Starting phenix.real_space_refine
on Wed Aug  5 21:34:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r3g_18864/08_2026/8r3g_18864.cif"
  }
  resolution = 4.4
  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=   0.001 sd=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     Se     48      7.20       5
     P      82      5.49       5
     S       8      5.16       5
     C    7285      2.51       5
     N    2090      2.21       5
     O    2472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11985
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2576
          Classifications: {'peptide': 335}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 837
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "E"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 844
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "B"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2576
          Classifications: {'peptide': 335}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324}
          Chain breaks: 1
  Restraints were copied for chains:
    D, C
  Time building chain proxies: 3.10, per 1000 atoms: 0.26
  Number of scatterers: 11985
  At special positions: 0
  Unit cell: (146.316, 130.698, 88.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Se     48     33.99
     S       8     16.00
     P      82     15.00
     O    2472      8.00
     N    2090      7.00
     C    7285      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: 0.85
  Conformation dependent library (CDL) restraints added in 392.7 milliseconds
  

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2480

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 12 sheets defined
      61.3% alpha, 13.1% beta
      38 base pairs and 72 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 12
    Processing helix  chain 'C' and resid 12 through 33
    Processing helix  chain 'C' and resid 36 through 44
    Processing helix  chain 'C' and resid 47 through 61
    Processing helix  chain 'C' and resid 74 through 92
      removed outlier: 5.160A  pdb=" N   ASP C  86 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   THR C  87 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS C  89 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL C  91 " --> pdb=" O   THR C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 105
    Processing helix  chain 'C' and resid 121 through 139
      removed outlier: 4.160A  pdb=" N   LYS C 125 " --> pdb=" O   PRO C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 160
    Processing helix  chain 'C' and resid 185 through 198
    Processing helix  chain 'C' and resid 211 through 221
    Processing helix  chain 'C' and resid 221 through 233
      removed outlier: 3.704A  pdb=" N   VAL C 227 " --> pdb=" O   SER C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 251
    Processing helix  chain 'C' and resid 254 through 264
    Processing helix  chain 'C' and resid 291 through 298
      removed outlier: 3.704A  pdb=" N   ASP C 296 " --> pdb=" O   ASP C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 309
      No H-bonds generated for 'chain 'C' and resid 307 through 309'
    Processing helix  chain 'C' and resid 310 through 318
    Processing helix  chain 'C' and resid 330 through 338
    Processing helix  chain 'A' and resid 2 through 12
      removed outlier: 3.683A  pdb=" N   LYS A  10 " --> pdb=" O   GLN A   6 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 33
    Processing helix  chain 'A' and resid 36 through 45
    Processing helix  chain 'A' and resid 47 through 61
    Processing helix  chain 'A' and resid 74 through 92
      removed outlier: 3.695A  pdb=" N   ASP A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASP A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 3.651A  pdb=" N   LEU A  96 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 139
      removed outlier: 4.160A  pdb=" N   LYS A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 160
    Processing helix  chain 'A' and resid 185 through 198
    Processing helix  chain 'A' and resid 211 through 221
    Processing helix  chain 'A' and resid 221 through 233
      removed outlier: 3.704A  pdb=" N   VAL A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 251
    Processing helix  chain 'A' and resid 254 through 264
    Processing helix  chain 'A' and resid 291 through 298
      removed outlier: 3.704A  pdb=" N   ASP A 296 " --> pdb=" O   ASP A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 310 through 318
    Processing helix  chain 'A' and resid 330 through 338
    Processing helix  chain 'B' and resid 2 through 12
    Processing helix  chain 'B' and resid 12 through 33
    Processing helix  chain 'B' and resid 36 through 44
    Processing helix  chain 'B' and resid 47 through 61
    Processing helix  chain 'B' and resid 74 through 92
      removed outlier: 5.159A  pdb=" N   ASP B  86 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   THR B  87 " --> pdb=" O   VAL B  83 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  89 " --> pdb=" O   GLU B  85 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL B  91 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 105
    Processing helix  chain 'B' and resid 121 through 139
      removed outlier: 4.160A  pdb=" N   LYS B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 160
    Processing helix  chain 'B' and resid 185 through 198
    Processing helix  chain 'B' and resid 211 through 221
    Processing helix  chain 'B' and resid 221 through 233
      removed outlier: 3.705A  pdb=" N   VAL B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 251
    Processing helix  chain 'B' and resid 254 through 264
    Processing helix  chain 'B' and resid 291 through 298
      removed outlier: 3.705A  pdb=" N   ASP B 296 " --> pdb=" O   ASP B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 309
      No H-bonds generated for 'chain 'B' and resid 307 through 309'
    Processing helix  chain 'B' and resid 310 through 318
    Processing helix  chain 'B' and resid 330 through 338
    Processing helix  chain 'D' and resid 2 through 12
      removed outlier: 3.682A  pdb=" N   LYS D  10 " --> pdb=" O   GLN D   6 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU D  11 " --> pdb=" O   ALA D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 33
    Processing helix  chain 'D' and resid 36 through 45
    Processing helix  chain 'D' and resid 47 through 61
