Starting phenix.real_space_refine
on Wed Feb 12 06:53:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jnf_9851/02_2025/6jnf_9851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jnf_9851/02_2025/6jnf_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_9851/02_2025/6jnf_9851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jnf_9851/02_2025/6jnf_9851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jnf_9851/02_2025/6jnf_9851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jnf_9851/02_2025/6jnf_9851.cif"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7271
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'46E': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    F, G, H, I, J
  Time building chain proxies: 4.94, per 1000 atoms: 0.68
  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: 1.60
  Conformation dependent library (CDL) restraints added in 938.6 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: 0.84
  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: 1.77

  Time building geometry restraints manager: 1.88 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:             0.360
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.060
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.800
-------------------------------------------------------------------------------
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= 0.544
  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 : 5.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.015   0.002   TRP D  36 
 HIS   0.007   0.001   HIS I  43 
 PHE   0.030   0.003   PHE A  92 
 TYR   0.024   0.002   TYR F 143 
 ARG   0.003   0.001   ARG F 330 

*********************** 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  : 0.867 
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: 0.6500 (p90) cc_final: 0.6296 (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: 0.8979 (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: 0.2121
  time to fit residues: 55.8910
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  : 0.898 
-------------------------------------------------------------------------------
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 74 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:   20.0000
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
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 = 0.177947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132364 restraints weight = 9043.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.130690 restraints weight = 9152.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.131344 restraints weight = 10782.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7422  Z= 0.189
  Angle     :  0.779  11.998  10053  Z= 0.382
  Chirality :  0.045   0.162   1141
  Planarity :  0.005   0.054   1272
  Dihedral  :  8.399  61.396   1003
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 24.55 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.86 (0.25), residues: 888
  helix: -3.07 (0.26), residues: 210
  sheet: -2.93 (0.25), residues: 366
  loop : -3.31 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  36 
 HIS   0.002   0.001   HIS A 102 
 PHE   0.011   0.001   PHE A 201 
 TYR   0.013   0.001   TYR I  30 
 ARG   0.004   0.000   ARG B  47 

*********************** 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
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8400 (p0) cc_final: 0.8141 (p0)
REVERT: A  164 MET cc_start: 0.7990 (mpp) cc_final: 0.7765 (mmm)
REVERT: A  167 LEU cc_start: 0.8790 (tt) cc_final: 0.7962 (mp)
REVERT: A  318 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8213 (pp)
REVERT: A  367 LEU cc_start: 0.8411 (tp) cc_final: 0.8207 (tp)
REVERT: A  369 MET cc_start: 0.8589 (ttm) cc_final: 0.8202 (ttt)
REVERT: C   87 PHE cc_start: 0.6710 (p90) cc_final: 0.6461 (p90)
REVERT: C   94 LYS cc_start: 0.8927 (tptt) cc_final: 0.8453 (tppt)
REVERT: D   40 MET cc_start: 0.8113 (tpp) cc_final: 0.7689 (tpp)
REVERT: D   42 TRP cc_start: 0.8348 (t60) cc_final: 0.7411 (t60)
REVERT: E   41 PHE cc_start: 0.9087 (m-80) cc_final: 0.8859 (m-80)
REVERT: F   87 ASP cc_start: 0.8413 (p0) cc_final: 0.8149 (p0)
REVERT: F  167 LEU cc_start: 0.8810 (tt) cc_final: 0.7993 (mp)
REVERT: F  318 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (pp)
  outliers start: 16
  outliers final: 12
  residues processed: 193
  average time/residue: 0.1889
  time to fit residues: 48.5360
Evaluate side-chains
  181 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  318 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain D residue   17 HIS
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue  194 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   40 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 56 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 43 optimal weight:    0.1980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.174240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128215 restraints weight = 8737.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.125197 restraints weight = 9521.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.126989 restraints weight = 9347.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2640

