Starting phenix.real_space_refine
on Wed Sep 17 17:11:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/09_2025/8yjl_39344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/09_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_39344/09_2025/8yjl_39344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/09_2025/8yjl_39344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/09_2025/8yjl_39344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/09_2025/8yjl_39344.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.50, per 1000 atoms: 0.25
  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: 0.95
  Conformation dependent library (CDL) restraints added in 332.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.27
  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: 1.89

  Time building geometry restraints manager: 1.25 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:             3.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.810
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.820
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.015   0.001   ARG D 261 
 TYR   0.024   0.003   TYR C 133 
 PHE   0.021   0.003   PHE D 283 
 TRP   0.015   0.002   TRP B  28 
 HIS   0.003   0.001   HIS A 246 

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

*********************** 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  : 0.461 
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: 0.0944
  time to fit residues: 20.7123
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  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0030
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
C  49 GLN
A  49 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.155771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.118999 restraints weight = 12513.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.122266 restraints weight = 10066.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.124254 restraints weight = 6586.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125136 restraints weight = 5349.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125517 restraints weight = 5183.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10123  Z= 0.153
  Angle     :  0.604   8.778  13909  Z= 0.325
  Chirality :  0.044   0.161   1601
  Planarity :  0.004   0.054   1589
  Dihedral  : 20.574 149.935   1871
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.54 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.23), residues: 1107
  helix: -0.81 (0.26), residues: 317
  sheet: -0.89 (0.26), residues: 356
  loop : -1.91 (0.25), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 320 
 TYR   0.013   0.001   TYR B 211 
 PHE   0.013   0.001   PHE D 316 
 TRP   0.004   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10120)
  covalent geometry    : angle       0.60344 (13903)
  SS BOND              : bond        0.01048 (    3)
  SS BOND              : angle       1.19139 (    6)
  hydrogen bonds       : bond        0.03857 (  489)
  hydrogen bonds       : angle       5.90305 ( 1349)

*********************** 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
  136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.385 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.6961 (pm20) cc_final: 0.6648 (pm20)
REVERT: C  108 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6462 (mm110)
REVERT: B   27 CYS cc_start: 0.7249 (t) cc_final: 0.6987 (p)
REVERT: A  244 MET cc_start: 0.8240 (tmm) cc_final: 0.7494 (ttt)
REVERT: D   37 MET cc_start: 0.8103 (ttm) cc_final: 0.7901 (ttm)
REVERT: D  221 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6868 (mm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 132
  average time/residue: 0.0972
  time to fit residues: 18.7035
Evaluate side-chains
  123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 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  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 71 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  71 ASN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.149484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.113962 restraints weight = 12589.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.115809 restraints weight = 8165.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.118827 restraints weight = 6723.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119215 restraints weight = 5100.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.119701 restraints weight = 5058.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10123  Z= 0.218
  Angle     :  0.635   9.552  13909  Z= 0.337
  Chirality :  0.045   0.151   1601
  Planarity :  0.004   0.047   1589
  Dihedral  : 20.456 136.022   1871
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.98 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.24), residues: 1107
  helix: -0.23 (0.28), residues: 316
  sheet: -1.13 (0.26), residues: 362
  loop : -1.69 (0.26), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  47 
 TYR   0.017   0.002   TYR B 211 
 PHE   0.013   0.002   PHE D 126 
 TRP   0.006   0.001   TRP C  28 
 HIS   0.002   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 (10120)
  covalent geometry    : angle       0.63504 (13903)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       1.08355 (    6)
  hydrogen bonds       : bond        0.03769 (  489)
  hydrogen bonds       : angle       5.91421 ( 1349)