    Processing helix  chain 'D' and resid 74 through 92
      removed outlier: 3.695A  pdb=" N   ASP D  86 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LYS D  89 " --> pdb=" O   GLU D  85 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASP D  90 " --> pdb=" O   ASP D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 105
      removed outlier: 3.651A  pdb=" N   LEU D  96 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 139
      removed outlier: 4.161A  pdb=" N   LYS D 125 " --> pdb=" O   PRO D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 160
    Processing helix  chain 'D' and resid 185 through 198
    Processing helix  chain 'D' and resid 211 through 221
    Processing helix  chain 'D' and resid 221 through 233
      removed outlier: 3.704A  pdb=" N   VAL D 227 " --> pdb=" O   SER D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 251
    Processing helix  chain 'D' and resid 254 through 264
    Processing helix  chain 'D' and resid 291 through 298
      removed outlier: 3.704A  pdb=" N   ASP D 296 " --> pdb=" O   ASP D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 309
      No H-bonds generated for 'chain 'D' and resid 307 through 309'
    Processing helix  chain 'D' and resid 310 through 318
    Processing helix  chain 'D' and resid 330 through 338
    Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 67
    Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113
      removed outlier: 6.555A  pdb=" N   ASP C 109 " --> pdb=" O   LEU C 326 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   THR C 328 " --> pdb=" O   ASP C 109 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE C 111 " --> pdb=" O   THR C 328 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE C 301 " --> pdb=" O   VAL C 325 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL C 327 " --> pdb=" O   ILE C 301 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA C 303 " --> pdb=" O   VAL C 327 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   ASP C 329 " --> pdb=" O   ALA C 303 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU C 237 " --> pdb=" O   ILE C 302 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   VAL C 304 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   HIS C 239 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 242 through 243
      removed outlier: 6.768A  pdb=" N   PHE C 275 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   GLU C 269 " --> pdb=" O   TYR C 273 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TYR C 273 " --> pdb=" O   GLU C 269 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ASN C 276 " --> pdb=" O   VAL C 281 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL C 281 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 67
    Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 113
      removed outlier: 6.555A  pdb=" N   ASP A 109 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   THR A 328 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE A 111 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE A 301 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL A 327 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA A 303 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   ASP A 329 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A 237 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   VAL A 304 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   HIS A 239 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243
      removed outlier: 6.767A  pdb=" N   PHE A 275 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   GLU A 269 " --> pdb=" O   TYR A 273 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TYR A 273 " --> pdb=" O   GLU A 269 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL A 281 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 67
    Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 113
      removed outlier: 6.555A  pdb=" N   ASP B 109 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   THR B 328 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ILE B 111 " --> pdb=" O   THR B 328 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ILE B 301 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL B 327 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ALA B 303 " --> pdb=" O   VAL B 327 " (cutoff:3.500A)
      removed outlier: 8.573A  pdb=" N   ASP B 329 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU B 237 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   VAL B 304 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   HIS B 239 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243
      removed outlier: 6.767A  pdb=" N   PHE B 275 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLU B 269 " --> pdb=" O   TYR B 273 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TYR B 273 " --> pdb=" O   GLU B 269 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL B 281 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 67
    Processing sheet with id=AB2, first strand: chain 'D' and resid 109 through 113
      removed outlier: 6.556A  pdb=" N   ASP D 109 " --> pdb=" O   LEU D 326 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   THR D 328 " --> pdb=" O   ASP D 109 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE D 111 " --> pdb=" O   THR D 328 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE D 301 " --> pdb=" O   VAL D 325 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL D 327 " --> pdb=" O   ILE D 301 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA D 303 " --> pdb=" O   VAL D 327 " (cutoff:3.500A)
      removed outlier: 8.571A  pdb=" N   ASP D 329 " --> pdb=" O   ALA D 303 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU D 237 " --> pdb=" O   ILE D 302 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   VAL D 304 " --> pdb=" O   LEU D 237 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   HIS D 239 " --> pdb=" O   VAL D 304 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 243
      removed outlier: 6.767A  pdb=" N   PHE D 275 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLU D 269 " --> pdb=" O   TYR D 273 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TYR D 273 " --> pdb=" O   GLU D 269 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASN D 276 " --> pdb=" O   VAL D 281 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL D 281 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)

    601 hydrogen bonds defined for protein.
