Starting phenix.real_space_refine
on Tue Mar  3 17:14:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jnf_9851/03_2026/6jnf_9851.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      20      5.16       5
     C    4681      2.51       5
     N    1215      2.21       5
     O    1354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7271
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2363
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 336
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 3, 'TRANS': 37}
    Chain: "C"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 342
          Classifications: {'peptide': 44}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
    Chain: "D"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 292
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "E"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 281
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
    Chain: "F"
      Number of atoms: 2363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2363
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 4
    Chain: "G"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 336
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 3, 'TRANS': 37}
    Chain: "H"
      Number of atoms: 342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 342
          Classifications: {'peptide': 44}
          Link IDs: {'PTRANS': 1, 'TRANS': 42}
    Chain: "I"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 292
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 1, 'TRANS': 32}
    Chain: "J"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 281
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'46E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.19
  Number of scatterers: 7271
  At special positions: 0
  Unit cell: (138.19, 114.943, 94.2795, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P       1     15.00
     O    1354      8.00
     N    1215      7.00
     C    4681      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: 0.55
  Conformation dependent library (CDL) restraints added in 255.5 milliseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 10 sheets defined
      26.4% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 4.218A  pdb=" N   GLN A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLY A 373 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 368 through 373'
    Processing helix  chain 'B' and resid 18 through 26
      removed outlier: 3.722A  pdb=" N   THR B  22 " --> pdb=" O   SER B  18 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   HIS B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 43
      removed outlier: 3.571A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR B  38 " --> pdb=" O   PRO B  34 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA B  42 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
      removed outlier: 3.573A  pdb=" N   LEU B  53 " --> pdb=" O   PHE B  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 102
      removed outlier: 3.541A  pdb=" N   THR C 101 " --> pdb=" O   ASN C  97 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU C 102 " --> pdb=" O   LEU C  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 97 through 102'
    Processing helix  chain 'C' and resid 110 through 130
      removed outlier: 3.710A  pdb=" N   LEU C 118 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU C 120 " --> pdb=" O   SER C 116 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LEU C 123 " --> pdb=" O   ALA C 119 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE C 124 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU C 125 " --> pdb=" O   GLN C 121 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE C 130 " --> pdb=" O   MET C 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 41
      removed outlier: 3.608A  pdb=" N   GLU D  22 " --> pdb=" O   GLN D  18 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR D  24 " --> pdb=" O   GLN D  20 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU D  25 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA D  29 " --> pdb=" O   LEU D  25 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   TYR D  30 " --> pdb=" O   LYS D  26 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL D  31 " --> pdb=" O   GLN D  27 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE D  34 " --> pdb=" O   TYR D  30 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP D  36 " --> pdb=" O   ALA D  32 " (cutoff:3.500A)
      Proline residue:  D  39  - end of helix
    Processing helix  chain 'D' and resid 44 through 49
      removed outlier: 4.051A  pdb=" N   TRP D  49 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 31 through 50
      removed outlier: 4.205A  pdb=" N   ILE E  35 " --> pdb=" O   PRO E  31 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY E  39 " --> pdb=" O   ILE E  35 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL E  43 " --> pdb=" O   GLY E  39 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 57
      removed outlier: 3.661A  pdb=" N   ASP E  55 " --> pdb=" O   SER E  51 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET E  56 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU E  57 " --> pdb=" O   LEU E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 51 through 57'
    Processing helix  chain 'F' and resid 67 through 72
    Processing helix  chain 'F' and resid 368 through 373
      removed outlier: 4.217A  pdb=" N   GLN F 372 " --> pdb=" O   LEU F 368 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLY F 373 " --> pdb=" O   MET F 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 368 through 373'
    Processing helix  chain 'G' and resid 18 through 26
      removed outlier: 3.723A  pdb=" N   THR G  22 " --> pdb=" O   SER G  18 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   HIS G  25 " --> pdb=" O   LEU G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 43