*********************** 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
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.337 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7197 (pm20) cc_final: 0.6782 (pm20)
REVERT: B   27 CYS cc_start: 0.7478 (t) cc_final: 0.7210 (p)
REVERT: B   68 MET cc_start: 0.8009 (mmt) cc_final: 0.7148 (mmt)
REVERT: B   86 ASP cc_start: 0.6891 (m-30) cc_final: 0.6642 (m-30)
REVERT: A  244 MET cc_start: 0.8258 (tmm) cc_final: 0.7766 (ttm)
REVERT: D   27 PHE cc_start: 0.6671 (t80) cc_final: 0.6463 (t80)
REVERT: D   40 TYR cc_start: 0.8887 (m-80) cc_final: 0.8673 (m-10)
REVERT: D  143 HIS cc_start: 0.7291 (t70) cc_final: 0.7038 (t70)
REVERT: D  221 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7084 (mm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1001
  time to fit residues: 20.3075
Evaluate side-chains
  133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  137 VAL
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
C 125 GLN
D 315 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.114309 restraints weight = 12735.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.117813 restraints weight = 9156.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.119125 restraints weight = 5898.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.119777 restraints weight = 5463.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.120560 restraints weight = 4823.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2653

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= 0.164
  Angle     :  0.586   9.447  13909  Z= 0.312
  Chirality :  0.043   0.159   1601
  Planarity :  0.003   0.037   1589
  Dihedral  : 20.443 135.718   1871
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.67 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.24), residues: 1107
  helix:  0.18 (0.29), residues: 317
  sheet: -1.09 (0.27), residues: 353
  loop : -1.59 (0.26), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 261 
 TYR   0.014   0.002   TYR B 211 
 PHE   0.010   0.001   PHE D 316 
 TRP   0.005   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (10120)
  covalent geometry    : angle       0.58552 (13903)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.91268 (    6)
  hydrogen bonds       : bond        0.03360 (  489)
  hydrogen bonds       : angle       5.66457 ( 1349)

*********************** 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
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.363 
Fit side-chains
REVERT: C   25 GLU cc_start: 0.7100 (pm20) cc_final: 0.6658 (pm20)
REVERT: C  135 CYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7511 (t)
REVERT: B   27 CYS cc_start: 0.7429 (t) cc_final: 0.7146 (p)
REVERT: B   68 MET cc_start: 0.7975 (mmt) cc_final: 0.7109 (mmt)
REVERT: B   86 ASP cc_start: 0.6897 (m-30) cc_final: 0.6661 (m-30)
REVERT: A   17 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7317 (mp0)
REVERT: A  244 MET cc_start: 0.8217 (tmm) cc_final: 0.7746 (ttm)
REVERT: D   40 TYR cc_start: 0.8889 (m-80) cc_final: 0.8350 (m-10)
REVERT: D  143 HIS cc_start: 0.7154 (t70) cc_final: 0.6804 (t70)
REVERT: D  221 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7126 (mm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1013
  time to fit residues: 20.3706
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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   94 ASP
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  135 CYS
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 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 64 optimal weight:    0.0980
   chunk 59 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
B 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.114501 restraints weight = 12648.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.118104 restraints weight = 8860.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.119573 restraints weight = 5743.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119854 restraints weight = 5322.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.121501 restraints weight = 4674.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2822

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= 0.161
  Angle     :  0.584   9.393  13909  Z= 0.309
  Chirality :  0.043   0.162   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.446 133.035   1871
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.43 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.24), residues: 1107
  helix:  0.39 (0.30), residues: 315
  sheet: -1.02 (0.27), residues: 348
  loop : -1.44 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 261 
 TYR   0.014   0.002   TYR B 211 
 PHE   0.009   0.001   PHE D 126 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10120)
  covalent geometry    : angle       0.58395 (13903)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       0.84991 (    6)
  hydrogen bonds       : bond        0.03266 (  489)
  hydrogen bonds       : angle       5.57532 ( 1349)