    1707 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      93 hydrogen bonds
      186 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      72 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.35: 3703
        1.35 -     1.51: 3821
        1.51 -     1.67: 4676
        1.67 -     1.84: 8
        1.84 -     2.00: 96
  Bond restraints: 12304
  Sorted by residual:
  bond pdb=" N   VAL D 206 "
       pdb=" CA  VAL D 206 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 7.50e-03 1.78e+04 2.13e+01
  bond pdb=" N   VAL A 206 "
       pdb=" CA  VAL A 206 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 7.50e-03 1.78e+04 2.10e+01
  bond pdb=" N   VAL C 206 "
       pdb=" CA  VAL C 206 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 7.50e-03 1.78e+04 1.99e+01
  bond pdb=" N   VAL B 206 "
       pdb=" CA  VAL B 206 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 7.50e-03 1.78e+04 1.99e+01
  bond pdb=" N   LEU B 107 "
       pdb=" CA  LEU B 107 "
    ideal  model  delta    sigma   weight residual
    1.455  1.507 -0.052 1.25e-02 6.40e+03 1.75e+01
  ... (remaining 12299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 14574
        2.15 -     4.30: 2087
        4.30 -     6.45: 212
        6.45 -     8.60: 22
        8.60 -    10.74: 28
  Bond angle restraints: 16923
  Sorted by residual:
  angle pdb=" C   PHE C 205 "
        pdb=" N   VAL C 206 "
        pdb=" CA  VAL C 206 "
      ideal   model   delta    sigma   weight residual
     122.59  114.90    7.69 7.20e-01 1.93e+00 1.14e+02
  angle pdb=" C   PHE B 205 "
        pdb=" N   VAL B 206 "
        pdb=" CA  VAL B 206 "
      ideal   model   delta    sigma   weight residual
     122.59  114.90    7.69 7.20e-01 1.93e+00 1.14e+02
  angle pdb=" C   PHE D 205 "
        pdb=" N   VAL D 206 "
        pdb=" CA  VAL D 206 "
      ideal   model   delta    sigma   weight residual
     122.59  116.43    6.16 7.20e-01 1.93e+00 7.31e+01
  angle pdb=" C   PHE A 205 "
        pdb=" N   VAL A 206 "
        pdb=" CA  VAL A 206 "
      ideal   model   delta    sigma   weight residual
     122.59  116.46    6.13 7.20e-01 1.93e+00 7.24e+01
  angle pdb=" N   ARG B 175 "
        pdb=" CA  ARG B 175 "
        pdb=" C   ARG B 175 "
      ideal   model   delta    sigma   weight residual
     110.53   99.79   10.74 1.32e+00 5.74e-01 6.62e+01
  ... (remaining 16918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 6931
       35.97 -    71.93: 435
       71.93 -   107.90: 18
      107.90 -   143.87: 0
      143.87 -   179.84: 2
  Dihedral angle restraints: 7386
    sinusoidal: 3546
      harmonic: 3840
  Sorted by residual:
  dihedral pdb=" C4'  DC E  19 "
           pdb=" C3'  DC E  19 "
           pdb=" O3'  DC E  19 "
           pdb=" P    DA E  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.16  179.84     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC F  19 "
           pdb=" C3'  DC F  19 "
           pdb=" O3'  DC F  19 "
           pdb=" P    DC F  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.75  176.25     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C   MSE D  88 "
           pdb=" N   MSE D  88 "
           pdb=" CA  MSE D  88 "
           pdb=" CB  MSE D  88 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.12    9.52     0      2.50e+00 1.60e-01 1.45e+01
  ... (remaining 7383 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1269
       0.084 -    0.169: 553
       0.169 -    0.253: 108
       0.253 -    0.337: 39
       0.337 -    0.422: 11
  Chirality restraints: 1980
  Sorted by residual:
  chirality pdb=" CA  VAL D 325 "
            pdb=" N   VAL D 325 "
            pdb=" C   VAL D 325 "
            pdb=" CB  VAL D 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.86   -0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CA  VAL A 325 "
            pdb=" N   VAL A 325 "
            pdb=" C   VAL A 325 "
            pdb=" CB  VAL A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.86   -0.42 2.00e-01 2.50e+01 4.42e+00
  chirality pdb=" CA  VAL C 325 "
            pdb=" N   VAL C 325 "
            pdb=" C   VAL C 325 "
            pdb=" CB  VAL C 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.86   -0.42 2.00e-01 2.50e+01 4.39e+00
  ... (remaining 1977 not shown)

  Planarity restraints: 1878
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D  87 "    0.022 2.00e-02 2.50e+03   4.81e-02 2.31e+01
        pdb=" C   THR D  87 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   THR D  87 "    0.032 2.00e-02 2.50e+03
        pdb=" N   MSE D  88 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  87 "   -0.022 2.00e-02 2.50e+03   4.81e-02 2.31e+01
        pdb=" C   THR A  87 "    0.083 2.00e-02 2.50e+03
        pdb=" O   THR A  87 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   MSE A  88 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 174 "    0.019 2.00e-02 2.50e+03   4.01e-02 1.61e+01
        pdb=" C   ALA A 174 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   ALA A 174 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ARG A 175 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1875 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1547
        2.77 -     3.31: 11645
        3.31 -     3.84: 20868
        3.84 -     4.37: 26612
        4.37 -     4.90: 39448
  Nonbonded interactions: 100120
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  33 "
            pdb=" OH  TYR B  78 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OE2 GLU C  33 "
            pdb=" OH  TYR C  78 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" NH2 ARG C  49 "
