Starting phenix.real_space_refine (version: dev)
on Thu May 12 22:00:21 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvq_22510/05_2022/7jvq_22510_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.013
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib"
  Total number of atoms: 8485
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2273
          Classifications: {'peptide': 286}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 275}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1989
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 214
          Unusual residues: {'PLM': 3, 'CLR': 5, 'OR9': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 5.35, per 1000 atoms: 0.63
  Number of scatterers: 8485
  At special positions: 0
  Unit cell: (95.316, 98.358, 121.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1541      8.00
     N    1449      7.00
     C    5439      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.16
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      39.4% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'R' and resid 22 through 50
    Processing helix  chain 'R' and resid 53 through 56
      No H-bonds generated for 'chain 'R' and resid 53 through 56'
    Processing helix  chain 'R' and resid 59 through 76
      removed outlier: 3.582A  pdb=" N   SER R  69 " --> pdb=" O   LEU R  66 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASP R  70 " --> pdb=" O   ALA R  67 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL R  75 " --> pdb=" O   LEU R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 87
    Processing helix  chain 'R' and resid 93 through 126
      removed outlier: 3.867A  pdb=" N   ASN R  97 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL R 100 " --> pdb=" O   ASN R  97 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   MET R 105 " --> pdb=" O   PHE R 102 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER R 107 " --> pdb=" O   ILE R 104 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR R 108 " --> pdb=" O   MET R 105 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ALA R 109 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU R 112 " --> pdb=" O   ALA R 109 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA R 124 " --> pdb=" O   ARG R 121 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE R 125 " --> pdb=" O   TYR R 122 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER R 126 " --> pdb=" O   TRP R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 134
    Processing helix  chain 'R' and resid 137 through 161
      removed outlier: 4.823A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 192 through 202
    Processing helix  chain 'R' and resid 204 through 241
    Processing helix  chain 'R' and resid 265 through 297
      Proline residue:  R 287  - end of helix
      removed outlier: 4.092A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 310 through 332
      removed outlier: 4.358A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU R 326 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 335 through 345
    Processing helix  chain 'A' and resid 10 through 39
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.640A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASP A 102 " --> pdb=" O   CYS A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 116 through 129
      removed outlier: 4.077A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 184 through 204
      removed outlier: 4.241A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 3.522A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.947A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing sheet with id=  A, first strand: chain 'A' and resid 211 through 215
      removed outlier: 7.286A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   HIS A 214 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ASN A  80 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   HIS A  82 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   VAL A  86 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.148A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.144A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.896A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.139A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.975A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.731A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.925A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.473A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1038 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: 2.44

  Time building geometry restraints manager: 3.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2456
        1.34 -     1.46: 2093
        1.46 -     1.59: 4046
        1.59 -     1.71: 0
        1.71 -     1.83: 76
  Bond restraints: 8671
  Sorted by residual:
  bond pdb=" C   ILE R 205 "
       pdb=" N   PRO R 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.28e-02 6.10e+03 3.52e+00
  bond pdb=" C   MET R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.30e-02 5.92e+03 3.46e+00
  bond pdb=" C   ILE R 157 "
       pdb=" N   PRO R 158 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.23e-02 6.61e+03 2.93e+00
  bond pdb=" C   THR R 136 "
       pdb=" N   PRO R 137 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.87e+00
  bond pdb=" C5  CLR R 502 "
       pdb=" C6  CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 2.00e-02 2.50e+03 2.60e+00
  ... (remaining 8666 not shown)

