Starting phenix.real_space_refine
on Sun May  3 06:48:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11nl_75864/05_2026/11nl_75864.map"
  }
  resolution = 2.41
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    2725      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11217
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 188
          Classifications: {'water': 188}
          Link IDs: {None: 187}
    Chain: "B"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 204
          Classifications: {'water': 204}
          Link IDs: {None: 203}
    Chain: "C"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 171
          Classifications: {'water': 171}
          Link IDs: {None: 170}
    Chain: "D"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 182
          Classifications: {'water': 182}
          Link IDs: {None: 181}
  Time building chain proxies: 2.85, per 1000 atoms: 0.25
  Number of scatterers: 11217
  At special positions: 0
  Unit cell: (98.49, 80.115, 107.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    2725      8.00
     N    1860      7.00
     C    6588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 552.3 milliseconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 8 sheets defined
      53.5% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 4.193A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.931A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 141
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 3.545A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 306 through 314
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 338
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 45
      removed outlier: 3.841A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.884A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 141
    Processing helix  chain 'B' and resid 159 through 180
      removed outlier: 3.551A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 260
      removed outlier: 3.511A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 306 through 314
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 338
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 45
      removed outlier: 4.054A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ARG C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.822A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 159 through 179
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 260
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 306 through 314
    Processing helix  chain 'C' and resid 319 through 338
    Processing helix  chain 'D' and resid 8 through 23
      removed outlier: 3.508A  pdb=" N   VAL D  23 " --> pdb=" O   ALA D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 4.168A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 81 through 85
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
      removed outlier: 3.544A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 260
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 306 through 314
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.863A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL A 267 " --> pdb=" O   THR A 298 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   SER A 300 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   PHE A 269 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.800A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.217A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.645A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 5.704A  pdb=" N   GLY C  28 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY C  75 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE C 144 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.845A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.618A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ALA D 145 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   GLU D 187 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLU D 189 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   CYS D 149 " --> pdb=" O   GLU D 189 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   LEU D 191 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   LEU D 151 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    551 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.69

  Time building geometry restraints manager: 1.22 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: 2182
        1.33 -     1.45: 2269
        1.45 -     1.57: 6164
        1.57 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" N   ILE C  46 "
       pdb=" CA  ILE C  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.045 1.08e-02 8.57e+03 1.77e+01
  bond pdb=" N   HIS D 156 "
       pdb=" CA  HIS D 156 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.06e-02 8.90e+03 1.31e+01
  bond pdb=" N   LEU D 320 "
       pdb=" CA  LEU D 320 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.16e-02 7.43e+03 1.12e+01
  bond pdb=" N   VAL A 264 "
       pdb=" CA  VAL A 264 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.042 1.27e-02 6.20e+03 1.09e+01
  bond pdb=" N   PRO A 230 "
       pdb=" CA  PRO A 230 "
    ideal  model  delta    sigma   weight residual
    1.464  1.434  0.030 9.30e-03 1.16e+04 1.04e+01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 13476
        1.42 -     2.85: 835
        2.85 -     4.27: 114
        4.27 -     5.70: 29
        5.70 -     7.12: 10
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" CA  PHE D 144 "
        pdb=" CB  PHE D 144 "
        pdb=" CG  PHE D 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.17   -4.37 1.00e+00 1.00e+00 1.91e+01
  angle pdb=" CA  PRO A 192 "
        pdb=" N   PRO A 192 "
        pdb=" CD  PRO A 192 "
      ideal   model   delta    sigma   weight residual
     112.00  106.24    5.76 1.40e+00 5.10e-01 1.69e+01