      removed outlier: 3.572A  pdb=" N   LEU G  37 " --> pdb=" O   ILE G  33 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR G  38 " --> pdb=" O   PRO G  34 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY G  40 " --> pdb=" O   VAL G  36 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA G  42 " --> pdb=" O   TYR G  38 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS G  43 " --> pdb=" O   LEU G  39 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 50 through 54
      removed outlier: 3.573A  pdb=" N   LEU G  53 " --> pdb=" O   PHE G  50 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 97 through 102
      removed outlier: 3.541A  pdb=" N   THR H 101 " --> pdb=" O   ASN H  97 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU H 102 " --> pdb=" O   LEU H  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 97 through 102'
    Processing helix  chain 'H' and resid 110 through 130
      removed outlier: 3.709A  pdb=" N   LEU H 118 " --> pdb=" O   SER H 114 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU H 120 " --> pdb=" O   SER H 116 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LEU H 123 " --> pdb=" O   ALA H 119 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE H 124 " --> pdb=" O   GLU H 120 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU H 125 " --> pdb=" O   GLN H 121 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE H 130 " --> pdb=" O   MET H 126 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 18 through 41
      removed outlier: 3.607A  pdb=" N   GLU I  22 " --> pdb=" O   GLN I  18 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR I  24 " --> pdb=" O   GLN I  20 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LEU I  25 " --> pdb=" O   THR I  21 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA I  29 " --> pdb=" O   LEU I  25 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   TYR I  30 " --> pdb=" O   LYS I  26 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL I  31 " --> pdb=" O   GLN I  27 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE I  34 " --> pdb=" O   TYR I  30 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP I  36 " --> pdb=" O   ALA I  32 " (cutoff:3.500A)
      Proline residue:  I  39  - end of helix
    Processing helix  chain 'I' and resid 44 through 49
      removed outlier: 4.052A  pdb=" N   TRP I  49 " --> pdb=" O   VAL I  45 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 31 through 50
      removed outlier: 4.205A  pdb=" N   ILE J  35 " --> pdb=" O   PRO J  31 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY J  39 " --> pdb=" O   ILE J  35 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL J  43 " --> pdb=" O   GLY J  39 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA J  44 " --> pdb=" O   ALA J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 51 through 57
      removed outlier: 3.660A  pdb=" N   ASP J  55 " --> pdb=" O   SER J  51 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET J  56 " --> pdb=" O   PRO J  52 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU J  57 " --> pdb=" O   LEU J  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 51 through 57'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121
      removed outlier: 3.874A  pdb=" N   LEU A 119 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLN A  99 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ALA A 121 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE A 104 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A  84 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG A  85 " --> pdb=" O   CYS A 355 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A  87 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A  91 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY A 356 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 338 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY A 342 " --> pdb=" O   CYS A 326 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 344 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   SER A 312 " --> pdb=" O   TYR A 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117
      removed outlier: 3.616A  pdb=" N   ILE A 131 " --> pdb=" O   PHE A 116 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127
      removed outlier: 3.604A  pdb=" N   PHE A 126 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASN A 142 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 139 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 153 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 167
      removed outlier: 4.071A  pdb=" N   LEU A 167 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A 182 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   VAL A 196 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 177
      removed outlier: 4.097A  pdb=" N   GLN A 203 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR A 234 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   SER A 258 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE A 256 " --> pdb=" O   GLN A 248 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 257 " --> pdb=" O   THR A 273 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU A 259 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ILE A 271 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR A 274 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER A 300 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 119 through 121
      removed outlier: 3.873A  pdb=" N   LEU F 119 " --> pdb=" O   GLN F  99 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLN F  99 " --> pdb=" O   LEU F 119 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ALA F 121 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   PHE F 104 " --> pdb=" O   ALA F  86 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU F  84 " --> pdb=" O   ILE F 106 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG F  85 " --> pdb=" O   CYS F 355 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP F  87 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA F  91 " --> pdb=" O   THR F 361 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY F 356 " --> pdb=" O   LEU F 339 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL F 338 " --> pdb=" O   ARG F 330 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY F 342 " --> pdb=" O   CYS F 326 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE F 344 " --> pdb=" O   VAL F 324 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   SER F 312 " --> pdb=" O   TYR F 309 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 117