*********************** 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
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7100 (pm20) cc_final: 0.6643 (pm20)
REVERT: C  135 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7473 (t)
REVERT: B   27 CYS cc_start: 0.7427 (t) cc_final: 0.7165 (p)
REVERT: B   68 MET cc_start: 0.7901 (mmt) cc_final: 0.7116 (mmt)
REVERT: B   86 ASP cc_start: 0.6860 (m-30) cc_final: 0.6644 (m-30)
REVERT: A   17 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7399 (mp0)
REVERT: A  244 MET cc_start: 0.8165 (tmm) cc_final: 0.7774 (ttm)
REVERT: D   40 TYR cc_start: 0.8904 (m-80) cc_final: 0.8467 (m-10)
REVERT: D  143 HIS cc_start: 0.7142 (t70) cc_final: 0.6793 (t70)
REVERT: D  221 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7152 (mm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1030
  time to fit residues: 20.1380
Evaluate side-chains
  136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  229 MET
Chi-restraints excluded: chain B residue   40 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 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 72 optimal weight:    4.9990
   chunk 85 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 96 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.150347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.114833 restraints weight = 12670.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.118341 restraints weight = 8835.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.120634 restraints weight = 5796.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.120972 restraints weight = 5075.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121478 restraints weight = 4383.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10123  Z= 0.153
  Angle     :  0.580   9.370  13909  Z= 0.307
  Chirality :  0.043   0.193   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.434 130.385   1871
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.56 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.25), residues: 1107
  helix:  0.49 (0.30), residues: 315
  sheet: -0.98 (0.27), residues: 372
  loop : -1.33 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 261 
 TYR   0.013   0.001   TYR B 211 
 PHE   0.009   0.001   PHE D 126 
 TRP   0.005   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10120)
  covalent geometry    : angle       0.58011 (13903)
  SS BOND              : bond        0.00104 (    3)
  SS BOND              : angle       0.92621 (    6)
  hydrogen bonds       : bond        0.03177 (  489)
  hydrogen bonds       : angle       5.51622 ( 1349)

*********************** 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
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7150 (pm20) cc_final: 0.6674 (pm20)
REVERT: C  135 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7457 (t)
REVERT: B    3 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7272 (tp30)
REVERT: B   27 CYS cc_start: 0.7402 (t) cc_final: 0.7161 (p)
REVERT: B   86 ASP cc_start: 0.6876 (m-30) cc_final: 0.6646 (m-30)
REVERT: A    8 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7729 (pp30)
REVERT: A   17 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7381 (mp0)
REVERT: A  199 MET cc_start: 0.7014 (tpp) cc_final: 0.6676 (mmm)
REVERT: A  244 MET cc_start: 0.8159 (tmm) cc_final: 0.7796 (ttm)
REVERT: D   40 TYR cc_start: 0.8917 (m-80) cc_final: 0.8594 (m-10)
REVERT: D  143 HIS cc_start: 0.7148 (t70) cc_final: 0.6799 (t70)
REVERT: D  221 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7151 (mm-30)
  outliers start: 29
  outliers final: 19
  residues processed: 143
  average time/residue: 0.0942
  time to fit residues: 19.4772
Evaluate side-chains
  142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
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    3 GLU
Chi-restraints excluded: chain B residue   40 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 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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
A  38 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 112 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 = 0.3830 r_free = 0.3830 target = 0.148401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.112975 restraints weight = 12632.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116551 restraints weight = 9019.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117576 restraints weight = 5868.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118154 restraints weight = 5661.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.118885 restraints weight = 4828.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10123  Z= 0.195
  Angle     :  0.615   9.189  13909  Z= 0.322
  Chirality :  0.044   0.239   1601
  Planarity :  0.003   0.034   1589
  Dihedral  : 20.495 125.520   1871
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.98 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.25), residues: 1107
  helix:  0.50 (0.30), residues: 315
  sheet: -1.14 (0.27), residues: 352
  loop : -1.36 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 261 
 TYR   0.015   0.002   TYR B 211 
 PHE   0.010   0.001   PHE B   2 
 TRP   0.007   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10120)
  covalent geometry    : angle       0.61449 (13903)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       1.04610 (    6)
  hydrogen bonds       : bond        0.03300 (  489)
  hydrogen bonds       : angle       5.63022 ( 1349)

