = 0.143438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.109290 restraints weight = 12817.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112627 restraints weight = 9139.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.114259 restraints weight = 5861.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  10120  Z= 0.361
  Angle     :  0.654   7.741  13903  Z= 0.347
  Chirality :  0.046   0.178   1601
  Planarity :  0.004   0.034   1589
  Dihedral  : 20.601 129.960   1871
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.25 %
    Favored  : 80.06 %
  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: -1.47 (0.24), residues: 1107
  helix:  0.17 (0.29), residues: 315
  sheet: -1.12 (0.27), residues: 347
  loop : -1.56 (0.26), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D 274 
 HIS   0.005   0.001   HIS D 143 
 PHE   0.014   0.002   PHE B   2 
 TYR   0.018   0.002   TYR B 211 
 ARG   0.004   0.000   ARG D 261 

*********************** 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
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7297 (pm20) cc_final: 0.6858 (pm20)
REVERT: C  135 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7514 (t)
REVERT: B    3 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7166 (tp30)
REVERT: B   27 CYS cc_start: 0.7539 (t) cc_final: 0.7261 (p)
REVERT: B   75 MET cc_start: 0.8574 (ttt) cc_final: 0.8371 (ttt)
REVERT: A   17 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6856 (mp0)
REVERT: D  130 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7668 (mm)
  outliers start: 26
  outliers final: 17
  residues processed: 139
  average time/residue: 0.2088
  time to fit residues: 41.8803
Evaluate side-chains
  133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
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  137 VAL
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 B residue  229 MET
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 A residue  139 MET
Chi-restraints excluded: chain D residue   67 MET
Chi-restraints excluded: chain D residue  130 LEU
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:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 81 optimal weight:    0.4980
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3812 r_free = 0.3812 target = 0.146470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.112837 restraints weight = 12797.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115984 restraints weight = 9069.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117652 restraints weight = 5953.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10120  Z= 0.225
  Angle     :  0.592   7.620  13903  Z= 0.316
  Chirality :  0.044   0.183   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.472 127.167   1871
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.87 %
    Favored  : 78.93 %
  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: -1.35 (0.24), residues: 1107
  helix:  0.37 (0.30), residues: 315
  sheet: -1.16 (0.27), residues: 352
  loop : -1.46 (0.27), 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 280 
 PHE   0.009   0.001   PHE C 169 
 TYR   0.015   0.002   TYR B 211 
 ARG   0.006   0.000   ARG D 261 

*********************** 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
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7164 (pm20) cc_final: 0.6710 (pm20)
REVERT: C  135 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7538 (t)
REVERT: B   27 CYS cc_start: 0.7427 (t) cc_final: 0.7167 (p)
REVERT: A    8 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (pt0)
REVERT: A   17 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7441 (mp0)
REVERT: D   40 TYR cc_start: 0.8935 (m-80) cc_final: 0.8628 (m-10)
  outliers start: 31
  outliers final: 17
  residues processed: 144
  average time/residue: 0.2219
  time to fit residues: 46.3169
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
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  137 VAL
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    8 GLN
Chi-restraints excluded: chain A residue   11 ILE
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 A residue  139 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain D residue  130 LEU
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:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 87 optimal weight:    0.2980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3805 r_free = 0.3805 target = 0.146007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.112296 restraints weight = 12976.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.115615 restraints weight = 9255.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.116862 restraints weight = 5991.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10120  Z= 0.240
  Angle     :  0.605   7.569  13903  Z= 0.318
  Chirality :  0.044   0.242   1601
  Planarity :  0.003   0.034   1589
  Dihedral  : 20.454 124.458   1871
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.08 %
    Favored  : 78.93 %
  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:  0.50 (0.30), residues: 315
  sheet: -1.11 (0.27), residues: 368
  loop : -1.39 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 280 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.015   0.002   TYR B 211 
 ARG   0.006   0.000   ARG D 261 

*********************** 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
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7175 (pm20) cc_final: 0.6686 (pm20)
REVERT: C  135 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7570 (t)
REVERT: B   27 CYS cc_start: 0.7458 (t) cc_final: 0.7160 (p)
REVERT: B  139 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7125 (ppp)
REVERT: A    8 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7941 (pt0)
REVERT: A   17 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7421 (mp0)
REVERT: D   40 TYR cc_start: 0.8946 (m-80) cc_final: 0.8467 (m-10)
REVERT: D  130 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7595 (mm)
  outliers start: 29
  outliers final: 20
  residues processed: 144
  average time/residue: 0.2098
  time to fit residues: 43.3028
Evaluate side-chains
  146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  229 MET
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 B residue  229 MET
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   11 ILE
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 A residue  139 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain D residue  130 LEU
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:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0870
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.9564

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  49 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3790 r_free = 0.3790 target = 0.144654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.111219 restraints weight = 12924.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.112945 restraints weight = 8340.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.115351 restraints weight = 6979.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10120  Z= 0.289
  Angle     :  0.635   8.231  13903  Z= 0.332
  Chirality :  0.045   0.281   1601
  Planarity :  0.003   0.034   1589
  Dihedral  : 20.480 120.440   1871
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.49 %
    Favored  : 78.10 %
  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: -1.27 (0.25), residues: 1107
  helix:  0.40 (0.29), residues: 315
  sheet: -1.12 (0.27), residues: 372
  loop : -1.37 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 280 
 PHE   0.010   0.001   PHE B   2 
 TYR   0.016   0.002   TYR B 211 
 ARG   0.007   0.000   ARG D 261 