      removed outlier: 3.616A  pdb=" N   ILE F 131 " --> pdb=" O   PHE F 116 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 126 through 127
      removed outlier: 3.602A  pdb=" N   PHE F 126 " --> pdb=" O   ASN F 142 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN F 142 " --> pdb=" O   PHE F 126 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL F 137 " --> pdb=" O   ILE F 157 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY F 139 " --> pdb=" O   LEU F 155 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL F 153 " --> pdb=" O   LEU F 141 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 166 through 167
      removed outlier: 4.071A  pdb=" N   LEU F 167 " --> pdb=" O   THR F 182 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR F 182 " --> pdb=" O   LEU F 167 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   VAL F 196 " --> pdb=" O   LEU F 183 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 176 through 177
      removed outlier: 4.097A  pdb=" N   GLN F 203 " --> pdb=" O   LEU F 211 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR F 234 " --> pdb=" O   GLY F 247 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   SER F 258 " --> pdb=" O   SER F 246 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE F 256 " --> pdb=" O   GLN F 248 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA F 257 " --> pdb=" O   THR F 273 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU F 259 " --> pdb=" O   ILE F 271 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE F 271 " --> pdb=" O   LEU F 259 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR F 274 " --> pdb=" O   SER F 300 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER F 300 " --> pdb=" O   THR F 274 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    558 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1185
        1.30 -     1.43: 1964
        1.43 -     1.55: 4237
        1.55 -     1.68: 4
        1.68 -     1.80: 32
  Bond restraints: 7422
  Sorted by residual:
  bond pdb=" C21 46E A 401 "
       pdb=" O21 46E A 401 "
    ideal  model  delta    sigma   weight residual
    1.331  1.402 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C31 46E A 401 "
       pdb=" O31 46E A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.396 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C   SER B  55 "
       pdb=" N   PRO B  56 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 7.94e+00
  bond pdb=" C   SER G  55 "
       pdb=" N   PRO G  56 "
    ideal  model  delta    sigma   weight residual
    1.334  1.399 -0.065 2.34e-02 1.83e+03 7.81e+00
  bond pdb=" C   GLN F 294 "
       pdb=" N   PRO F 295 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.19e+00
  ... (remaining 7417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 9838
        3.59 -     7.18: 183
        7.18 -    10.78: 26
       10.78 -    14.37: 3
       14.37 -    17.96: 3
  Bond angle restraints: 10053
  Sorted by residual:
  angle pdb=" N   ILE A 293 "
        pdb=" CA  ILE A 293 "
        pdb=" C   ILE A 293 "
      ideal   model   delta    sigma   weight residual
     113.20  106.10    7.10 9.60e-01 1.09e+00 5.46e+01
  angle pdb=" N   ILE F 293 "
        pdb=" CA  ILE F 293 "
        pdb=" C   ILE F 293 "
      ideal   model   delta    sigma   weight residual
     113.20  106.10    7.10 9.60e-01 1.09e+00 5.46e+01
  angle pdb=" O11 46E A 401 "
        pdb=" P   46E A 401 "
        pdb=" O13 46E A 401 "
      ideal   model   delta    sigma   weight residual
      93.37  111.27  -17.90 3.00e+00 1.11e-01 3.56e+01
  angle pdb=" C   VAL A 205 "
        pdb=" N   THR A 206 "
        pdb=" CA  THR A 206 "
      ideal   model   delta    sigma   weight residual
     121.80  135.59  -13.79 2.44e+00 1.68e-01 3.19e+01
  angle pdb=" C   VAL F 205 "
        pdb=" N   THR F 206 "
        pdb=" CA  THR F 206 "
      ideal   model   delta    sigma   weight residual
     121.80  135.50  -13.70 2.44e+00 1.68e-01 3.15e+01
  ... (remaining 10048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3738
       17.79 -    35.59: 503
       35.59 -    53.38: 90
       53.38 -    71.17: 25
       71.17 -    88.97: 17
  Dihedral angle restraints: 4373
    sinusoidal: 1719
      harmonic: 2654
  Sorted by residual:
  dihedral pdb=" CA  VAL A 205 "
           pdb=" C   VAL A 205 "
           pdb=" N   THR A 206 "
           pdb=" CA  THR A 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.16   28.84     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  VAL F 205 "
           pdb=" C   VAL F 205 "
           pdb=" N   THR F 206 "
           pdb=" CA  THR F 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.17   28.83     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ARG B  47 "
           pdb=" C   ARG B  47 "
           pdb=" N   PRO B  48 "
           pdb=" CA  PRO B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.29  -28.71     0      5.00e+00 4.00e-02 3.30e+01
  ... (remaining 4370 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 822
       0.060 -    0.120: 235
       0.120 -    0.180: 71
       0.180 -    0.241: 9
       0.241 -    0.301: 4
  Chirality restraints: 1141
  Sorted by residual:
  chirality pdb=" CB  VAL F 332 "
            pdb=" CA  VAL F 332 "
            pdb=" CG1 VAL F 332 "
            pdb=" CG2 VAL F 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  ASN F 321 "
            pdb=" N   ASN F 321 "
            pdb=" C   ASN F 321 "
            pdb=" CB  ASN F 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1138 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 333 "   -0.048 5.00e-02 4.00e+02   7.24e-02 8.40e+00
        pdb=" N   PRO A 334 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 334 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 334 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 333 "    0.048 5.00e-02 4.00e+02   7.20e-02 8.29e+00