*********************** 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
  150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 GLU cc_start: 0.7201 (pm20) cc_final: 0.6677 (pm20)
REVERT: C  135 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7496 (t)
REVERT: B    3 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7287 (tp30)
REVERT: B   27 CYS cc_start: 0.7464 (t) cc_final: 0.7204 (p)
REVERT: B   86 ASP cc_start: 0.6937 (m-30) cc_final: 0.6714 (m-30)
REVERT: B  139 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7144 (ppp)
REVERT: A    8 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7851 (pp30)
REVERT: A   17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7418 (mp0)
REVERT: A  199 MET cc_start: 0.6876 (tpp) cc_final: 0.6506 (mmm)
REVERT: D   40 TYR cc_start: 0.8938 (m-80) cc_final: 0.8512 (m-10)
REVERT: D  143 HIS cc_start: 0.7248 (t70) cc_final: 0.6920 (t-90)
REVERT: D  221 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7207 (mm-30)
  outliers start: 29
  outliers final: 19
  residues processed: 138
  average time/residue: 0.0962
  time to fit residues: 19.2879
Evaluate side-chains
  143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue   94 ASP
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  135 CYS
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 88 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 112 optimal weight:    0.0470
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
C 108 GLN
D  48 GLN
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 253 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.151090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.115897 restraints weight = 12594.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.119408 restraints weight = 8790.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.121038 restraints weight = 5721.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.121486 restraints weight = 5243.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122051 restraints weight = 4599.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10123  Z= 0.135
  Angle     :  0.580   9.389  13909  Z= 0.306
  Chirality :  0.043   0.245   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.411 121.991   1871
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.25), residues: 1107
  helix:  0.63 (0.30), residues: 315
  sheet: -0.97 (0.27), residues: 372
  loop : -1.26 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 261 
 TYR   0.013   0.001   TYR B 211 
 PHE   0.010   0.001   PHE C 169 
 TRP   0.005   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10120)
  covalent geometry    : angle       0.57946 (13903)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       0.83256 (    6)
  hydrogen bonds       : bond        0.03047 (  489)
  hydrogen bonds       : angle       5.42969 ( 1349)

*********************** 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: 27
    poor density    : 122
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7507 (t)
REVERT: B    3 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7249 (tp30)
REVERT: B   27 CYS cc_start: 0.7396 (t) cc_final: 0.7137 (p)
REVERT: B   86 ASP cc_start: 0.6879 (m-30) cc_final: 0.6616 (m-30)
REVERT: B  139 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7038 (ppp)
REVERT: A    8 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (pt0)
REVERT: A   17 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7357 (mp0)
REVERT: D   40 TYR cc_start: 0.8941 (m-80) cc_final: 0.8625 (m-10)
REVERT: D   75 MET cc_start: 0.8418 (mmm) cc_final: 0.8139 (mmm)
REVERT: D  143 HIS cc_start: 0.7139 (t70) cc_final: 0.6885 (t70)
  outliers start: 27
  outliers final: 14
  residues processed: 138
  average time/residue: 0.0972
  time to fit residues: 19.2430
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
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  137 VAL
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   17 GLU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 VAL
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 28 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0030
   overall best weight:    0.6790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.149534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114092 restraints weight = 12594.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117587 restraints weight = 8900.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.118743 restraints weight = 5784.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.119029 restraints weight = 5554.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.122651 restraints weight = 4842.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10123  Z= 0.164
  Angle     :  0.604   9.262  13909  Z= 0.316
  Chirality :  0.044   0.300   1601
  Planarity :  0.003   0.032   1589
  Dihedral  : 20.393 117.492   1871
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.25), residues: 1107
  helix:  0.72 (0.30), residues: 315
  sheet: -1.00 (0.27), residues: 368
  loop : -1.23 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 320 
 TYR   0.014   0.002   TYR B 211 
 PHE   0.009   0.001   PHE D 126 
 TRP   0.007   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10120)
  covalent geometry    : angle       0.60358 (13903)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.92095 (    6)
  hydrogen bonds       : bond        0.03181 (  489)
  hydrogen bonds       : angle       5.50736 ( 1349)