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= 0.276
  Angle     :  0.809  12.023  10053  Z= 0.392
  Chirality :  0.046   0.184   1141
  Planarity :  0.005   0.047   1272
  Dihedral  :  8.063  67.784   1001
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.98 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 25.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.98 (0.27), residues: 888
  helix: -1.74 (0.33), residues: 204
  sheet: -2.63 (0.26), residues: 366
  loop : -2.94 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 260 
 HIS   0.002   0.001   HIS G  43 
 PHE   0.022   0.002   PHE B  35 
 TYR   0.012   0.002   TYR A 217 
 ARG   0.003   0.000   ARG B  47 

*********************** 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
  206 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  318 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8391 (pp)
REVERT: A  369 MET cc_start: 0.8702 (ttm) cc_final: 0.8391 (ttt)
REVERT: C   87 PHE cc_start: 0.6511 (p90) cc_final: 0.6116 (p90)
REVERT: C   94 LYS cc_start: 0.8961 (tptt) cc_final: 0.8476 (tppt)
REVERT: D   42 TRP cc_start: 0.8838 (t60) cc_final: 0.7445 (t60)
REVERT: E   25 GLN cc_start: 0.7767 (tp-100) cc_final: 0.6850 (mp10)
REVERT: E   41 PHE cc_start: 0.9164 (m-80) cc_final: 0.8915 (m-80)
REVERT: F  217 TYR cc_start: 0.8314 (t80) cc_final: 0.8091 (t80)
REVERT: F  219 ARG cc_start: 0.8469 (ttt180) cc_final: 0.8013 (ttt-90)
REVERT: F  318 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8411 (pp)
REVERT: F  369 MET cc_start: 0.8722 (ttm) cc_final: 0.8410 (ttt)
REVERT: I   44 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8103 (mm)
  outliers start: 35
  outliers final: 25
  residues processed: 189
  average time/residue: 0.1754
  time to fit residues: 44.9255
Evaluate side-chains
  190 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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  318 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 C residue  114 SER
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  234 THR
Chi-restraints excluded: chain F residue  318 LEU
Chi-restraints excluded: chain F residue  351 THR
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   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   44 LEU
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 6 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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**
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 = 0.4199 r_free = 0.4199 target = 0.177778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.132350 restraints weight = 8761.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130440 restraints weight = 9515.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.131242 restraints weight = 10059.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2976

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= 0.212
  Angle     :  0.784  11.832  10053  Z= 0.376
  Chirality :  0.046   0.183   1141
  Planarity :  0.004   0.051   1272
  Dihedral  :  7.505  75.234   1001
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 28.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.28), residues: 888
  helix: -0.98 (0.36), residues: 202
  sheet: -2.26 (0.26), residues: 366
  loop : -2.77 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 260 
 HIS   0.003   0.000   HIS D  43 
 PHE   0.024   0.001   PHE G  35 
 TYR   0.014   0.001   TYR A 217 
 ARG   0.002   0.000   ARG G  47 

*********************** 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
  195 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8310 (p0) cc_final: 0.7987 (p0)
REVERT: A  367 LEU cc_start: 0.8424 (tp) cc_final: 0.8220 (tp)
REVERT: A  369 MET cc_start: 0.8652 (ttm) cc_final: 0.8378 (ttt)
REVERT: C   87 PHE cc_start: 0.6549 (p90) cc_final: 0.6331 (p90)
REVERT: C   94 LYS cc_start: 0.8908 (tptt) cc_final: 0.8464 (tppt)
REVERT: C  122 GLN cc_start: 0.7720 (pt0) cc_final: 0.7289 (tt0)
REVERT: D   42 TRP cc_start: 0.8760 (t60) cc_final: 0.7398 (t60)
REVERT: E   25 GLN cc_start: 0.7694 (tp-100) cc_final: 0.6801 (mp10)
REVERT: E   41 PHE cc_start: 0.9078 (m-80) cc_final: 0.8836 (m-80)
REVERT: F   87 ASP cc_start: 0.8344 (p0) cc_final: 0.8023 (p0)
REVERT: F  219 ARG cc_start: 0.8256 (ttt180) cc_final: 0.8005 (ttt-90)
REVERT: F  369 MET cc_start: 0.8569 (ttm) cc_final: 0.8310 (ttt)
REVERT: H  122 GLN cc_start: 0.7645 (pt0) cc_final: 0.7225 (tt0)
  outliers start: 28
  outliers final: 23
  residues processed: 184
  average time/residue: 0.1726
  time to fit residues: 43.3556
Evaluate side-chains
  186 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  234 THR
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  357 LEU
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  114 SER
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  333 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   88 VAL
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   45 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.5788