  angle pdb=" CA  PHE A 144 "
        pdb=" CB  PHE A 144 "
        pdb=" CG  PHE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  117.81   -4.01 1.00e+00 1.00e+00 1.61e+01
  angle pdb=" CA  VAL B 208 "
        pdb=" C   VAL B 208 "
        pdb=" O   VAL B 208 "
      ideal   model   delta    sigma   weight residual
     121.17  117.05    4.12 1.06e+00 8.90e-01 1.51e+01
  angle pdb=" CA  PRO A 188 "
        pdb=" N   PRO A 188 "
        pdb=" CD  PRO A 188 "
      ideal   model   delta    sigma   weight residual
     112.00  106.59    5.41 1.40e+00 5.10e-01 1.49e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 6053
       17.71 -    35.42: 342
       35.42 -    53.13: 69
       53.13 -    70.84: 26
       70.84 -    88.55: 14
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  PHE B 299 "
           pdb=" C   PHE B 299 "
           pdb=" N   SER B 300 "
           pdb=" CA  SER B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.37   16.63     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  GLU D 121 "
           pdb=" CG  GLU D 121 "
           pdb=" CD  GLU D 121 "
           pdb=" OE1 GLU D 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.55  -88.55     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CG  ARG C 200 "
           pdb=" CD  ARG C 200 "
           pdb=" NE  ARG C 200 "
           pdb=" CZ  ARG C 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.98  -43.98     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1202
       0.048 -    0.095: 337
       0.095 -    0.142: 88
       0.142 -    0.190: 15
       0.190 -    0.237: 2
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  LEU C  61 "
            pdb=" N   LEU C  61 "
            pdb=" C   LEU C  61 "
            pdb=" CB  LEU C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  PHE A 144 "
            pdb=" N   PHE A 144 "
            pdb=" C   PHE A 144 "
            pdb=" CB  PHE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-01
  chirality pdb=" CA  PHE D 144 "
            pdb=" N   PHE D 144 "
            pdb=" C   PHE D 144 "
            pdb=" CB  PHE D 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 260 "   -0.021 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        pdb=" C   VAL C 260 "    0.071 2.00e-02 2.50e+03
        pdb=" O   VAL C 260 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PRO C 261 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 260 "    0.019 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   VAL A 260 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   VAL A 260 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PRO A 261 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 187 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO C 188 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 188 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 188 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2108
        2.77 -     3.30: 11171
        3.30 -     3.83: 21054
        3.83 -     4.37: 26324
        4.37 -     4.90: 41596
  Nonbonded interactions: 102253
  Sorted by model distance:
  nonbonded pdb=" O   GLN D  60 "
            pdb=" OG1 THR D  64 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   GLN C  60 "
            pdb=" OG1 THR C  64 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   ALA D  32 "
            pdb=" O   HOH D 401 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR B  84 "
            pdb=" OD2 ASP B 140 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   PRO D   5 "
            pdb=" O   HOH D 402 "
     model   vdw
     2.313 3.040
  ... (remaining 102248 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.300
  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:9.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
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      :  0.006   0.068  10672  Z= 0.324
  Angle     :  0.774   7.123  14464  Z= 0.475
  Chirality :  0.048   0.237   1644
  Planarity :  0.007   0.058   1880
  Dihedral  : 12.900  88.547   3984
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  0.36 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.53 (0.23), residues: 1364
  helix:  1.27 (0.19), residues: 708
  sheet: -1.22 (0.34), residues: 220
  loop : -0.10 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG B  21 
 TYR   0.021   0.002   TYR D 213 
 PHE   0.022   0.002   PHE D 144 
 TRP   0.037   0.005   TRP A 147 
 HIS   0.011   0.002   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 (10672)
  covalent geometry    : angle       0.77353 (14464)
  hydrogen bonds       : bond        0.14397 (  551)
  hydrogen bonds       : angle       5.81526 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6869 (mtp180) cc_final: 0.6297 (mmp80)
REVERT: A   95 GLN cc_start: 0.7409 (tt0) cc_final: 0.7131 (tp40)
REVERT: A  152 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7764 (pttm)
REVERT: A  199 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7719 (mmtm)
REVERT: A  303 ARG cc_start: 0.6839 (ttp80) cc_final: 0.6461 (mtm180)
REVERT: A  317 LYS cc_start: 0.7305 (mttm) cc_final: 0.7083 (mtpp)
REVERT: A  339 GLN cc_start: 0.8281 (mt0) cc_final: 0.8015 (mt0)
REVERT: B  152 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7640 (ptmm)
REVERT: B  199 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7784 (mmpt)
REVERT: B  242 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6812 (mmtt)
REVERT: B  303 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6824 (mmm160)
REVERT: C   41 LYS cc_start: 0.7407 (mmtm) cc_final: 0.6781 (mmmm)
REVERT: C   42 ARG cc_start: 0.6441 (mtp180) cc_final: 0.5917 (mmm160)
REVERT: C  193 ASP cc_start: 0.7568 (m-30) cc_final: 0.7353 (m-30)
REVERT: C  237 HIS cc_start: 0.7433 (t70) cc_final: 0.6990 (m-70)
REVERT: C  242 LYS cc_start: 0.7630 (mttm) cc_final: 0.7109 (tmtt)