        pdb=" N   PRO F 334 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO F 334 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO F 334 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 206 "    0.045 5.00e-02 4.00e+02   6.79e-02 7.39e+00
        pdb=" N   PRO A 207 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2410
        2.82 -     3.34: 6024
        3.34 -     3.86: 10495
        3.86 -     4.38: 11252
        4.38 -     4.90: 20355
  Nonbonded interactions: 50536
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN F 203 "
            pdb=" O   ILE I  41 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   PHE J  27 "
            pdb=" OG  SER J  30 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   PHE E  27 "
            pdb=" OG  SER E  30 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG  SER A 246 "
            pdb=" N   GLY A 247 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" OG  SER F 246 "
            pdb=" N   GLY F 247 "
     model   vdw
     2.335 3.120
  ... (remaining 50531 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 47 through 373)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'J'
}

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:             0.430
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.120
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
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      :  0.009   0.071   7422  Z= 0.379
  Angle     :  1.227  17.959  10053  Z= 0.617
  Chirality :  0.063   0.301   1141
  Planarity :  0.007   0.072   1272
  Dihedral  : 17.480  88.966   2653
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.41 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.16 (0.22), residues: 888
  helix: -4.57 (0.14), residues: 202
  sheet: -3.78 (0.22), residues: 366
  loop : -3.66 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 330 
 TYR   0.024   0.002   TYR F 143 
 PHE   0.030   0.003   PHE A  92 
 TRP   0.015   0.002   TRP D  36 
 HIS   0.007   0.001   HIS I  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00855 ( 7422)
  covalent geometry    : angle       1.22736 (10053)
  hydrogen bonds       : bond        0.33245 (  204)
  hydrogen bonds       : angle      10.46351 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 196
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 GLN cc_start: 0.8420 (pp30) cc_final: 0.7844 (pp30)
REVERT: A  217 TYR cc_start: 0.8576 (t80) cc_final: 0.8194 (t80)
REVERT: A  219 ARG cc_start: 0.8833 (ttt180) cc_final: 0.8501 (ttp-170)
REVERT: B   26 ASN cc_start: 0.7181 (t0) cc_final: 0.6845 (t0)
REVERT: C   87 PHE cc_start: 0.6499 (p90) cc_final: 0.6297 (p90)
REVERT: C   94 LYS cc_start: 0.9047 (tptt) cc_final: 0.8429 (tppt)
REVERT: D   42 TRP cc_start: 0.8507 (t60) cc_final: 0.7847 (t-100)
REVERT: E   41 PHE cc_start: 0.9204 (m-80) cc_final: 0.8978 (m-80)
REVERT: F  203 GLN cc_start: 0.8300 (pp30) cc_final: 0.7892 (pp30)
REVERT: F  214 GLU cc_start: 0.8795 (pp20) cc_final: 0.8585 (pp20)
REVERT: F  219 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8572 (ttp-170)
REVERT: J   41 PHE cc_start: 0.9164 (m-80) cc_final: 0.8887 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 202
  average time/residue: 0.0922
  time to fit residues: 24.5984
Evaluate side-chains
  161 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  65 ASN
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.173115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.127500 restraints weight = 8812.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125478 restraints weight = 9399.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.126649 restraints weight = 9760.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.127728 restraints weight = 5720.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.128588 restraints weight = 5060.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7422  Z= 0.210
  Angle     :  0.841  11.961  10053  Z= 0.415
  Chirality :  0.047   0.171   1141
  Planarity :  0.005   0.055   1272
  Dihedral  :  9.120  73.120   1003
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.74 %
    Favored  : 86.26 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 22.76 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.26), residues: 888
  helix: -2.94 (0.27), residues: 210
  sheet: -3.06 (0.25), residues: 366
  loop : -3.25 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  47 
 TYR   0.014   0.002   TYR I  30 
 PHE   0.019   0.002   PHE F  92 
 TRP   0.010   0.001   TRP I  36 
 HIS   0.002   0.001   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 7422)
  covalent geometry    : angle       0.84123 (10053)
  hydrogen bonds       : bond        0.06000 (  204)
  hydrogen bonds       : angle       6.46750 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8023 (mpp) cc_final: 0.7794 (mmm)
REVERT: A  203 GLN cc_start: 0.8035 (pp30) cc_final: 0.7628 (pp30)
REVERT: A  217 TYR cc_start: 0.8265 (t80) cc_final: 0.8063 (t80)
REVERT: A  318 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8356 (pp)
REVERT: A  369 MET cc_start: 0.8645 (ttm) cc_final: 0.8242 (ttt)
REVERT: B   26 ASN cc_start: 0.7252 (t0) cc_final: 0.7049 (t0)
REVERT: B   35 PHE cc_start: 0.8856 (t80) cc_final: 0.8640 (t80)
REVERT: C   87 PHE cc_start: 0.6727 (p90) cc_final: 0.6463 (p90)
REVERT: C   94 LYS cc_start: 0.8945 (tptt) cc_final: 0.8459 (tppt)
REVERT: D   40 MET cc_start: 0.8307 (tpp) cc_final: 0.7831 (tpp)
REVERT: D   42 TRP cc_start: 0.8771 (t60) cc_final: 0.7655 (t60)
REVERT: F  164 MET cc_start: 0.8002 (mpp) cc_final: 0.7773 (mmm)
REVERT: F  203 GLN cc_start: 0.8013 (pp30) cc_final: 0.7624 (pp30)
REVERT: F  236 TYR cc_start: 0.8305 (t80) cc_final: 0.7961 (t80)
REVERT: F  318 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8357 (pp)
REVERT: G   35 PHE cc_start: 0.8833 (t80) cc_final: 0.8619 (t80)
REVERT: J   38 ASN cc_start: 0.8586 (m110) cc_final: 0.8355 (m110)
REVERT: J   41 PHE cc_start: 0.9006 (m-80) cc_final: 0.8737 (m-80)
  outliers start: 33
  outliers final: 24
  residues processed: 191
  average time/residue: 0.0710
  time to fit residues: 18.6296