            pdb=" N6   DA E  28 "
     model   vdw
     2.253 3.200
  nonbonded pdb=" OE2 GLU A  33 "
            pdb=" OH  TYR A  78 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OE2 GLU D  33 "
            pdb=" OH  TYR D  78 "
     model   vdw
     2.259 3.040
  ... (remaining 100115 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.030
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.140
  Find NCS groups from input model:        0.100
  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:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5176
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      :  0.013   0.099  12304  Z= 0.857
  Angle     :  1.535  10.744  16923  Z= 1.069
  Chirality :  0.100   0.422   1980
  Planarity :  0.007   0.048   1878
  Dihedral  : 19.042 179.837   4906
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.16 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.21), residues: 1324
  helix: -0.91 (0.16), residues: 732
  sheet: -0.59 (0.35), residues: 156
  loop : -0.21 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG B 167 
 TYR   0.049   0.010   TYR A 317 
 PHE   0.028   0.006   PHE B  57 
 TRP   0.010   0.005   TRP C 122 
 HIS   0.015   0.005   HIS C 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01334 /  0.86 (12304)
  covalent geometry    : angle       1.53470 /  1.07 (16923)
  hydrogen bonds       : bond        0.18693 / 12.29 (  694)
  hydrogen bonds       : angle       7.14085 /  5.11 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 393
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   20 GLN cc_start: 0.8013 (mt0) cc_final: 0.7509 (mm-40)
REVERT: C  132 VAL cc_start: 0.8206 (t) cc_final: 0.7906 (p)
REVERT: C  152 THR cc_start: 0.8581 (m) cc_final: 0.8276 (p)
REVERT: C  173 PRO cc_start: 0.6274 (Cg_endo) cc_final: 0.5877 (Cg_exo)
REVERT: C  304 VAL cc_start: 0.7403 (t) cc_final: 0.7123 (m)
REVERT: A  145 VAL cc_start: 0.7381 (t) cc_final: 0.6906 (t)
REVERT: B   29 ILE cc_start: 0.8635 (mt) cc_final: 0.8288 (mm)
REVERT: B  101 LEU cc_start: 0.7635 (tp) cc_final: 0.7318 (tp)
REVERT: B  132 VAL cc_start: 0.8259 (t) cc_final: 0.7994 (p)
REVERT: B  152 THR cc_start: 0.8727 (m) cc_final: 0.8386 (p)
REVERT: B  304 VAL cc_start: 0.7345 (t) cc_final: 0.7086 (m)
REVERT: D   12 LEU cc_start: 0.8142 (mt) cc_final: 0.6562 (mt)
REVERT: D   19 MSE cc_start: 0.5087 (mtp) cc_final: 0.4782 (ttp)
REVERT: D  145 VAL cc_start: 0.7442 (t) cc_final: 0.7099 (t)
REVERT: D  295 ILE cc_start: 0.8004 (pt) cc_final: 0.7697 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 395
  average time/residue: 0.1091
  time to fit residues: 59.3662
Evaluate side-chains
  203 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.0270
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9240

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C   3 GLN
A 252 ASN
B   3 GLN
B   6 GLN
D 252 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.091866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.074269 restraints weight = 53277.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.077104 restraints weight = 34164.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.079200 restraints weight = 23858.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.080984 restraints weight = 17984.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.082137 restraints weight = 14080.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  12304  Z= 0.201
  Angle     :  0.768   8.698  16923  Z= 0.417
  Chirality :  0.048   0.233   1980
  Planarity :  0.006   0.078   1878
  Dihedral  : 21.067 170.037   2326
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.23), residues: 1324
  helix:  0.73 (0.18), residues: 748
  sheet: -0.65 (0.37), residues: 164
  loop :  0.04 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  49 
 TYR   0.025   0.002   TYR C 274 
 PHE   0.038   0.004   PHE D 139 
 TRP   0.005   0.001   TRP B 122 
 HIS   0.003   0.001   HIS D 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.20 (12304)
  covalent geometry    : angle       0.76798 /  0.42 (16923)
  hydrogen bonds       : bond        0.06198 /  4.20 (  694)
  hydrogen bonds       : angle       4.96470 /  3.62 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 LEU cc_start: 0.9033 (mm) cc_final: 0.8480 (mm)
REVERT: C   20 GLN cc_start: 0.8546 (mt0) cc_final: 0.7962 (mm110)
REVERT: C   35 ILE cc_start: 0.7395 (mm) cc_final: 0.7031 (mm)
REVERT: C  201 TYR cc_start: 0.6099 (p90) cc_final: 0.5720 (p90)
REVERT: A  145 VAL cc_start: 0.8444 (t) cc_final: 0.8105 (t)
REVERT: A  175 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8396 (tpp80)
REVERT: A  274 TYR cc_start: 0.6790 (m-80) cc_final: 0.6447 (m-80)
REVERT: A  326 LEU cc_start: 0.6039 (tp) cc_final: 0.5795 (tt)
REVERT: B  171 PHE cc_start: 0.5500 (m-80) cc_final: 0.4940 (m-10)
REVERT: B  201 TYR cc_start: 0.5774 (p90) cc_final: 0.5512 (p90)
REVERT: D   12 LEU cc_start: 0.8904 (mt) cc_final: 0.8507 (mp)
REVERT: D  114 SER cc_start: 0.8324 (m) cc_final: 0.7641 (t)
REVERT: D  145 VAL cc_start: 0.8495 (t) cc_final: 0.8142 (t)
REVERT: D  175 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8155 (tpp80)
REVERT: D  326 LEU cc_start: 0.6049 (tp) cc_final: 0.5797 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.0900
  time to fit residues: 31.7889
Evaluate side-chains
  164 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 115 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 70 optimal weight:   30.0000