REVERT: C  295 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7541 (m-90)
REVERT: C  303 ARG cc_start: 0.6762 (mtm-85) cc_final: 0.6079 (ttt-90)
REVERT: C  341 LYS cc_start: 0.7631 (mttt) cc_final: 0.7362 (mtmm)
REVERT: D   95 GLN cc_start: 0.7865 (tt0) cc_final: 0.7585 (tt0)
REVERT: D  199 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7684 (mttm)
REVERT: D  234 THR cc_start: 0.7307 (m) cc_final: 0.7100 (p)
REVERT: D  303 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.6551 (mtp85)
REVERT: D  311 LYS cc_start: 0.8172 (tttt) cc_final: 0.7958 (ttpp)
REVERT: D  341 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7850 (mmpt)
  outliers start: 13
  outliers final: 5
  residues processed: 204
  average time/residue: 0.8629
  time to fit residues: 185.1904
Evaluate side-chains
  102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  320 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 324 GLN
A 334 ASN
** B   2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS
B  54 ASN
B  95 GLN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
C 168 ASN
C 219 HIS
C 319 ASN
D 231 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.127232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.096972 restraints weight = 11698.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.60
r_work: 0.2995 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10672  Z= 0.192
  Angle     :  0.635   8.518  14464  Z= 0.334
  Chirality :  0.046   0.155   1644
  Planarity :  0.006   0.052   1880
  Dihedral  :  5.602  57.641   1484
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  7.82 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.29 (0.22), residues: 1364
  helix:  2.06 (0.19), residues: 704
  sheet: -1.33 (0.39), residues: 144
  loop : -0.09 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  21 
 TYR   0.035   0.003   TYR C 213 
 PHE   0.018   0.003   PHE B 144 
 TRP   0.023   0.003   TRP A 313 
 HIS   0.008   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (10672)
  covalent geometry    : angle       0.63530 (14464)
  hydrogen bonds       : bond        0.06030 (  551)
  hydrogen bonds       : angle       4.17867 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6350 (mmp80)
REVERT: A   52 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7194 (tt0)
REVERT: A   86 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7354 (mttm)
REVERT: A   95 GLN cc_start: 0.7605 (tt0) cc_final: 0.7140 (tp-100)
REVERT: A  152 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7735 (pttp)
REVERT: A  199 LYS cc_start: 0.8166 (ptmt) cc_final: 0.7492 (mmtm)
REVERT: A  303 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6521 (mtm180)
REVERT: A  317 LYS cc_start: 0.7369 (mttm) cc_final: 0.6890 (tptm)
REVERT: B  107 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8627 (ttmm)
REVERT: B  132 GLU cc_start: 0.8230 (mp0) cc_final: 0.8013 (mp0)
REVERT: B  152 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7715 (ptmm)
REVERT: B  199 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7742 (mmpt)
REVERT: B  242 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6901 (mmtt)
REVERT: B  311 LYS cc_start: 0.7236 (tttm) cc_final: 0.6589 (tmmt)
REVERT: C   42 ARG cc_start: 0.6665 (mtp180) cc_final: 0.5916 (mmp-170)
REVERT: C  155 GLU cc_start: 0.6993 (pm20) cc_final: 0.6762 (pt0)
REVERT: C  193 ASP cc_start: 0.7977 (m-30) cc_final: 0.7659 (m-30)
REVERT: C  237 HIS cc_start: 0.7475 (t70) cc_final: 0.7211 (m-70)
REVERT: C  242 LYS cc_start: 0.7766 (mttm) cc_final: 0.7219 (tmtt)
REVERT: C  247 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: C  295 TRP cc_start: 0.9040 (OUTLIER) cc_final: 0.7369 (m-90)
REVERT: C  303 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6398 (ttt-90)
REVERT: C  341 LYS cc_start: 0.8106 (mttt) cc_final: 0.7870 (mtmm)
REVERT: D   52 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6668 (tp30)
REVERT: D   95 GLN cc_start: 0.8097 (tt0) cc_final: 0.7789 (tt0)
REVERT: D  152 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7914 (pttp)
REVERT: D  199 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7746 (mttm)
REVERT: D  234 THR cc_start: 0.8047 (m) cc_final: 0.7835 (p)
REVERT: D  303 ARG cc_start: 0.7672 (ttt-90) cc_final: 0.7005 (mtp180)
REVERT: D  341 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7997 (mmpt)
  outliers start: 27
  outliers final: 11
  residues processed: 125
  average time/residue: 0.8876
  time to fit residues: 116.9850
Evaluate side-chains
  96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  152 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   chunk 97 optimal weight:    0.3980
   chunk 123 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
A 339 GLN
B   2 HIS
B  95 GLN
B 306 GLN
D 287 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.129732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.100494 restraints weight = 11888.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.54
r_work: 0.3050 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10672  Z= 0.107
  Angle     :  0.471   8.208  14464  Z= 0.247
  Chirality :  0.039   0.142   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.085  59.664   1482
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  8.72 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.68 (0.23), residues: 1364
  helix:  2.49 (0.19), residues: 712
  sheet: -1.64 (0.37), residues: 164
  loop :  0.12 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.015   0.002   TYR C 213 
 PHE   0.013   0.001   PHE B 144 
 TRP   0.013   0.002   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10672)
  covalent geometry    : angle       0.47065 (14464)
  hydrogen bonds       : bond        0.04460 (  551)
  hydrogen bonds       : angle       3.87724 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8399 (t) cc_final: 0.7891 (m)
REVERT: A   42 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6356 (mmp80)