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.173070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129289 restraints weight = 8733.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127573 restraints weight = 10002.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128390 restraints weight = 10659.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.3128

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= 0.254
  Angle     :  0.801  14.263  10053  Z= 0.385
  Chirality :  0.047   0.238   1141
  Planarity :  0.004   0.057   1272
  Dihedral  :  7.420  79.763   1001
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.85 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.03 %
    Favored  : 66.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.29), residues: 888
  helix: -0.63 (0.37), residues: 208
  sheet: -2.11 (0.26), residues: 366
  loop : -2.67 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 260 
 HIS   0.003   0.001   HIS D  17 
 PHE   0.015   0.001   PHE F  92 
 TYR   0.015   0.001   TYR F 217 
 ARG   0.002   0.000   ARG F  85 

*********************** 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
  201 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 163
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.8042 (mtp180)
REVERT: A  369 MET cc_start: 0.8570 (ttm) cc_final: 0.8284 (ttt)
REVERT: C   94 LYS cc_start: 0.8887 (tptt) cc_final: 0.8484 (tppt)
REVERT: C  122 GLN cc_start: 0.7696 (pt0) cc_final: 0.7349 (tt0)
REVERT: D   18 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8377 (tp40)
REVERT: D   22 GLU cc_start: 0.8341 (pm20) cc_final: 0.7808 (pm20)
REVERT: E   25 GLN cc_start: 0.7701 (tp-100) cc_final: 0.6900 (mp10)
REVERT: E   38 ASN cc_start: 0.8160 (m110) cc_final: 0.7932 (m110)
REVERT: E   41 PHE cc_start: 0.9072 (m-80) cc_final: 0.8837 (m-80)
REVERT: F  164 MET cc_start: 0.7935 (mmm) cc_final: 0.7644 (mpp)
REVERT: F  318 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8455 (pp)
REVERT: F  369 MET cc_start: 0.8509 (ttm) cc_final: 0.8221 (ttt)
REVERT: H  122 GLN cc_start: 0.7637 (pt0) cc_final: 0.7285 (tt0)
REVERT: J   38 ASN cc_start: 0.8237 (m110) cc_final: 0.8027 (m110)
  outliers start: 38
  outliers final: 32
  residues processed: 186
  average time/residue: 0.1749
  time to fit residues: 44.5629
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  : 0.815 
-------------------------------------------------------------------------------
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  234 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  333 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  114 SER
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  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  357 LEU
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 I residue   17 HIS
Chi-restraints excluded: chain I residue   45 VAL
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain J residue   34 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.177608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134450 restraints weight = 8719.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132331 restraints weight = 10424.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134463 restraints weight = 8398.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3363

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= 0.212
  Angle     :  0.810  16.964  10053  Z= 0.379
  Chirality :  0.046   0.233   1141
  Planarity :  0.004   0.057   1272
  Dihedral  :  7.084  80.649   1001
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 30.31 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.30), residues: 888
  helix: -0.25 (0.39), residues: 200
  sheet: -1.87 (0.27), residues: 366
  loop : -2.40 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 260 
 HIS   0.001   0.000   HIS I  43 
 PHE   0.013   0.001   PHE A 359 
 TYR   0.017   0.001   TYR A 217 
 ARG   0.001   0.000   ARG F 219 