  Histogram of bond angle deviations from ideal:
      100.09 -   107.06: 236
      107.06 -   114.03: 4996
      114.03 -   121.01: 3967
      121.01 -   127.98: 2485
      127.98 -   134.96: 76
  Bond angle restraints: 11760
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  130.99   -9.45 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" C   ILE R 294 "
        pdb=" N   LEU R 295 "
        pdb=" CA  LEU R 295 "
      ideal   model   delta    sigma   weight residual
     121.62  126.94   -5.32 1.57e+00 4.06e-01 1.15e+01
  angle pdb=" N   LEU R 286 "
        pdb=" CA  LEU R 286 "
        pdb=" C   LEU R 286 "
      ideal   model   delta    sigma   weight residual
     109.81  116.93   -7.12 2.21e+00 2.05e-01 1.04e+01
  angle pdb=" N   LEU R 295 "
        pdb=" CA  LEU R 295 "
        pdb=" C   LEU R 295 "
      ideal   model   delta    sigma   weight residual
     113.77  118.01   -4.24 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     123.93  128.85   -4.92 1.54e+00 4.22e-01 1.02e+01
  ... (remaining 11755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 4896
       14.88 -    29.75: 195
       29.75 -    44.63: 40
       44.63 -    59.50: 2
       59.50 -    74.38: 3
  Dihedral angle restraints: 5136
    sinusoidal: 2080
      harmonic: 3056
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.67  -70.67     1      1.00e+01 1.00e-02 6.42e+01
  dihedral pdb=" CA  MET R 135 "
           pdb=" C   MET R 135 "
           pdb=" N   THR R 136 "
           pdb=" CA  THR R 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.08   24.92     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  LEU B 198 "
           pdb=" C   LEU B 198 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 5133 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1149
       0.084 -    0.168: 148
       0.168 -    0.252: 20
       0.252 -    0.336: 5
       0.336 -    0.420: 6
  Chirality restraints: 1328
  Sorted by residual:
  chirality pdb=" C14 CLR R 506 "
            pdb=" C13 CLR R 506 "
            pdb=" C15 CLR R 506 "
            pdb=" C8  CLR R 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.40 2.00e-01 2.50e+01 3.95e+00
  chirality pdb=" C14 CLR R 503 "
            pdb=" C13 CLR R 503 "
            pdb=" C15 CLR R 503 "
            pdb=" C8  CLR R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.71    0.40 2.00e-01 2.50e+01 3.94e+00
  ... (remaining 1325 not shown)

  Planarity restraints: 1462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 207 "    0.020 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   VAL R 207 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   VAL R 207 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ALA R 208 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 218 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.27e+00
        pdb=" C   TYR R 218 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   TYR R 218 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG R 219 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 114 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.03e+00
        pdb=" C   LEU R 114 "    0.049 2.00e-02 2.50e+03
        pdb=" O   LEU R 114 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   CYS R 115 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1459 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1845
        2.79 -     3.32: 7504
        3.32 -     3.85: 13417
        3.85 -     4.37: 15625
        4.37 -     4.90: 27685
  Nonbonded interactions: 66076
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.268 2.440
  nonbonded pdb=" OH  TYR A 170 "
            pdb=" OD2 ASP A 195 "
     model   vdw
     2.270 2.440
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.329 2.440
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.344 2.440
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.358 2.520
  ... (remaining 66071 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5439      2.51       5
     N    1449      2.21       5
     O    1541      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.210
  Check model and map are aligned:         0.120
  Convert atoms to be neutral:             0.070
  Process input model:                     25.630
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  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:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
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      :  0.004   0.057   8671  Z= 0.282
  Angle     :  0.923   9.957  11760  Z= 0.510
  Chirality :  0.064   0.420   1328
  Planarity :  0.007   0.060   1462
  Dihedral  :  8.708  74.381   3140
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.23), residues: 1031
  helix: -1.60 (0.21), residues: 408
  sheet: -0.36 (0.34), residues: 219
  loop : -2.01 (0.26), residues: 404