REVERT: A   44 GLN cc_start: 0.6134 (mm110) cc_final: 0.5784 (tm-30)
REVERT: A   52 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7256 (tt0)
REVERT: A   86 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7400 (mttt)
REVERT: A   95 GLN cc_start: 0.7606 (tt0) cc_final: 0.7110 (tp-100)
REVERT: A  152 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7662 (pttp)
REVERT: A  199 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7517 (mmpt)
REVERT: A  303 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6519 (mtm180)
REVERT: A  317 LYS cc_start: 0.7323 (mttm) cc_final: 0.6840 (tptm)
REVERT: B   34 GLU cc_start: 0.7048 (mp0) cc_final: 0.6719 (mt-10)
REVERT: B  107 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8561 (ttmm)
REVERT: B  152 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7633 (ptmm)
REVERT: B  199 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7597 (mmpt)
REVERT: B  242 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6974 (mmtt)
REVERT: B  311 LYS cc_start: 0.7216 (tttm) cc_final: 0.6607 (tmmt)
REVERT: C   42 ARG cc_start: 0.6792 (mtp180) cc_final: 0.6050 (mmm160)
REVERT: C  193 ASP cc_start: 0.7920 (m-30) cc_final: 0.7587 (m-30)
REVERT: C  237 HIS cc_start: 0.7466 (t70) cc_final: 0.7240 (m-70)
REVERT: C  242 LYS cc_start: 0.7737 (mttm) cc_final: 0.7230 (tmtt)
REVERT: C  247 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: C  295 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.6894 (m-90)
REVERT: C  303 ARG cc_start: 0.7008 (mtm-85) cc_final: 0.6305 (ttt-90)
REVERT: C  341 LYS cc_start: 0.8052 (mttt) cc_final: 0.7750 (mtmm)
REVERT: D   95 GLN cc_start: 0.8124 (tt0) cc_final: 0.7820 (tt0)
REVERT: D  199 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7668 (mttm)
REVERT: D  303 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.6933 (mtp180)
REVERT: D  341 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8046 (mmpt)
  outliers start: 23
  outliers final: 8
  residues processed: 112
  average time/residue: 0.8723
  time to fit residues: 103.1016
Evaluate side-chains
  98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0050
   chunk 28 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 319 ASN
B  54 ASN
B  95 GLN
C  85 GLN
D 166 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.128584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.099238 restraints weight = 11859.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.54
r_work: 0.3031 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10672  Z= 0.110
  Angle     :  0.471   5.176  14464  Z= 0.247
  Chirality :  0.039   0.141   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  4.952  58.311   1482
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  :  8.63 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.83 (0.23), residues: 1364
  helix:  2.66 (0.19), residues: 712
  sheet: -1.57 (0.36), residues: 184
  loop :  0.19 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 258 
 TYR   0.019   0.001   TYR C 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.014   0.002   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10672)
  covalent geometry    : angle       0.47143 (14464)
  hydrogen bonds       : bond        0.04429 (  551)
  hydrogen bonds       : angle       3.75608 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 0.447 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6484 (mmp80)
REVERT: A   44 GLN cc_start: 0.6244 (mm110) cc_final: 0.5956 (tm-30)
REVERT: A   52 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7265 (tt0)
REVERT: A   66 ASP cc_start: 0.7595 (t70) cc_final: 0.7269 (t0)
REVERT: A   86 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7375 (mttm)
REVERT: A   95 GLN cc_start: 0.7653 (tt0) cc_final: 0.7139 (tp-100)
REVERT: A  152 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7716 (pttp)
REVERT: A  199 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7571 (mmpt)
REVERT: A  303 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6566 (mtm180)
REVERT: A  317 LYS cc_start: 0.7354 (mttm) cc_final: 0.6820 (tptm)
REVERT: B   34 GLU cc_start: 0.7088 (mp0) cc_final: 0.6770 (mt-10)
REVERT: B  107 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8533 (ttmm)
REVERT: B  152 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7675 (ptmm)
REVERT: B  199 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7638 (mmtm)
REVERT: B  242 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7081 (mmtt)
REVERT: B  311 LYS cc_start: 0.7287 (tttm) cc_final: 0.6668 (tmmt)
REVERT: B  318 GLU cc_start: 0.7383 (mp0) cc_final: 0.7153 (pm20)
REVERT: B  343 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8111 (p)
REVERT: C   42 ARG cc_start: 0.6825 (mtp180) cc_final: 0.6043 (mmm160)
REVERT: C   60 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7383 (tt0)
REVERT: C   63 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8165 (mp)
REVERT: C  193 ASP cc_start: 0.7968 (m-30) cc_final: 0.7643 (m-30)
REVERT: C  237 HIS cc_start: 0.7510 (t70) cc_final: 0.7273 (m-70)
REVERT: C  242 LYS cc_start: 0.7755 (mttm) cc_final: 0.7268 (tmtt)
REVERT: C  247 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: C  295 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.6810 (m-90)
REVERT: C  303 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6411 (ttt-90)
REVERT: C  341 LYS cc_start: 0.8071 (mttt) cc_final: 0.7732 (mtmm)
REVERT: D   52 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6693 (tp30)
REVERT: D   95 GLN cc_start: 0.8130 (tt0) cc_final: 0.7849 (tt0)
REVERT: D  107 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8789 (ttmm)
REVERT: D  199 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7701 (mttm)
REVERT: D  303 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.6976 (mtp180)
REVERT: D  341 LYS cc_start: 0.8282 (mmtt) cc_final: 0.8039 (mmpt)