*********************** 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
  142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7460 (t)
REVERT: C  244 MET cc_start: 0.7866 (mtt) cc_final: 0.7551 (mtt)
REVERT: B    3 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7250 (tp30)
REVERT: B   27 CYS cc_start: 0.7439 (t) cc_final: 0.7147 (p)
REVERT: B   86 ASP cc_start: 0.6847 (m-30) cc_final: 0.6602 (m-30)
REVERT: B  139 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6998 (ppp)
REVERT: A    8 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7913 (pt0)
REVERT: A   17 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7408 (mp0)
REVERT: D   40 TYR cc_start: 0.8949 (m-80) cc_final: 0.8549 (m-10)
REVERT: D  143 HIS cc_start: 0.7213 (t70) cc_final: 0.6961 (t70)
REVERT: D  276 HIS cc_start: 0.7902 (p-80) cc_final: 0.6786 (m90)
  outliers start: 25
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0929
  time to fit residues: 18.6879
Evaluate side-chains
  139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
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   94 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  137 VAL
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   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 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 0 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0050
   chunk 104 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.149590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114137 restraints weight = 12514.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117629 restraints weight = 8905.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119263 restraints weight = 5801.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.119644 restraints weight = 5343.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.120265 restraints weight = 4664.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10123  Z= 0.164
  Angle     :  0.609   9.240  13909  Z= 0.318
  Chirality :  0.044   0.325   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.376 116.006   1871
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.25), residues: 1107
  helix:  0.68 (0.30), residues: 316
  sheet: -0.98 (0.27), residues: 368
  loop : -1.25 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 320 
 TYR   0.015   0.002   TYR B 211 
 PHE   0.009   0.001   PHE C 169 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10120)
  covalent geometry    : angle       0.60881 (13903)
  SS BOND              : bond        0.00151 (    3)
  SS BOND              : angle       0.97061 (    6)
  hydrogen bonds       : bond        0.03163 (  489)
  hydrogen bonds       : angle       5.53304 ( 1349)

********************** 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
  142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: C  135 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7511 (t)
REVERT: C  244 MET cc_start: 0.8061 (mtt) cc_final: 0.7743 (mtt)
REVERT: B    3 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7288 (tp30)
REVERT: B   27 CYS cc_start: 0.7451 (t) cc_final: 0.7151 (p)
REVERT: B   86 ASP cc_start: 0.6872 (m-30) cc_final: 0.6632 (m-30)
REVERT: B  139 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6989 (ppp)
REVERT: A   17 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7420 (mp0)
REVERT: D   40 TYR cc_start: 0.8977 (m-80) cc_final: 0.8553 (m-10)
REVERT: D   75 MET cc_start: 0.8341 (mmm) cc_final: 0.8084 (mmm)
REVERT: D  276 HIS cc_start: 0.7901 (p-80) cc_final: 0.6805 (m90)
  outliers start: 25
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0961
  time to fit residues: 18.9844
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue   94 ASP
Chi-restraints excluded: chain C residue  135 CYS
Chi-restraints excluded: chain C residue  137 VAL
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   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  199 MET
Chi-restraints excluded: chain D residue  130 LEU
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 95 optimal weight:    0.8980
   chunk 110 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 74 optimal weight:    0.1980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** D 253 HIS ** 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 = 0.3852 r_free = 0.3852 target = 0.150482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.115281 restraints weight = 12575.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.118681 restraints weight = 8838.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.121182 restraints weight = 5801.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.121385 restraints weight = 5126.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122308 restraints weight = 4357.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10123  Z= 0.147
  Angle     :  0.609   9.297  13909  Z= 0.318
  Chirality :  0.044   0.307   1601
  Planarity :  0.003   0.033   1589
  Dihedral  : 20.348 114.178   1871
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.73 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.25), residues: 1107
  helix:  0.74 (0.30), residues: 316
  sheet: -0.90 (0.27), residues: 368
  loop : -1.19 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 320 
 TYR   0.015   0.001   TYR B 211 
 PHE   0.010   0.001   PHE C 169 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10120)
  covalent geometry    : angle       0.60856 (13903)
  SS BOND              : bond        0.00139 (    3)
  SS BOND              : angle       0.93279 (    6)
  hydrogen bonds       : bond        0.03126 (  489)
  hydrogen bonds       : angle       5.47688 ( 1349)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.20 seconds
wall clock time: 28 minutes 18.47 seconds (1698.47 seconds total)