*********************** 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
  211 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 167
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8295 (p0) cc_final: 0.7975 (p0)
REVERT: A  156 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8071 (tt0)
REVERT: A  369 MET cc_start: 0.8352 (ttm) cc_final: 0.8067 (ttt)
REVERT: C   94 LYS cc_start: 0.8825 (tptt) cc_final: 0.8484 (tppt)
REVERT: E   25 GLN cc_start: 0.7513 (tp-100) cc_final: 0.6783 (mp10)
REVERT: E   38 ASN cc_start: 0.8205 (m-40) cc_final: 0.7961 (m110)
REVERT: E   41 PHE cc_start: 0.9036 (m-80) cc_final: 0.8817 (m-80)
REVERT: F   87 ASP cc_start: 0.8350 (p0) cc_final: 0.8028 (p0)
REVERT: F  156 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8061 (tt0)
REVERT: F  369 MET cc_start: 0.8285 (ttm) cc_final: 0.8011 (ttt)
REVERT: J   38 ASN cc_start: 0.8189 (m110) cc_final: 0.7987 (m110)
  outliers start: 44
  outliers final: 34
  residues processed: 196
  average time/residue: 0.1585
  time to fit residues: 43.1554
Evaluate side-chains
  194 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
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  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  318 LEU
Chi-restraints excluded: chain A residue  333 LEU
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   93 THR
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain D residue   40 MET
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  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  333 LEU
Chi-restraints excluded: chain F residue  339 LEU
Chi-restraints excluded: chain F residue  351 THR
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   88 VAL
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   32 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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
D  18 GLN
F 109 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.173258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.127203 restraints weight = 8741.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125382 restraints weight = 9924.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.127234 restraints weight = 9481.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3396

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= 0.325
  Angle     :  0.869  17.439  10053  Z= 0.414
  Chirality :  0.049   0.243   1141
  Planarity :  0.005   0.055   1272
  Dihedral  :  7.572  79.817   1001
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.41 %
    Favored  : 85.59 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 30.82 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.30), residues: 888
  helix: -0.12 (0.39), residues: 202
  sheet: -2.03 (0.26), residues: 366
  loop : -2.41 (0.39), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 260 
 HIS   0.002   0.001   HIS G  43 
 PHE   0.019   0.002   PHE F  92 
 TYR   0.020   0.002   TYR F 217 
 ARG   0.004   0.000   ARG A  85 

*********************** 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
  204 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 162
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8178 (tt0)
REVERT: A  369 MET cc_start: 0.8503 (ttm) cc_final: 0.8159 (ttt)
REVERT: C   87 PHE cc_start: 0.6377 (p90) cc_final: 0.6099 (p90)
REVERT: C   94 LYS cc_start: 0.8889 (tptt) cc_final: 0.8487 (tppt)
REVERT: E   25 GLN cc_start: 0.7658 (tp-100) cc_final: 0.6928 (mp10)
REVERT: E   38 ASN cc_start: 0.8159 (m-40) cc_final: 0.7934 (m110)
REVERT: E   41 PHE cc_start: 0.9099 (m-80) cc_final: 0.8893 (m-80)
REVERT: F  156 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8189 (tt0)
REVERT: F  369 MET cc_start: 0.8457 (ttm) cc_final: 0.8131 (ttt)
REVERT: J   38 ASN cc_start: 0.8200 (m110) cc_final: 0.7979 (m110)
  outliers start: 42
  outliers final: 33
  residues processed: 187
  average time/residue: 0.1782
  time to fit residues: 45.2816
Evaluate side-chains
  192 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  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  318 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  114 SER
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  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   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   45 VAL
Chi-restraints excluded: chain J residue   32 LEU
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 66 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.0784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.177225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.131833 restraints weight = 8695.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131429 restraints weight = 9679.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.132334 restraints weight = 8926.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3579