  outliers start: 31
  outliers final: 10
  residues processed: 117
  average time/residue: 0.9181
  time to fit residues: 113.1520
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 127 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
C 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.095731 restraints weight = 11789.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.59
r_work: 0.2981 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10672  Z= 0.145
  Angle     :  0.513   5.776  14464  Z= 0.270
  Chirality :  0.041   0.155   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.063  55.957   1480
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  :  8.72 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.73 (0.23), residues: 1364
  helix:  2.63 (0.19), residues: 704
  sheet: -1.63 (0.36), residues: 184
  loop :  0.10 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 258 
 TYR   0.024   0.002   TYR D 213 
 PHE   0.017   0.002   PHE B 144 
 TRP   0.016   0.002   TRP B 147 
 HIS   0.005   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10672)
  covalent geometry    : angle       0.51346 (14464)
  hydrogen bonds       : bond        0.05311 (  551)
  hydrogen bonds       : angle       3.88311 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 SER cc_start: 0.8379 (t) cc_final: 0.7930 (m)
REVERT: A   42 ARG cc_start: 0.6944 (mtp180) cc_final: 0.6466 (mmp80)
REVERT: A   44 GLN cc_start: 0.6435 (mm110) cc_final: 0.6234 (tm-30)
REVERT: A   52 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7275 (tt0)
REVERT: A   66 ASP cc_start: 0.7616 (t70) cc_final: 0.7297 (t0)
REVERT: A   86 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7359 (mttm)
REVERT: A   95 GLN cc_start: 0.7689 (tt0) cc_final: 0.7141 (tp-100)
REVERT: A  152 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7688 (pttp)
REVERT: A  173 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7542 (t80)
REVERT: A  199 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7510 (mmtm)
REVERT: A  303 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6513 (mtm180)
REVERT: A  317 LYS cc_start: 0.7482 (mttm) cc_final: 0.7074 (mtpp)
REVERT: A  318 GLU cc_start: 0.7001 (mp0) cc_final: 0.6354 (mp0)
REVERT: B   34 GLU cc_start: 0.7122 (mp0) cc_final: 0.6741 (mt-10)
REVERT: B   45 SER cc_start: 0.8023 (p) cc_final: 0.7782 (m)
REVERT: B  107 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8615 (ttmm)
REVERT: B  152 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7620 (ptmm)
REVERT: B  199 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7654 (mmtm)
REVERT: B  242 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7071 (mmtt)
REVERT: B  311 LYS cc_start: 0.7438 (tttm) cc_final: 0.6846 (tmmt)
REVERT: B  317 LYS cc_start: 0.7053 (mmtt) cc_final: 0.6675 (mttp)
REVERT: B  343 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8086 (p)
REVERT: C   42 ARG cc_start: 0.6879 (mtp180) cc_final: 0.5966 (mmm160)
REVERT: C   60 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7439 (tt0)
REVERT: C   63 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: C  193 ASP cc_start: 0.8001 (m-30) cc_final: 0.7666 (m-30)
REVERT: C  237 HIS cc_start: 0.7569 (t70) cc_final: 0.7314 (m-70)
REVERT: C  242 LYS cc_start: 0.7805 (mttm) cc_final: 0.7268 (tmtt)
REVERT: C  247 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7984 (mt-10)
REVERT: C  303 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.6483 (tmt-80)
REVERT: C  341 LYS cc_start: 0.8087 (mttt) cc_final: 0.7817 (mtmm)
REVERT: D   52 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6645 (tp30)
REVERT: D   95 GLN cc_start: 0.8100 (tt0) cc_final: 0.7813 (tt0)
REVERT: D  107 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8755 (ttmm)
REVERT: D  199 LYS cc_start: 0.8320 (mmpt) cc_final: 0.7728 (mttt)
REVERT: D  288 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8227 (mtmm)
REVERT: D  303 ARG cc_start: 0.7548 (ttt-90) cc_final: 0.7048 (mtp180)
  outliers start: 35
  outliers final: 15
  residues processed: 124
  average time/residue: 0.8924
  time to fit residues: 116.8447
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 126 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.127732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.098094 restraints weight = 11809.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.55
r_work: 0.3017 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10672  Z= 0.110
  Angle     :  0.463   5.402  14464  Z= 0.242
  Chirality :  0.039   0.138   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  4.873  56.684   1480
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.53 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.84 (0.23), residues: 1364
  helix:  2.71 (0.19), residues: 712
  sheet: -1.62 (0.36), residues: 184
  loop :  0.16 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.017   0.001   TYR C 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.013   0.001   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10672)
  covalent geometry    : angle       0.46279 (14464)
  hydrogen bonds       : bond        0.04397 (  551)
  hydrogen bonds       : angle       3.76473 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 SER cc_start: 0.8413 (t) cc_final: 0.7964 (m)
REVERT: A   42 ARG cc_start: 0.6945 (mtp180) cc_final: 0.6531 (mmp80)
REVERT: A   66 ASP cc_start: 0.7578 (t70) cc_final: 0.7251 (t0)
REVERT: A   86 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7344 (mttm)
REVERT: A   95 GLN cc_start: 0.7685 (tt0) cc_final: 0.7107 (tp-100)
REVERT: A  152 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7701 (pttp)
REVERT: A  173 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.7545 (t80)
REVERT: A  199 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7551 (mmpt)
REVERT: A  303 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6454 (mtm180)