Evaluate side-chains
  186 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  351 THR
Chi-restraints excluded: chain F residue  353 ILE
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  104 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   40 MET
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.172166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128492 restraints weight = 8738.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.126014 restraints weight = 10598.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127320 restraints weight = 8835.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.131827 restraints weight = 5988.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131851 restraints weight = 4374.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7422  Z= 0.219
  Angle     :  0.834  12.209  10053  Z= 0.408
  Chirality :  0.047   0.181   1141
  Planarity :  0.005   0.047   1272
  Dihedral  :  8.698  71.125   1003
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.30 %
    Favored  : 85.70 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.55 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.08 (0.28), residues: 888
  helix: -1.76 (0.33), residues: 206
  sheet: -2.79 (0.26), residues: 368
  loop : -2.91 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  47 
 TYR   0.010   0.002   TYR A  79 
 PHE   0.019   0.002   PHE F  92 
 TRP   0.012   0.001   TRP B  41 
 HIS   0.002   0.001   HIS G  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 7422)
  covalent geometry    : angle       0.83423 (10053)
  hydrogen bonds       : bond        0.05574 (  204)
  hydrogen bonds       : angle       6.07450 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.8857 (tt) cc_final: 0.8654 (tt)
REVERT: A  203 GLN cc_start: 0.7982 (pp30) cc_final: 0.7698 (pp30)
REVERT: A  318 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8458 (pp)
REVERT: A  369 MET cc_start: 0.8327 (ttm) cc_final: 0.8048 (ttt)
REVERT: C   94 LYS cc_start: 0.8861 (tptt) cc_final: 0.8491 (tppt)
REVERT: D   42 TRP cc_start: 0.8672 (t60) cc_final: 0.7293 (t60)
REVERT: E   25 GLN cc_start: 0.7683 (tp-100) cc_final: 0.6666 (mp10)
REVERT: F  155 LEU cc_start: 0.8900 (tt) cc_final: 0.8687 (tt)
REVERT: F  203 GLN cc_start: 0.8002 (pp30) cc_final: 0.7697 (pp30)
REVERT: F  217 TYR cc_start: 0.8133 (t80) cc_final: 0.7927 (t80)
REVERT: F  236 TYR cc_start: 0.8395 (t80) cc_final: 0.8081 (t80)
REVERT: F  318 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8467 (pp)
REVERT: F  369 MET cc_start: 0.8385 (ttm) cc_final: 0.8070 (ttt)
REVERT: H  120 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: J   41 PHE cc_start: 0.8933 (m-80) cc_final: 0.8640 (m-80)
  outliers start: 40
  outliers final: 31
  residues processed: 193
  average time/residue: 0.0751
  time to fit residues: 19.9942
Evaluate side-chains
  192 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  333 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  353 ILE
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  104 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   40 MET
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 85 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 GLN
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.174552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129020 restraints weight = 8802.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.125108 restraints weight = 9110.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127245 restraints weight = 9396.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.127975 restraints weight = 5714.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.129041 restraints weight = 5192.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7422  Z= 0.167
  Angle     :  0.811  13.352  10053  Z= 0.389
  Chirality :  0.047   0.203   1141
  Planarity :  0.004   0.052   1272
  Dihedral  :  8.153  77.247   1003
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.49 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.29), residues: 888
  helix: -1.03 (0.37), residues: 200
  sheet: -2.47 (0.26), residues: 366
  loop : -2.58 (0.39), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  47 
 TYR   0.012   0.001   TYR A 217 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.010   0.001   TRP B  41 
 HIS   0.002   0.000   HIS G  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7422)
  covalent geometry    : angle       0.81099 (10053)
  hydrogen bonds       : bond        0.04633 (  204)
  hydrogen bonds       : angle       5.81017 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 169
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.8873 (tt) cc_final: 0.8664 (tt)
REVERT: A  219 ARG cc_start: 0.8458 (ttt180) cc_final: 0.7988 (ttt-90)
REVERT: A  318 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8349 (pp)
REVERT: A  369 MET cc_start: 0.8631 (ttm) cc_final: 0.8357 (ttt)
REVERT: C   94 LYS cc_start: 0.8951 (tptt) cc_final: 0.8473 (tppt)
REVERT: D   42 TRP cc_start: 0.8780 (t60) cc_final: 0.7445 (t60)
REVERT: E   25 GLN cc_start: 0.7711 (tp-100) cc_final: 0.6901 (mp10)
REVERT: F  155 LEU cc_start: 0.8918 (tt) cc_final: 0.8698 (tt)
REVERT: F  236 TYR cc_start: 0.8349 (t80) cc_final: 0.7996 (t80)
REVERT: F  318 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8372 (pp)
REVERT: F  369 MET cc_start: 0.8674 (ttm) cc_final: 0.8408 (ttt)
REVERT: I   42 TRP cc_start: 0.8619 (t60) cc_final: 0.7211 (t60)
REVERT: J   41 PHE cc_start: 0.9034 (m-80) cc_final: 0.8688 (m-80)
  outliers start: 37
  outliers final: 33
  residues processed: 189
  average time/residue: 0.0742
  time to fit residues: 19.5331
Evaluate side-chains
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  259 LEU
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  333 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  353 ILE
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  104 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0060
   chunk 26 optimal weight:    0.0770
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5754

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  38 ASN