   chunk 21 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 109 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.092366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.074708 restraints weight = 51250.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.077648 restraints weight = 32516.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.079889 restraints weight = 22564.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.081522 restraints weight = 16809.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.082719 restraints weight = 13275.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12304  Z= 0.162
  Angle     :  0.678   8.795  16923  Z= 0.372
  Chirality :  0.045   0.262   1980
  Planarity :  0.005   0.074   1878
  Dihedral  : 21.053 177.282   2326
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.23), residues: 1324
  helix:  0.77 (0.18), residues: 758
  sheet: -0.11 (0.38), residues: 156
  loop : -0.26 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 138 
 TYR   0.016   0.002   TYR D 215 
 PHE   0.024   0.003   PHE D 271 
 TRP   0.004   0.001   TRP B 122 
 HIS   0.003   0.001   HIS A 192 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.16 (12304)
  covalent geometry    : angle       0.67796 /  0.37 (16923)
  hydrogen bonds       : bond        0.05112 /  3.44 (  694)
  hydrogen bonds       : angle       4.71434 /  3.44 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 LEU cc_start: 0.9151 (mm) cc_final: 0.8289 (mm)
REVERT: C   20 GLN cc_start: 0.8583 (mt0) cc_final: 0.7921 (mm110)
REVERT: C   35 ILE cc_start: 0.7660 (mm) cc_final: 0.7384 (mm)
REVERT: C   54 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8277 (mm-30)
REVERT: C  132 VAL cc_start: 0.9398 (p) cc_final: 0.8648 (t)
REVERT: C  201 TYR cc_start: 0.6354 (p90) cc_final: 0.5874 (p90)
REVERT: C  327 VAL cc_start: 0.8800 (t) cc_final: 0.8553 (t)
REVERT: A  114 SER cc_start: 0.8415 (m) cc_final: 0.7676 (t)
REVERT: A  175 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8382 (tpp80)
REVERT: B   54 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8413 (mm-30)
REVERT: B  171 PHE cc_start: 0.7128 (m-80) cc_final: 0.6617 (m-10)
REVERT: B  237 LEU cc_start: 0.9045 (tp) cc_final: 0.8733 (tp)
REVERT: B  327 VAL cc_start: 0.8723 (t) cc_final: 0.8265 (t)
REVERT: D   12 LEU cc_start: 0.8829 (mt) cc_final: 0.8609 (mt)
REVERT: D  114 SER cc_start: 0.8468 (m) cc_final: 0.7767 (t)
REVERT: D  175 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8243 (tpp80)
REVERT: D  201 TYR cc_start: 0.7722 (p90) cc_final: 0.7521 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0890
  time to fit residues: 27.2146
Evaluate side-chains
  155 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0570
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 115 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.6098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 239 HIS
B   6 GLN
B 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.089296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.071955 restraints weight = 53766.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.074756 restraints weight = 34048.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.076930 restraints weight = 23685.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.078482 restraints weight = 17641.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.079759 restraints weight = 14017.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12304  Z= 0.152
  Angle     :  0.664  16.580  16923  Z= 0.358
  Chirality :  0.043   0.249   1980
  Planarity :  0.004   0.067   1878
  Dihedral  : 21.041 179.175   2326
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.23), residues: 1324
  helix:  0.80 (0.19), residues: 754
  sheet: -0.26 (0.37), residues: 164
  loop : -0.24 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  30 
 TYR   0.020   0.002   TYR B  78 
 PHE   0.027   0.003   PHE A 318 
 TRP   0.004   0.001   TRP D 122 
 HIS   0.003   0.001   HIS D 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 (12304)
  covalent geometry    : angle       0.66411 /  0.36 (16923)
  hydrogen bonds       : bond        0.04539 /  3.06 (  694)
  hydrogen bonds       : angle       4.59664 /  3.35 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 LEU cc_start: 0.9029 (mm) cc_final: 0.7897 (mm)
REVERT: C   35 ILE cc_start: 0.7567 (mm) cc_final: 0.7247 (mm)
REVERT: C   54 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: C  201 TYR cc_start: 0.6280 (p90) cc_final: 0.5849 (p90)
REVERT: A   12 LEU cc_start: 0.9333 (mp) cc_final: 0.9103 (mp)
REVERT: A  175 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8228 (tpp80)
REVERT: B   35 ILE cc_start: 0.9003 (tp) cc_final: 0.6210 (tp)
REVERT: B   54 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8433 (mm-30)
REVERT: B   88 MSE cc_start: 0.7894 (tpp) cc_final: 0.7277 (tpp)
REVERT: B   92 LEU cc_start: 0.6746 (mt) cc_final: 0.6231 (mt)
REVERT: B  148 THR cc_start: 0.8491 (t) cc_final: 0.8129 (t)
REVERT: B  237 LEU cc_start: 0.9024 (tp) cc_final: 0.8803 (tp)
REVERT: B  327 VAL cc_start: 0.8941 (t) cc_final: 0.8490 (t)
REVERT: D   12 LEU cc_start: 0.8831 (mt) cc_final: 0.8569 (mt)
REVERT: D  175 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.7587 (tpp80)
REVERT: D  201 TYR cc_start: 0.7846 (p90) cc_final: 0.7610 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0942
  time to fit residues: 28.5949
Evaluate side-chains
  153 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 121 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 109 optimal weight:    0.4980
   chunk 126 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    1.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN