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= 0.216
  Angle     :  0.851  20.670  10053  Z= 0.396
  Chirality :  0.046   0.167   1141
  Planarity :  0.004   0.056   1272
  Dihedral  :  7.108  80.460   1001
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 31.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.30), residues: 888
  helix: -0.03 (0.40), residues: 200
  sheet: -1.88 (0.26), residues: 380
  loop : -2.20 (0.40), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 260 
 HIS   0.003   0.001   HIS I  43 
 PHE   0.014   0.001   PHE A 359 
 TYR   0.023   0.001   TYR F 217 
 ARG   0.003   0.000   ARG G  47 

*********************** 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
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8348 (p0) cc_final: 0.8014 (p0)
REVERT: A  167 LEU cc_start: 0.8694 (tt) cc_final: 0.7977 (mp)
REVERT: A  203 GLN cc_start: 0.8093 (pp30) cc_final: 0.7831 (tm-30)
REVERT: A  369 MET cc_start: 0.8364 (ttm) cc_final: 0.8043 (ttt)
REVERT: C   94 LYS cc_start: 0.8845 (tptt) cc_final: 0.8472 (tppt)
REVERT: E   25 GLN cc_start: 0.7587 (tp-100) cc_final: 0.6917 (mp10)
REVERT: F   87 ASP cc_start: 0.8358 (p0) cc_final: 0.8024 (p0)
REVERT: F  167 LEU cc_start: 0.8803 (tt) cc_final: 0.8145 (mp)
REVERT: F  168 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7387 (mt-10)
REVERT: F  369 MET cc_start: 0.8337 (ttm) cc_final: 0.8025 (ttt)
REVERT: G   47 ARG cc_start: 0.7003 (mpp80) cc_final: 0.6756 (mpp80)
  outliers start: 37
  outliers final: 33
  residues processed: 186
  average time/residue: 0.1865
  time to fit residues: 47.5408
Evaluate side-chains
  194 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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  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  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   93 THR
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain D residue   40 MET
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  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   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain I residue   17 HIS
Chi-restraints excluded: chain I residue   43 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 54 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**
** 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 = 0.4196 r_free = 0.4196 target = 0.177787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.131830 restraints weight = 8749.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.128399 restraints weight = 9684.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.130927 restraints weight = 8320.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3683

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= 0.222
  Angle     :  0.848  18.948  10053  Z= 0.396
  Chirality :  0.046   0.166   1141
  Planarity :  0.004   0.053   1272
  Dihedral  :  6.876  80.261   1001
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.81 %
    Favored  : 89.19 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 32.99 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.30), residues: 888
  helix: -0.02 (0.39), residues: 200
  sheet: -1.76 (0.27), residues: 380
  loop : -2.19 (0.39), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 260 
 HIS   0.001   0.000   HIS B  43 
 PHE   0.015   0.001   PHE A 359 
 TYR   0.020   0.001   TYR F 217 
 ARG   0.002   0.000   ARG B  47 

*********************** 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
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 166
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ASP cc_start: 0.8338 (p0) cc_final: 0.7988 (p0)
REVERT: A  167 LEU cc_start: 0.8713 (tt) cc_final: 0.7976 (mp)
REVERT: A  203 GLN cc_start: 0.8067 (pp30) cc_final: 0.7863 (tm-30)
REVERT: A  369 MET cc_start: 0.8418 (ttm) cc_final: 0.8066 (ttt)
REVERT: C   94 LYS cc_start: 0.8926 (tptt) cc_final: 0.8492 (tppt)
REVERT: D   18 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8137 (tp40)
REVERT: E   25 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7036 (mp10)
REVERT: F   87 ASP cc_start: 0.8314 (p0) cc_final: 0.7945 (p0)
REVERT: F  167 LEU cc_start: 0.8808 (tt) cc_final: 0.8104 (mp)
REVERT: F  168 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: F  369 MET cc_start: 0.8397 (ttm) cc_final: 0.8046 (ttt)
REVERT: G   47 ARG cc_start: 0.7171 (mpp80) cc_final: 0.6955 (mpp80)
REVERT: J   56 MET cc_start: 0.8307 (tpt) cc_final: 0.7861 (tpt)
  outliers start: 33
  outliers final: 31
  residues processed: 188
  average time/residue: 0.1802
  time to fit residues: 45.8316
Evaluate side-chains
  193 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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  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  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   93 THR
Chi-restraints excluded: chain C residue  114 SER
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  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   88 VAL
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 57 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:   30.0000
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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**
** 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 = 0.4180 r_free = 0.4180 target = 0.176213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.129775 restraints weight = 8814.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128482 restraints weight = 9927.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.129741 restraints weight = 8876.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3750