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 311 GLN
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.178935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.133620 restraints weight = 8725.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.133367 restraints weight = 9564.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134686 restraints weight = 8781.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135214 restraints weight = 5178.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.135640 restraints weight = 4963.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7422  Z= 0.123
  Angle     :  0.778  15.108  10053  Z= 0.368
  Chirality :  0.045   0.241   1141
  Planarity :  0.004   0.052   1272
  Dihedral  :  7.183  81.851   1001
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 31.59 %
    Favored  : 65.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.29), residues: 888
  helix: -0.71 (0.37), residues: 202
  sheet: -2.04 (0.27), residues: 364
  loop : -2.57 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  47 
 TYR   0.019   0.001   TYR F 217 
 PHE   0.013   0.001   PHE A 359 
 TRP   0.010   0.001   TRP B  41 
 HIS   0.001   0.000   HIS G  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7422)
  covalent geometry    : angle       0.77810 (10053)
  hydrogen bonds       : bond        0.03567 (  204)
  hydrogen bonds       : angle       5.45173 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8216 (p0) cc_final: 0.7849 (p0)
REVERT: A  164 MET cc_start: 0.8005 (mpp) cc_final: 0.7698 (mmm)
REVERT: A  167 LEU cc_start: 0.8763 (tt) cc_final: 0.8083 (mp)
REVERT: A  369 MET cc_start: 0.8279 (ttm) cc_final: 0.8040 (ttt)
REVERT: C   94 LYS cc_start: 0.8853 (tptt) cc_final: 0.8483 (tppt)
REVERT: C  122 GLN cc_start: 0.7681 (pt0) cc_final: 0.7334 (tt0)
REVERT: D   18 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7993 (tp40)
REVERT: D   42 TRP cc_start: 0.8643 (t60) cc_final: 0.7242 (t60)
REVERT: E   25 GLN cc_start: 0.7599 (tp-100) cc_final: 0.6794 (mp10)
REVERT: E   38 ASN cc_start: 0.8230 (m-40) cc_final: 0.8011 (m110)
REVERT: F   87 ASP cc_start: 0.8237 (p0) cc_final: 0.7874 (p0)
REVERT: F  164 MET cc_start: 0.7956 (mpp) cc_final: 0.7641 (mmm)
REVERT: F  167 LEU cc_start: 0.8775 (tt) cc_final: 0.8102 (mp)
REVERT: F  369 MET cc_start: 0.8411 (ttm) cc_final: 0.8148 (ttt)
REVERT: H  122 GLN cc_start: 0.7643 (pt0) cc_final: 0.7303 (tt0)
REVERT: I   42 TRP cc_start: 0.8428 (t60) cc_final: 0.7175 (t60)
REVERT: J   41 PHE cc_start: 0.8996 (m-80) cc_final: 0.8707 (m-80)
  outliers start: 24
  outliers final: 17
  residues processed: 191
  average time/residue: 0.0614
  time to fit residues: 16.5008
Evaluate side-chains
  185 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 GLN
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.176662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133520 restraints weight = 8733.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.131369 restraints weight = 10616.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.133069 restraints weight = 9602.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133617 restraints weight = 5845.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.134247 restraints weight = 5287.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7422  Z= 0.145
  Angle     :  0.800  16.439  10053  Z= 0.376
  Chirality :  0.046   0.230   1141
  Planarity :  0.004   0.053   1272
  Dihedral  :  7.030  82.473   1001
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 30.56 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.30), residues: 888
  helix: -0.37 (0.38), residues: 202
  sheet: -1.88 (0.27), residues: 366
  loop : -2.48 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  47 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.016   0.001   PHE A 359 
 TRP   0.010   0.001   TRP B  41 
 HIS   0.004   0.000   HIS I  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7422)
  covalent geometry    : angle       0.79998 (10053)
  hydrogen bonds       : bond        0.03929 (  204)
  hydrogen bonds       : angle       5.35650 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8321 (p0) cc_final: 0.7963 (p0)
REVERT: A  219 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7941 (ttt-90)
REVERT: A  369 MET cc_start: 0.8276 (ttm) cc_final: 0.8019 (ttt)
REVERT: C   94 LYS cc_start: 0.8854 (tptt) cc_final: 0.8485 (tppt)
REVERT: D   42 TRP cc_start: 0.8677 (t60) cc_final: 0.7241 (t60)
REVERT: E   25 GLN cc_start: 0.7628 (tp-100) cc_final: 0.6957 (mp10)
REVERT: F   87 ASP cc_start: 0.8331 (p0) cc_final: 0.7965 (p0)
REVERT: F  318 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8356 (pp)
REVERT: F  369 MET cc_start: 0.8372 (ttm) cc_final: 0.8080 (ttt)
REVERT: H  122 GLN cc_start: 0.7647 (pt0) cc_final: 0.7306 (tt0)
REVERT: J   41 PHE cc_start: 0.9062 (m-80) cc_final: 0.8790 (m-80)
  outliers start: 34
  outliers final: 24
  residues processed: 195
  average time/residue: 0.0702
  time to fit residues: 19.2205
Evaluate side-chains
  187 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  351 THR
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 47 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  18 GLN
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.177392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131906 restraints weight = 8705.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.129138 restraints weight = 9985.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.131280 restraints weight = 9494.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.131771 restraints weight = 5985.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.132512 restraints weight = 5479.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7422  Z= 0.145
  Angle     :  0.819  18.591  10053  Z= 0.382
  Chirality :  0.046   0.216   1141
  Planarity :  0.004   0.051   1272
  Dihedral  :  6.880  82.295   1001
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.70 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 31.84 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.30), residues: 888
  helix: -0.19 (0.39), residues: 202