B  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.087147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.069777 restraints weight = 52575.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.072349 restraints weight = 33509.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.074442 restraints weight = 23578.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.076042 restraints weight = 17694.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.077071 restraints weight = 14021.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.5111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12304  Z= 0.169
  Angle     :  0.638   8.798  16923  Z= 0.351
  Chirality :  0.042   0.251   1980
  Planarity :  0.005   0.070   1878
  Dihedral  : 21.013 178.805   2326
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.23), residues: 1324
  helix:  0.99 (0.19), residues: 752
  sheet: -0.05 (0.37), residues: 164
  loop : -0.38 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 175 
 TYR   0.024   0.002   TYR C  78 
 PHE   0.049   0.004   PHE D 139 
 TRP   0.006   0.001   TRP B 122 
 HIS   0.001   0.000   HIS D 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.17 (12304)
  covalent geometry    : angle       0.63838 /  0.35 (16923)
  hydrogen bonds       : bond        0.04443 /  3.00 (  694)
  hydrogen bonds       : angle       4.56573 /  3.31 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   16 LEU cc_start: 0.9122 (mm) cc_final: 0.7911 (mm)
REVERT: C   35 ILE cc_start: 0.8014 (mm) cc_final: 0.7789 (tt)
REVERT: C   54 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: C  201 TYR cc_start: 0.6567 (p90) cc_final: 0.6083 (p90)
REVERT: A   12 LEU cc_start: 0.9365 (mp) cc_final: 0.9111 (mt)
REVERT: A   51 LEU cc_start: 0.9021 (tp) cc_final: 0.8722 (mt)
REVERT: A  175 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8250 (tpp80)
REVERT: A  204 LEU cc_start: 0.8549 (mt) cc_final: 0.8309 (mt)
REVERT: A  327 VAL cc_start: 0.8036 (p) cc_final: 0.7833 (m)
REVERT: B   54 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8478 (mm-30)
REVERT: B   66 ILE cc_start: 0.8067 (mp) cc_final: 0.7843 (mp)
REVERT: B   88 MSE cc_start: 0.7704 (tpp) cc_final: 0.7096 (tpp)
REVERT: B   92 LEU cc_start: 0.6907 (mt) cc_final: 0.6550 (mt)
REVERT: B  132 VAL cc_start: 0.9543 (p) cc_final: 0.9283 (t)
REVERT: B  237 LEU cc_start: 0.9008 (tp) cc_final: 0.8777 (tp)
REVERT: B  241 ILE cc_start: 0.8488 (mm) cc_final: 0.8229 (mm)
REVERT: D   12 LEU cc_start: 0.9016 (mt) cc_final: 0.8755 (mt)
REVERT: D   51 LEU cc_start: 0.9021 (tp) cc_final: 0.8700 (mt)
REVERT: D   88 MSE cc_start: 0.6200 (ttm) cc_final: 0.5752 (ttt)
REVERT: D  175 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8288 (tpp80)
REVERT: D  204 LEU cc_start: 0.8554 (mt) cc_final: 0.8294 (mt)
REVERT: D  327 VAL cc_start: 0.8428 (p) cc_final: 0.8141 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1109
  time to fit residues: 31.9814
Evaluate side-chains
  148 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    1.0784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.085962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.068740 restraints weight = 55841.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.071320 restraints weight = 35067.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.073339 restraints weight = 24586.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.074774 restraints weight = 18493.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.076024 restraints weight = 14834.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.5430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12304  Z= 0.140
  Angle     :  0.624   9.382  16923  Z= 0.344
  Chirality :  0.041   0.250   1980
  Planarity :  0.004   0.070   1878
  Dihedral  : 20.960 178.282   2326
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.23), residues: 1324
  helix:  1.04 (0.18), residues: 754
  sheet:  0.08 (0.37), residues: 160
  loop : -0.49 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 175 
 TYR   0.011   0.002   TYR B 201 
 PHE   0.040   0.003   PHE D 139 
 TRP   0.004   0.001   TRP B 122 
 HIS   0.002   0.000   HIS D 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.14 (12304)
  covalent geometry    : angle       0.62373 /  0.34 (16923)
  hydrogen bonds       : bond        0.04098 /  2.76 (  694)
  hydrogen bonds       : angle       4.55167 /  3.30 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   54 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8454 (mm-30)
REVERT: C  156 VAL cc_start: 0.9556 (t) cc_final: 0.9027 (t)
REVERT: C  201 TYR cc_start: 0.6558 (p90) cc_final: 0.6142 (p90)
REVERT: A   51 LEU cc_start: 0.9162 (tp) cc_final: 0.8639 (mt)
REVERT: A  175 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8191 (tpp80)
REVERT: A  327 VAL cc_start: 0.8391 (p) cc_final: 0.8127 (m)
REVERT: B   54 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8342 (mm-30)
REVERT: B   88 MSE cc_start: 0.7820 (tpp) cc_final: 0.7265 (tpp)
REVERT: B   92 LEU cc_start: 0.6999 (mt) cc_final: 0.6596 (mt)
REVERT: B  241 ILE cc_start: 0.8503 (mm) cc_final: 0.8266 (mm)
REVERT: D   26 LEU cc_start: 0.9247 (tp) cc_final: 0.9038 (tp)
REVERT: D   51 LEU cc_start: 0.9156 (tp) cc_final: 0.8638 (mt)
REVERT: D  327 VAL cc_start: 0.8515 (p) cc_final: 0.8276 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1065
  time to fit residues: 31.2910
Evaluate side-chains
  145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 70 optimal weight:   30.0000
   chunk 54 optimal weight:    6.9990
   chunk 137 optimal weight:    0.2980