*********************** 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
  151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7329 (pm20) cc_final: 0.6842 (pm20)
REVERT: C  135 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7623 (t)
REVERT: B    3 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7238 (tp30)
REVERT: B   27 CYS cc_start: 0.7499 (t) cc_final: 0.7205 (p)
REVERT: B  139 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7070 (ppp)
REVERT: A    8 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7932 (pt0)
REVERT: A   17 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7432 (mp0)
REVERT: D   40 TYR cc_start: 0.8955 (m-80) cc_final: 0.8560 (m-10)
REVERT: D   67 MET cc_start: 0.6997 (mtm) cc_final: 0.6795 (mtm)
REVERT: D  130 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7539 (mm)
  outliers start: 33
  outliers final: 20
  residues processed: 140
  average time/residue: 0.2072
  time to fit residues: 41.9384
Evaluate side-chains
  142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  158 VAL
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 B residue  229 MET
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   11 ILE
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 A residue  139 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain D residue  130 LEU
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:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0470
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3808 r_free = 0.3808 target = 0.145945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112279 restraints weight = 12897.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.115280 restraints weight = 9284.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116340 restraints weight = 6136.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10120  Z= 0.228
  Angle     :  0.612   7.875  13903  Z= 0.322
  Chirality :  0.044   0.302   1601
  Planarity :  0.003   0.035   1589
  Dihedral  : 20.433 118.497   1871
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.18 %
    Favored  : 78.41 %
  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: -1.20 (0.25), residues: 1107
  helix:  0.48 (0.30), residues: 315
  sheet: -1.06 (0.27), residues: 372
  loop : -1.36 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 280 
 PHE   0.010   0.001   PHE C 169 
 TYR   0.015   0.002   TYR B 211 
 ARG   0.007   0.000   ARG D 261 

*********************** 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
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7284 (pm20) cc_final: 0.6770 (pm20)
REVERT: B    3 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7248 (tp30)
REVERT: B   27 CYS cc_start: 0.7473 (t) cc_final: 0.7196 (p)
REVERT: B  139 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7021 (ppp)
REVERT: A    8 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7919 (pt0)
REVERT: A   17 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7396 (mp0)
REVERT: D   40 TYR cc_start: 0.8971 (m-80) cc_final: 0.8668 (m-10)
REVERT: D  130 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7586 (mm)
REVERT: D  331 SER cc_start: 0.8243 (p) cc_final: 0.7968 (p)
  outliers start: 33
  outliers final: 24
  residues processed: 143
  average time/residue: 0.2121
  time to fit residues: 44.0048
Evaluate side-chains
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  158 VAL
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 B residue  229 MET
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 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 A residue  139 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain D residue  130 LEU
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:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 113 optimal weight:    0.3980
   chunk 75 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3812 r_free = 0.3812 target = 0.146190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112419 restraints weight = 12962.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115584 restraints weight = 9347.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.116878 restraints weight = 6104.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10120  Z= 0.231
  Angle     :  0.633  13.934  13903  Z= 0.327
  Chirality :  0.044   0.345   1601
  Planarity :  0.003   0.034   1589
  Dihedral  : 20.404 116.400   1871
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.70 %
    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: -1.18 (0.25), residues: 1107
  helix:  0.48 (0.29), residues: 316
  sheet: -1.04 (0.27), residues: 372
  loop : -1.37 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 280 
 PHE   0.010   0.001   PHE D 126 
 TYR   0.015   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 320 

********************** 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
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7311 (pm20) cc_final: 0.6771 (pm20)
REVERT: B    3 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7276 (tp30)
REVERT: B   27 CYS cc_start: 0.7450 (t) cc_final: 0.7179 (p)
REVERT: B  139 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6996 (ppp)
REVERT: A    8 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (pt0)
REVERT: A   17 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7398 (mp0)
REVERT: D   40 TYR cc_start: 0.8980 (m-80) cc_final: 0.8577 (m-10)
REVERT: D  130 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7566 (mm)
  outliers start: 27
  outliers final: 21
  residues processed: 138
  average time/residue: 0.2014
  time to fit residues: 40.4893
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  158 VAL
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 B residue  229 MET
Chi-restraints excluded: chain A residue    8 GLN
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 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 A residue  139 MET
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain D residue  130 LEU
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 101 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 102 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
** D  48 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 = 0.148118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112691 restraints weight = 12696.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.116232 restraints weight = 9075.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117820 restraints weight = 5845.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10120  Z= 0.259
  Angle     :  0.632   8.032  13903  Z= 0.330
  Chirality :  0.045   0.323   1601
  Planarity :  0.003   0.034   1589
  Dihedral  : 20.404 114.514   1871
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.80 %
    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: -1.19 (0.25), residues: 1107
  helix:  0.51 (0.30), residues: 316
  sheet: -1.06 (0.27), residues: 374
  loop : -1.38 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 280 
 PHE   0.010   0.001   PHE D 126 
 TYR   0.016   0.002   TYR B 211 
 ARG   0.003   0.000   ARG D 320 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2745.19 seconds
wall clock time: 50 minutes 28.94 seconds (3028.94 seconds total)