  sheet: -1.72 (0.27), residues: 366
  loop : -2.41 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  47 
 TYR   0.018   0.001   TYR A 217 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.010   0.001   TRP B  41 
 HIS   0.001   0.000   HIS G  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7422)
  covalent geometry    : angle       0.81898 (10053)
  hydrogen bonds       : bond        0.03694 (  204)
  hydrogen bonds       : angle       5.22978 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8288 (p0) cc_final: 0.7924 (p0)
REVERT: A  156 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8001 (tt0)
REVERT: A  219 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7932 (mtp180)
REVERT: A  369 MET cc_start: 0.8366 (ttm) cc_final: 0.8093 (ttt)
REVERT: C   94 LYS cc_start: 0.8871 (tptt) cc_final: 0.8474 (tppt)
REVERT: D   42 TRP cc_start: 0.8759 (t60) cc_final: 0.7258 (t60)
REVERT: E   25 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7079 (mp10)
REVERT: F   87 ASP cc_start: 0.8332 (p0) cc_final: 0.7969 (p0)
REVERT: F  164 MET cc_start: 0.7752 (mmm) cc_final: 0.7479 (mpp)
REVERT: F  167 LEU cc_start: 0.8764 (tt) cc_final: 0.8039 (mp)
REVERT: F  369 MET cc_start: 0.8443 (ttm) cc_final: 0.8125 (ttt)
REVERT: G   47 ARG cc_start: 0.7185 (mpp80) cc_final: 0.6982 (mpp80)
REVERT: J   41 PHE cc_start: 0.9085 (m-80) cc_final: 0.8879 (m-80)
REVERT: J   56 MET cc_start: 0.8374 (tpt) cc_final: 0.7875 (tpt)
  outliers start: 35
  outliers final: 28
  residues processed: 190
  average time/residue: 0.0660
  time to fit residues: 17.4764
Evaluate side-chains
  189 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.175945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.130808 restraints weight = 8844.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129877 restraints weight = 9840.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.131505 restraints weight = 9273.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.131856 restraints weight = 5789.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132690 restraints weight = 5399.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7422  Z= 0.170
  Angle     :  0.834  20.099  10053  Z= 0.391
  Chirality :  0.047   0.170   1141
  Planarity :  0.004   0.049   1272
  Dihedral  :  7.019  81.458   1001
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 32.10 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.30), residues: 888
  helix: -0.07 (0.39), residues: 202
  sheet: -1.71 (0.27), residues: 366
  loop : -2.42 (0.39), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  47 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.016   0.002   PHE A 359 
 TRP   0.010   0.001   TRP B  41 
 HIS   0.002   0.000   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7422)
  covalent geometry    : angle       0.83450 (10053)
  hydrogen bonds       : bond        0.04083 (  204)
  hydrogen bonds       : angle       5.29881 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8007 (tt0)
REVERT: A  369 MET cc_start: 0.8232 (ttm) cc_final: 0.7980 (ttt)
REVERT: C   94 LYS cc_start: 0.8900 (tptt) cc_final: 0.8525 (tppt)
REVERT: D   42 TRP cc_start: 0.8650 (t60) cc_final: 0.7215 (t60)
REVERT: E   25 GLN cc_start: 0.7608 (tp-100) cc_final: 0.6969 (mp10)
REVERT: F  156 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7999 (tt0)
REVERT: F  164 MET cc_start: 0.7760 (mmm) cc_final: 0.7539 (mpp)
REVERT: F  369 MET cc_start: 0.8309 (ttm) cc_final: 0.8011 (ttt)
REVERT: G   47 ARG cc_start: 0.7040 (mpp80) cc_final: 0.6825 (mpp80)
REVERT: J   41 PHE cc_start: 0.9049 (m-80) cc_final: 0.8829 (m-80)
  outliers start: 40
  outliers final: 35
  residues processed: 190
  average time/residue: 0.0669
  time to fit residues: 17.9636
Evaluate side-chains
  194 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain F residue   49 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  101 SER
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  156 GLN
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  259 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    0.0770
   chunk 60 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0000
   chunk 55 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    0.7746

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

Flipped N/Q/H residues before XYZ refinement:
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.179420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133916 restraints weight = 8622.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.131973 restraints weight = 10302.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133121 restraints weight = 8721.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.137297 restraints weight = 6013.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.137257 restraints weight = 4737.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7422  Z= 0.133
  Angle     :  0.808  19.184  10053  Z= 0.377
  Chirality :  0.045   0.163   1141
  Planarity :  0.004   0.050   1272
  Dihedral  :  6.608  82.216   1001
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 32.99 %
    Favored  : 63.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.30), residues: 888
  helix:  0.07 (0.39), residues: 202
  sheet: -1.52 (0.28), residues: 366
  loop : -2.43 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  47 
 TYR   0.019   0.001   TYR A 217 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.011   0.001   TRP B  41 
 HIS   0.001   0.000   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7422)
  covalent geometry    : angle       0.80843 (10053)
  hydrogen bonds       : bond        0.03247 (  204)
  hydrogen bonds       : angle       5.09960 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 166
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8194 (p0) cc_final: 0.7838 (p0)
REVERT: A  156 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7971 (tt0)
REVERT: A  167 LEU cc_start: 0.8709 (tt) cc_final: 0.8011 (mp)
REVERT: A  369 MET cc_start: 0.8137 (ttm) cc_final: 0.7887 (ttt)
REVERT: C   94 LYS cc_start: 0.8873 (tptt) cc_final: 0.8507 (tppt)