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.083266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.066334 restraints weight = 56298.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.068866 restraints weight = 35546.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.070779 restraints weight = 24941.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.072203 restraints weight = 18876.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.073168 restraints weight = 15178.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.5820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12304  Z= 0.171
  Angle     :  0.632   8.176  16923  Z= 0.349
  Chirality :  0.042   0.248   1980
  Planarity :  0.004   0.072   1878
  Dihedral  : 20.949 177.389   2326
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.23), residues: 1324
  helix:  1.10 (0.18), residues: 750
  sheet:  0.16 (0.38), residues: 158
  loop : -0.57 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 250 
 TYR   0.015   0.002   TYR D  78 
 PHE   0.043   0.003   PHE D 139 
 TRP   0.009   0.001   TRP B 122 
 HIS   0.004   0.001   HIS C 192 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 (12304)
  covalent geometry    : angle       0.63204 /  0.35 (16923)
  hydrogen bonds       : bond        0.04276 /  2.86 (  694)
  hydrogen bonds       : angle       4.53423 /  3.27 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8771 (mt-10)
REVERT: A  175 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8117 (tpp80)
REVERT: A  327 VAL cc_start: 0.8451 (p) cc_final: 0.8178 (m)
REVERT: B   88 MSE cc_start: 0.7993 (tpp) cc_final: 0.7549 (tpp)
REVERT: B   92 LEU cc_start: 0.7076 (mt) cc_final: 0.6847 (mt)
REVERT: B  237 LEU cc_start: 0.9068 (tp) cc_final: 0.8866 (tp)
REVERT: D   51 LEU cc_start: 0.8938 (tp) cc_final: 0.8699 (mt)
REVERT: D  175 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8201 (tpp80)
REVERT: D  204 LEU cc_start: 0.8663 (mt) cc_final: 0.8460 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0966
  time to fit residues: 26.6590
Evaluate side-chains
  135 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 96 optimal weight:    0.3980
   chunk 125 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   chunk 73 optimal weight:   20.0000
   chunk 113 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.085590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.068869 restraints weight = 54915.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.071391 restraints weight = 35387.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.073361 restraints weight = 24896.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.074792 restraints weight = 18801.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.075856 restraints weight = 15108.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.6001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12304  Z= 0.135
  Angle     :  0.629  12.208  16923  Z= 0.340
  Chirality :  0.041   0.251   1980
  Planarity :  0.004   0.072   1878
  Dihedral  : 20.907 177.363   2326
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.23), residues: 1324
  helix:  1.13 (0.19), residues: 752
  sheet:  0.10 (0.38), residues: 160
  loop : -0.69 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 250 
 TYR   0.023   0.002   TYR C 201 
 PHE   0.042   0.003   PHE D 139 
 TRP   0.006   0.001   TRP B 122 
 HIS   0.002   0.001   HIS C 192 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.14 (12304)
  covalent geometry    : angle       0.62919 /  0.34 (16923)
  hydrogen bonds       : bond        0.03934 /  2.65 (  694)
  hydrogen bonds       : angle       4.49410 /  3.27 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  135 MSE cc_start: 0.5827 (ptt) cc_final: 0.5580 (ptp)
REVERT: C  160 MSE cc_start: 0.4593 (mtp) cc_final: 0.2635 (mtp)
REVERT: A   88 MSE cc_start: 0.6680 (ptp) cc_final: 0.6408 (ptp)
REVERT: A  175 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8139 (tpp80)
REVERT: A  204 LEU cc_start: 0.8552 (mt) cc_final: 0.8348 (mt)
REVERT: A  327 VAL cc_start: 0.8184 (p) cc_final: 0.7775 (m)
REVERT: B   54 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8260 (mm-30)
REVERT: B  144 ILE cc_start: 0.6797 (mp) cc_final: 0.6573 (mp)
REVERT: D  154 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8670 (mt-10)
REVERT: D  175 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8181 (tpp80)
REVERT: D  290 MSE cc_start: 0.5418 (mmp) cc_final: 0.4938 (mmt)
REVERT: D  291 GLN cc_start: 0.8824 (mt0) cc_final: 0.8145 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0913
  time to fit residues: 25.9720
Evaluate side-chains
  140 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.083890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.066953 restraints weight = 54425.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.069593 restraints weight = 33792.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.071647 restraints weight = 23230.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.073050 restraints weight = 17296.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.074241 restraints weight = 13836.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.6178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12304  Z= 0.140
  Angle     :  0.646  12.861  16923  Z= 0.350
  Chirality :  0.042   0.251   1980
  Planarity :  0.004   0.074   1878
  Dihedral  : 20.877 177.164   2326
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.23), residues: 1324
  helix:  1.08 (0.19), residues: 752
  sheet:  0.31 (0.39), residues: 152
  loop : -0.81 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 250 