REVERT: A  317 LYS cc_start: 0.7344 (mttm) cc_final: 0.6664 (tptm)
REVERT: A  318 GLU cc_start: 0.7016 (mp0) cc_final: 0.6514 (mp0)
REVERT: B   34 GLU cc_start: 0.7091 (mp0) cc_final: 0.6760 (mt-10)
REVERT: B   45 SER cc_start: 0.8000 (p) cc_final: 0.7744 (m)
REVERT: B  107 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8544 (ttmm)
REVERT: B  152 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7642 (ptmm)
REVERT: B  199 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7591 (mmtm)
REVERT: B  242 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7104 (mmtt)
REVERT: B  311 LYS cc_start: 0.7429 (tttm) cc_final: 0.6801 (tmmt)
REVERT: B  317 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6736 (mttp)
REVERT: B  343 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8092 (p)
REVERT: C   42 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6049 (mmm160)
REVERT: C   60 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7453 (tt0)
REVERT: C   63 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8203 (mp)
REVERT: C  193 ASP cc_start: 0.7977 (m-30) cc_final: 0.7673 (m-30)
REVERT: C  237 HIS cc_start: 0.7556 (t70) cc_final: 0.7304 (m-70)
REVERT: C  242 LYS cc_start: 0.7814 (mttm) cc_final: 0.7294 (tmtt)
REVERT: C  247 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7955 (mt-10)
REVERT: C  303 ARG cc_start: 0.7273 (mtm-85) cc_final: 0.6527 (ttt-90)
REVERT: C  341 LYS cc_start: 0.8130 (mttt) cc_final: 0.7781 (mtmm)
REVERT: D   52 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6664 (tp30)
REVERT: D   95 GLN cc_start: 0.8113 (tt0) cc_final: 0.7850 (tt0)
REVERT: D  107 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8773 (ttmm)
REVERT: D  199 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7703 (mttt)
REVERT: D  303 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.6996 (mtp180)
  outliers start: 28
  outliers final: 15
  residues processed: 109
  average time/residue: 0.9533
  time to fit residues: 109.5699
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 99 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 135 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.133270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.107317 restraints weight = 12358.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.38
r_work: 0.3202 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10672  Z= 0.109
  Angle     :  0.462   5.991  14464  Z= 0.241
  Chirality :  0.039   0.139   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  4.833  56.135   1480
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.16 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.91 (0.23), residues: 1364
  helix:  2.78 (0.19), residues: 712
  sheet: -1.59 (0.36), residues: 184
  loop :  0.17 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.019   0.001   TYR C 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.013   0.002   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10672)
  covalent geometry    : angle       0.46244 (14464)
  hydrogen bonds       : bond        0.04419 (  551)
  hydrogen bonds       : angle       3.69960 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 SER cc_start: 0.8427 (t) cc_final: 0.8050 (m)
REVERT: A   42 ARG cc_start: 0.6869 (mtp180) cc_final: 0.6417 (mmp80)
REVERT: A   66 ASP cc_start: 0.7514 (t70) cc_final: 0.7184 (t0)
REVERT: A   86 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7397 (mttm)
REVERT: A   95 GLN cc_start: 0.7682 (tt0) cc_final: 0.7110 (tp-100)
REVERT: A  152 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7696 (pttp)
REVERT: A  173 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: A  199 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7519 (mmpt)
REVERT: A  303 ARG cc_start: 0.7155 (ttp80) cc_final: 0.6482 (mtm180)
REVERT: A  317 LYS cc_start: 0.7331 (mttm) cc_final: 0.7094 (mtpm)
REVERT: A  318 GLU cc_start: 0.7099 (mp0) cc_final: 0.6516 (mp0)
REVERT: B   34 GLU cc_start: 0.7058 (mp0) cc_final: 0.6802 (mt-10)
REVERT: B   45 SER cc_start: 0.8042 (p) cc_final: 0.7761 (m)
REVERT: B  107 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (ttmm)
REVERT: B  152 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7620 (ptmm)
REVERT: B  199 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7624 (mmtm)
REVERT: B  242 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7174 (mmtt)
REVERT: B  311 LYS cc_start: 0.7411 (tttm) cc_final: 0.6786 (tmmt)
REVERT: B  317 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6896 (mttp)
REVERT: B  343 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8115 (p)
REVERT: C   42 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6123 (mmm160)
REVERT: C   60 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7389 (tt0)
REVERT: C  193 ASP cc_start: 0.7949 (m-30) cc_final: 0.7651 (m-30)
REVERT: C  242 LYS cc_start: 0.7883 (mttm) cc_final: 0.7405 (tmtt)
REVERT: C  247 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7892 (mt-10)
REVERT: C  303 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6571 (tmt-80)
REVERT: C  341 LYS cc_start: 0.8081 (mttt) cc_final: 0.7823 (mtmm)
REVERT: D   52 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6698 (tp30)
REVERT: D  107 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (ttmm)
REVERT: D  199 LYS cc_start: 0.8238 (mmpt) cc_final: 0.7692 (mttt)
REVERT: D  303 ARG cc_start: 0.7331 (ttt-90) cc_final: 0.6974 (mtp180)
  outliers start: 26
  outliers final: 16
  residues processed: 110
  average time/residue: 0.9370
  time to fit residues: 108.6236
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   52 GLU
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 114 optimal weight:    0.3980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.128726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.099829 restraints weight = 11817.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.55