REVERT: D   42 TRP cc_start: 0.8630 (t60) cc_final: 0.7085 (t60)
REVERT: E   25 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7038 (mp10)
REVERT: E   56 MET cc_start: 0.8133 (tpt) cc_final: 0.7672 (tpt)
REVERT: F   87 ASP cc_start: 0.8250 (p0) cc_final: 0.7894 (p0)
REVERT: F  156 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7975 (tt0)
REVERT: F  164 MET cc_start: 0.7747 (mmm) cc_final: 0.7516 (mpp)
REVERT: F  167 LEU cc_start: 0.8668 (tt) cc_final: 0.8052 (mp)
REVERT: F  369 MET cc_start: 0.8200 (ttm) cc_final: 0.7918 (ttt)
REVERT: G   47 ARG cc_start: 0.6989 (mpp80) cc_final: 0.6756 (mpp80)
REVERT: J   41 PHE cc_start: 0.9040 (m-80) cc_final: 0.8827 (m-80)
  outliers start: 31
  outliers final: 28
  residues processed: 188
  average time/residue: 0.0712
  time to fit residues: 18.6303
Evaluate side-chains
  192 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  156 GLN
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  259 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue   22 THR
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  127 GLU
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 0 optimal weight:   20.0000
   chunk 48 optimal weight:    0.4980
   chunk 38 optimal weight:    8.9990
   chunk 78 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** E  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.179972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133326 restraints weight = 8704.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131539 restraints weight = 9512.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.133314 restraints weight = 8740.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133950 restraints weight = 5657.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134595 restraints weight = 5202.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7422  Z= 0.133
  Angle     :  0.803  17.845  10053  Z= 0.375
  Chirality :  0.045   0.166   1141
  Planarity :  0.004   0.052   1272
  Dihedral  :  6.437  82.758   1001
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 34.02 %
    Favored  : 62.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.30), residues: 888
  helix:  0.25 (0.40), residues: 200
  sheet: -1.46 (0.27), residues: 380
  loop : -2.23 (0.39), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.018   0.001   TYR A 217 
 PHE   0.015   0.001   PHE A 359 
 TRP   0.011   0.001   TRP B  41 
 HIS   0.001   0.000   HIS F 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7422)
  covalent geometry    : angle       0.80296 (10053)
  hydrogen bonds       : bond        0.03168 (  204)
  hydrogen bonds       : angle       5.01583 (  558)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8268 (p0) cc_final: 0.7924 (p0)
REVERT: A  156 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7958 (tt0)
REVERT: A  167 LEU cc_start: 0.8722 (tt) cc_final: 0.7995 (mp)
REVERT: A  369 MET cc_start: 0.8221 (ttm) cc_final: 0.7942 (ttt)
REVERT: C   94 LYS cc_start: 0.8939 (tptt) cc_final: 0.8411 (tppt)
REVERT: D   18 GLN cc_start: 0.8372 (tp40) cc_final: 0.8148 (tp40)
REVERT: D   42 TRP cc_start: 0.8663 (t60) cc_final: 0.7127 (t60)
REVERT: E   25 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7093 (mp10)
REVERT: E   56 MET cc_start: 0.8210 (tpt) cc_final: 0.7771 (tpt)
REVERT: F   87 ASP cc_start: 0.8283 (p0) cc_final: 0.7928 (p0)
REVERT: F  156 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7973 (tt0)
REVERT: F  164 MET cc_start: 0.7814 (mmm) cc_final: 0.7565 (mpp)
REVERT: F  167 LEU cc_start: 0.8678 (tt) cc_final: 0.8059 (mp)
REVERT: F  369 MET cc_start: 0.8290 (ttm) cc_final: 0.7975 (ttt)
REVERT: J   41 PHE cc_start: 0.9070 (m-80) cc_final: 0.8805 (m-80)
  outliers start: 26
  outliers final: 22
  residues processed: 187
  average time/residue: 0.0733
  time to fit residues: 19.5033
Evaluate side-chains
  186 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 HIS
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue   93 THR
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  101 SER
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  156 GLN
Chi-restraints excluded: chain F residue  234 THR
Chi-restraints excluded: chain F residue  259 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  357 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.0030
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0060
   chunk 59 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0370
   chunk 45 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0370
   chunk 2 optimal weight:    0.0470
   overall best weight:    0.0260

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

Flipped N/Q/H residues before XYZ refinement:
D  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.187398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.141868 restraints weight = 8711.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.141234 restraints weight = 9239.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143043 restraints weight = 8372.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143350 restraints weight = 5377.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.144029 restraints weight = 5143.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7422  Z= 0.127
  Angle     :  0.781  17.292  10053  Z= 0.362
  Chirality :  0.044   0.161   1141
  Planarity :  0.004   0.053   1272
  Dihedral  :  5.878  87.179    999
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 34.40 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.30), residues: 888
  helix:  0.36 (0.40), residues: 200
  sheet: -1.24 (0.28), residues: 374
  loop : -2.16 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  47 
 TYR   0.020   0.001   TYR A 217 
 PHE   0.012   0.001   PHE A 359 
 TRP   0.015   0.001   TRP B  41 
 HIS   0.001   0.000   HIS G  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7422)
  covalent geometry    : angle       0.78093 (10053)
  hydrogen bonds       : bond        0.02158 (  204)
  hydrogen bonds       : angle       4.69096 (  558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1205.96 seconds
wall clock time: 21 minutes 26.02 seconds (1286.02 seconds total)