 TYR   0.009   0.001   TYR B 273 
 PHE   0.041   0.003   PHE D 139 
 TRP   0.006   0.001   TRP C 122 
 HIS   0.002   0.000   HIS B 192 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.14 (12304)
  covalent geometry    : angle       0.64551 /  0.35 (16923)
  hydrogen bonds       : bond        0.03947 /  2.69 (  694)
  hydrogen bonds       : angle       4.61039 /  3.32 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  193 MSE cc_start: 0.5612 (tpt) cc_final: 0.4959 (tpp)
REVERT: A   12 LEU cc_start: 0.9217 (mm) cc_final: 0.9005 (mm)
REVERT: A   88 MSE cc_start: 0.6999 (ptp) cc_final: 0.6735 (ptp)
REVERT: A  175 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8086 (tpp80)
REVERT: A  204 LEU cc_start: 0.8649 (mt) cc_final: 0.8436 (mt)
REVERT: A  327 VAL cc_start: 0.7907 (p) cc_final: 0.7682 (p)
REVERT: B   54 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8384 (mm-30)
REVERT: B  120 SER cc_start: 0.8731 (p) cc_final: 0.8376 (m)
REVERT: D  175 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8168 (tpp80)
REVERT: D  204 LEU cc_start: 0.8601 (mt) cc_final: 0.8375 (mt)
REVERT: D  290 MSE cc_start: 0.5187 (mmp) cc_final: 0.4710 (mmt)
REVERT: D  291 GLN cc_start: 0.8977 (mt0) cc_final: 0.8274 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0912
  time to fit residues: 25.5329
Evaluate side-chains
  143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0000
   chunk 60 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.084127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.067549 restraints weight = 55139.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.069981 restraints weight = 35179.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.071946 restraints weight = 24650.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.073374 restraints weight = 18651.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.074326 restraints weight = 14965.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.6371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12304  Z= 0.142
  Angle     :  0.634  11.158  16923  Z= 0.348
  Chirality :  0.041   0.251   1980
  Planarity :  0.004   0.077   1878
  Dihedral  : 20.851 176.598   2326
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.23), residues: 1324
  helix:  1.05 (0.19), residues: 752
  sheet:  0.39 (0.39), residues: 148
  loop : -0.81 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 250 
 TYR   0.009   0.001   TYR B 273 
 PHE   0.041   0.003   PHE D 139 
 TRP   0.006   0.001   TRP B 122 
 HIS   0.002   0.000   HIS C 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.14 (12304)
  covalent geometry    : angle       0.63447 /  0.35 (16923)
  hydrogen bonds       : bond        0.04015 /  2.72 (  694)
  hydrogen bonds       : angle       4.64831 /  3.36 ( 1893)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LEU cc_start: 0.9205 (mm) cc_final: 0.8946 (mm)
REVERT: A   88 MSE cc_start: 0.6794 (ptp) cc_final: 0.6485 (ptp)
REVERT: A  175 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8172 (tpp80)
REVERT: A  327 VAL cc_start: 0.8069 (p) cc_final: 0.6480 (m)
REVERT: B   54 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8277 (mm-30)
REVERT: B  120 SER cc_start: 0.8444 (p) cc_final: 0.7669 (m)
REVERT: D   71 MSE cc_start: 0.1461 (ptp) cc_final: 0.1157 (ptp)
REVERT: D  135 MSE cc_start: 0.6943 (tpp) cc_final: 0.6649 (tpp)
REVERT: D  145 VAL cc_start: 0.8844 (t) cc_final: 0.8587 (t)
REVERT: D  175 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8220 (tpp80)
REVERT: D  236 MSE cc_start: 0.3074 (mtt) cc_final: 0.2280 (mtt)
REVERT: D  291 GLN cc_start: 0.8931 (mt0) cc_final: 0.8323 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0755
  time to fit residues: 21.0838
Evaluate side-chains
  140 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 123 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0970
   chunk 103 optimal weight:    0.0570
   chunk 134 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 88 optimal weight:    0.1980
   chunk 70 optimal weight:   30.0000
   chunk 67 optimal weight:   30.0000
   overall best weight:    0.3096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.085371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.068503 restraints weight = 53865.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.071193 restraints weight = 33672.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.073240 restraints weight = 23309.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.074630 restraints weight = 17338.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.075821 restraints weight = 13832.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.6494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12304  Z= 0.130
  Angle     :  0.619   8.012  16923  Z= 0.339
  Chirality :  0.041   0.255   1980
  Planarity :  0.004   0.074   1878
  Dihedral  : 20.789 176.523   2326
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.23), residues: 1324
  helix:  1.08 (0.19), residues: 752
  sheet:  0.41 (0.40), residues: 148
  loop : -0.76 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  52 
 TYR   0.007   0.001   TYR B 273 
 PHE   0.040   0.003   PHE D 139 
 TRP   0.006   0.001   TRP C 122 
 HIS   0.001   0.000   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.13 (12304)
  covalent geometry    : angle       0.61950 /  0.34 (16923)
  hydrogen bonds       : bond        0.03831 /  2.60 (  694)
  hydrogen bonds       : angle       4.57420 /  3.30 ( 1893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1946.21 seconds
wall clock time: 34 minutes 25.40 seconds (2065.40 seconds total)