r_work: 0.3051 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10672  Z= 0.101
  Angle     :  0.448   6.457  14464  Z= 0.232
  Chirality :  0.039   0.132   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  4.759  56.532   1480
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.25 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  2.00 (0.23), residues: 1364
  helix:  2.85 (0.19), residues: 712
  sheet: -1.58 (0.36), residues: 184
  loop :  0.23 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.016   0.001   TYR A 213 
 PHE   0.014   0.001   PHE B 144 
 TRP   0.011   0.001   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10672)
  covalent geometry    : angle       0.44787 (14464)
  hydrogen bonds       : bond        0.04125 (  551)
  hydrogen bonds       : angle       3.66680 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 SER cc_start: 0.8432 (t) cc_final: 0.8060 (m)
REVERT: A   42 ARG cc_start: 0.6898 (mtp180) cc_final: 0.6437 (mmp80)
REVERT: A   66 ASP cc_start: 0.7538 (t70) cc_final: 0.7185 (t0)
REVERT: A   86 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7549 (mtpp)
REVERT: A   95 GLN cc_start: 0.7727 (tt0) cc_final: 0.7140 (tp-100)
REVERT: A  152 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7724 (pttp)
REVERT: A  155 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6281 (pm20)
REVERT: A  173 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7535 (t80)
REVERT: A  199 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7574 (mmpt)
REVERT: A  303 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6480 (mtm180)
REVERT: A  317 LYS cc_start: 0.7313 (mttm) cc_final: 0.6636 (tptm)
REVERT: A  318 GLU cc_start: 0.7154 (mp0) cc_final: 0.6615 (mp0)
REVERT: B   34 GLU cc_start: 0.7101 (mp0) cc_final: 0.6801 (mt-10)
REVERT: B   45 SER cc_start: 0.8096 (p) cc_final: 0.7806 (m)
REVERT: B  107 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8476 (ttmm)
REVERT: B  152 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7661 (ptmm)
REVERT: B  199 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7604 (mmtm)
REVERT: B  242 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7068 (mmtt)
REVERT: B  311 LYS cc_start: 0.7478 (tttm) cc_final: 0.6824 (tmmt)
REVERT: B  317 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6856 (mttp)
REVERT: C   42 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6133 (mmm160)
REVERT: C   60 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7434 (tt0)
REVERT: C  193 ASP cc_start: 0.7970 (m-30) cc_final: 0.7644 (m-30)
REVERT: C  242 LYS cc_start: 0.7920 (mttm) cc_final: 0.7383 (tmtt)
REVERT: C  247 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: C  303 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6540 (tmt-80)
REVERT: C  341 LYS cc_start: 0.8100 (mttt) cc_final: 0.7804 (mtmm)
REVERT: D   95 GLN cc_start: 0.8306 (tt0) cc_final: 0.8089 (tt0)
REVERT: D  107 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8743 (ttmm)
REVERT: D  199 LYS cc_start: 0.8320 (mmpt) cc_final: 0.7759 (mttm)
REVERT: D  303 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.6961 (mtp180)
  outliers start: 26
  outliers final: 15
  residues processed: 114
  average time/residue: 0.9251
  time to fit residues: 111.3055
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  107 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue  107 LYS
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 104 optimal weight:    0.0470
   chunk 58 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0170
   chunk 72 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
C 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.101307 restraints weight = 11663.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.51
r_work: 0.3060 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10672  Z= 0.089
  Angle     :  0.428   6.815  14464  Z= 0.221
  Chirality :  0.038   0.122   1644
  Planarity :  0.003   0.033   1880
  Dihedral  :  4.620  57.006   1480
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.79 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  2.14 (0.24), residues: 1364
  helix:  2.96 (0.19), residues: 712
  sheet: -1.52 (0.37), residues: 184
  loop :  0.30 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 258 
 TYR   0.013   0.001   TYR C 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.010   0.001   TRP D 147 
 HIS   0.002   0.000   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (10672)
  covalent geometry    : angle       0.42809 (14464)
  hydrogen bonds       : bond        0.03684 (  551)
  hydrogen bonds       : angle       3.54804 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 SER cc_start: 0.8481 (t) cc_final: 0.8084 (m)
REVERT: A   42 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6344 (mmp80)
REVERT: A   66 ASP cc_start: 0.7490 (t70) cc_final: 0.7145 (t0)
REVERT: A   86 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7555 (mtpp)
REVERT: A   95 GLN cc_start: 0.7685 (tt0) cc_final: 0.7086 (tp-100)
REVERT: A  152 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7711 (pttp)
REVERT: A  199 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7559 (mmpt)
REVERT: A  303 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6504 (mtm180)
REVERT: A  317 LYS cc_start: 0.7245 (mttm) cc_final: 0.7041 (mtpm)
REVERT: A  318 GLU cc_start: 0.7140 (mp0) cc_final: 0.6420 (mp0)
REVERT: B   34 GLU cc_start: 0.7028 (mp0) cc_final: 0.6771 (mt-10)
REVERT: B   45 SER cc_start: 0.8040 (p) cc_final: 0.7704 (m)
REVERT: B  152 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7619 (ptmm)
REVERT: B  199 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7537 (mmtm)
REVERT: B  242 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7101 (mmtt)
REVERT: B  311 LYS cc_start: 0.7391 (tttm) cc_final: 0.6717 (tmmt)
REVERT: B  317 LYS cc_start: 0.7136 (mmtt) cc_final: 0.6849 (mttp)