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= 0.269
  Angle     :  0.858  17.955  10053  Z= 0.406
  Chirality :  0.047   0.172   1141
  Planarity :  0.004   0.053   1272
  Dihedral  :  7.066  79.590   1001
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 32.10 %
    Favored  : 63.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.30), residues: 888
  helix:  0.11 (0.40), residues: 198
  sheet: -1.80 (0.27), residues: 380
  loop : -2.04 (0.40), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 260 
 HIS   0.001   0.000   HIS G  43 
 PHE   0.016   0.002   PHE F 359 
 TYR   0.021   0.002   TYR F 217 
 ARG   0.003   0.000   ARG G  47 

********************** 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
  202 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8778 (tt) cc_final: 0.7988 (mp)
REVERT: A  203 GLN cc_start: 0.8096 (pp30) cc_final: 0.7881 (tm-30)
REVERT: A  369 MET cc_start: 0.8386 (ttm) cc_final: 0.8042 (ttt)
REVERT: C   94 LYS cc_start: 0.8921 (tptt) cc_final: 0.8501 (tppt)
REVERT: D   18 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8079 (tp40)
REVERT: D   22 GLU cc_start: 0.7871 (pm20) cc_final: 0.7334 (pm20)
REVERT: E   25 GLN cc_start: 0.7626 (tp-100) cc_final: 0.6955 (mp10)
REVERT: F  155 LEU cc_start: 0.8696 (tp) cc_final: 0.8403 (tt)
REVERT: F  369 MET cc_start: 0.8462 (ttm) cc_final: 0.8091 (ttt)
REVERT: G   47 ARG cc_start: 0.7157 (mpp80) cc_final: 0.6946 (mpp80)
  outliers start: 37
  outliers final: 37
  residues processed: 186
  average time/residue: 0.1649
  time to fit residues: 42.4832
Evaluate side-chains
  199 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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  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  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  114 SER
Chi-restraints excluded: chain C residue  118 LEU
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  259 LEU
Chi-restraints excluded: chain F residue  333 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   88 VAL
Chi-restraints excluded: chain H residue   93 THR
Chi-restraints excluded: chain H residue  118 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0970
   chunk 46 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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**
** 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 = 0.4229 r_free = 0.4229 target = 0.181139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.135695 restraints weight = 8594.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136002 restraints weight = 9517.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.137019 restraints weight = 8743.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3942

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= 0.191
  Angle     :  0.819  17.609  10053  Z= 0.383
  Chirality :  0.046   0.161   1141
  Planarity :  0.004   0.055   1272
  Dihedral  :  6.492  81.550   1001
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 33.38 %
    Favored  : 63.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.30), residues: 888
  helix:  0.21 (0.41), residues: 198
  sheet: -1.56 (0.27), residues: 380
  loop : -2.06 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 260 
 HIS   0.001   0.000   HIS A 102 
 PHE   0.013   0.001   PHE F 359 
 TYR   0.022   0.001   TYR F 217 
 ARG   0.002   0.000   ARG G  47 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2350.27 seconds
wall clock time: 42 minutes 49.70 seconds (2569.70 seconds total)