REVERT: C   42 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6142 (mmm160)
REVERT: C   60 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7463 (tt0)
REVERT: C  193 ASP cc_start: 0.7971 (m-30) cc_final: 0.7636 (m-30)
REVERT: C  242 LYS cc_start: 0.7928 (mttm) cc_final: 0.7419 (tmtt)
REVERT: C  247 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7950 (mt-10)
REVERT: C  303 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6560 (ttt-90)
REVERT: C  311 LYS cc_start: 0.7338 (tmtm) cc_final: 0.7018 (tmtp)
REVERT: C  341 LYS cc_start: 0.8020 (mttt) cc_final: 0.7760 (mtmm)
REVERT: D  199 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7666 (mttm)
REVERT: D  303 ARG cc_start: 0.7427 (ttt-90) cc_final: 0.6948 (mtp180)
REVERT: D  318 GLU cc_start: 0.7667 (pt0) cc_final: 0.7342 (mp0)
  outliers start: 18
  outliers final: 12
  residues processed: 108
  average time/residue: 0.8966
  time to fit residues: 102.2929
Evaluate side-chains
  107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 10 optimal weight:    0.2980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
D  95 GLN
D 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.124370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.094518 restraints weight = 11831.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.57
r_work: 0.2960 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10672  Z= 0.166
  Angle     :  0.536   7.245  14464  Z= 0.279
  Chirality :  0.042   0.160   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.093  54.423   1480
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.06 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.80 (0.23), residues: 1364
  helix:  2.74 (0.19), residues: 704
  sheet: -1.67 (0.36), residues: 184
  loop :  0.09 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 258 
 TYR   0.025   0.002   TYR D 213 
 PHE   0.017   0.002   PHE B 144 
 TRP   0.015   0.002   TRP C 147 
 HIS   0.006   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (10672)
  covalent geometry    : angle       0.53575 (14464)
  hydrogen bonds       : bond        0.05583 (  551)
  hydrogen bonds       : angle       3.85383 ( 1602)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   38 SER cc_start: 0.8389 (t) cc_final: 0.8037 (m)
REVERT: A   42 ARG cc_start: 0.6798 (mtp180) cc_final: 0.6368 (mmp80)
REVERT: A   66 ASP cc_start: 0.7634 (t70) cc_final: 0.7320 (t0)
REVERT: A   86 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7556 (mttp)
REVERT: A   95 GLN cc_start: 0.7759 (tt0) cc_final: 0.7153 (tp-100)
REVERT: A  152 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7653 (pttp)
REVERT: A  199 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7545 (mmtm)
REVERT: A  303 ARG cc_start: 0.7246 (ttp80) cc_final: 0.6510 (mtm180)
REVERT: A  317 LYS cc_start: 0.7535 (mttm) cc_final: 0.7237 (mtpm)
REVERT: A  318 GLU cc_start: 0.7291 (mp0) cc_final: 0.6695 (mp0)
REVERT: B   34 GLU cc_start: 0.7160 (mp0) cc_final: 0.6767 (mt-10)
REVERT: B   45 SER cc_start: 0.8049 (p) cc_final: 0.7729 (m)
REVERT: B  152 LYS cc_start: 0.8457 (ttmt) cc_final: 0.7629 (ptmm)
REVERT: B  199 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7681 (mmtm)
REVERT: B  242 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7144 (mmtt)
REVERT: B  311 LYS cc_start: 0.7517 (tttm) cc_final: 0.6916 (tmmt)
REVERT: B  317 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6960 (mttp)
REVERT: B  318 GLU cc_start: 0.7439 (mp0) cc_final: 0.7047 (pm20)
REVERT: C   42 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6074 (mmm160)
REVERT: C   60 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7396 (tt0)
REVERT: C  193 ASP cc_start: 0.7990 (m-30) cc_final: 0.7681 (m-30)
REVERT: C  242 LYS cc_start: 0.7945 (mttm) cc_final: 0.7374 (tmtt)
REVERT: C  247 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: C  303 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6583 (ttt-90)
REVERT: C  341 LYS cc_start: 0.8088 (mttt) cc_final: 0.7838 (mtmm)
REVERT: D  199 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7749 (mttt)
REVERT: D  303 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.7054 (mtp180)
  outliers start: 17
  outliers final: 13
  residues processed: 108
  average time/residue: 0.9165
  time to fit residues: 104.4329
Evaluate side-chains
  105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue   60 GLN
Chi-restraints excluded: chain C residue  173 TYR
Chi-restraints excluded: chain C residue  250 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  343 THR
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue  139 LYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 134 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 125 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.127292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.097559 restraints weight = 11741.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.54
r_work: 0.3007 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10672  Z= 0.110
  Angle     :  0.466   6.531  14464  Z= 0.243
  Chirality :  0.039   0.135   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  4.869  55.405   1480
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.24 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.92 (0.23), residues: 1364
  helix:  2.82 (0.19), residues: 712
  sheet: -1.66 (0.36), residues: 184
  loop :  0.15 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.018   0.001   TYR D 213 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.013   0.002   TRP B 147 
 HIS   0.003   0.001   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10672)
  covalent geometry    : angle       0.46627 (14464)
  hydrogen bonds       : bond        0.04444 (  551)
  hydrogen bonds       : angle       3.73195 ( 1602)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4288.23 seconds
wall clock time: 74 minutes 4.90 seconds (4444.90 seconds total)