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 3
  residues processed: 216
  average time/residue: 1.1519
  time to fit residues: 264.5918
Evaluate side-chains
  126 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 2
  average time/residue: 0.1121
  time to fit residues: 1.5679
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
R 334 ASN
A  23 ASN
A  64 HIS
B  88 ASN
B 259 GLN
N  31 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.071   8671  Z= 0.347
  Angle     :  0.641  10.191  11760  Z= 0.341
  Chirality :  0.045   0.163   1328
  Planarity :  0.005   0.044   1462
  Dihedral  :  5.474  38.036   1233
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer Outliers :  3.88 %
  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: -0.41 (0.25), residues: 1031
  helix:  0.77 (0.25), residues: 388
  sheet:  0.02 (0.33), residues: 222
  loop : -1.40 (0.28), residues: 421

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 35
  outliers final: 16
  residues processed: 160
  average time/residue: 1.0171
  time to fit residues: 174.9292
Evaluate side-chains
  131 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.957 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 12
  residues processed: 7
  average time/residue: 0.1118
  time to fit residues: 2.6177
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0060
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 91 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 268 ASN
N  31 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8671  Z= 0.157
  Angle     :  0.498   6.066  11760  Z= 0.265
  Chirality :  0.040   0.152   1328
  Planarity :  0.004   0.041   1462
  Dihedral  :  5.010  34.761   1233
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer Outliers :  4.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.20 (0.25), residues: 1031
  helix:  1.64 (0.26), residues: 388
  sheet:  0.14 (0.33), residues: 217
  loop : -1.31 (0.28), residues: 426

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
  outliers start: 36
  outliers final: 17
  residues processed: 145
  average time/residue: 0.9875
  time to fit residues: 154.5016
Evaluate side-chains
  132 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.997 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 13
  residues processed: 5
  average time/residue: 0.1531
  time to fit residues: 2.4959
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0050
   chunk 48 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.3800

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8671  Z= 0.220
  Angle     :  0.517   6.115  11760  Z= 0.274
  Chirality :  0.041   0.173   1328
  Planarity :  0.004   0.054   1462
  Dihedral  :  4.995  35.424   1233
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer Outliers :  4.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.35 (0.26), residues: 1031
  helix:  1.81 (0.26), residues: 382
  sheet:  0.14 (0.33), residues: 215
  loop : -1.17 (0.28), residues: 434

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
  outliers start: 40
  outliers final: 22
  residues processed: 142
  average time/residue: 1.0306
  time to fit residues: 157.7414
Evaluate side-chains
  142 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.989 
Switching outliers to nearest non-outliers
  outliers start: 22
  outliers final: 17
  residues processed: 7
  average time/residue: 0.1348
  time to fit residues: 2.8071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.0060
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 242 GLN
N  31 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8671  Z= 0.141
  Angle     :  0.474   6.411  11760  Z= 0.248
  Chirality :  0.039   0.140   1328
  Planarity :  0.004   0.045   1462
  Dihedral  :  4.706  32.502   1233
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer Outliers :  3.55 %
  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:  0.60 (0.26), residues: 1031
  helix:  2.06 (0.26), residues: 382
  sheet:  0.18 (0.33), residues: 219
  loop : -1.03 (0.29), residues: 430

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 32
  outliers final: 23
  residues processed: 149
  average time/residue: 1.0439
  time to fit residues: 167.2983
Evaluate side-chains
  136 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.945 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 20
  residues processed: 6
  average time/residue: 0.1663
  time to fit residues: 2.6385
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
A 242 GLN
G  44 HIS
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8671  Z= 0.258
  Angle     :  0.541   6.867  11760  Z= 0.285
  Chirality :  0.042   0.180   1328
  Planarity :  0.005   0.075   1462
  Dihedral  :  5.059  33.723   1233
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer Outliers :  4.22 %
  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:  0.37 (0.26), residues: 1031
  helix:  1.75 (0.26), residues: 384
  sheet: -0.03 (0.33), residues: 225
  loop : -0.99 (0.29), residues: 422

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 38
  outliers final: 23
  residues processed: 140
  average time/residue: 0.9728
  time to fit residues: 147.1660
Evaluate side-chains
  134 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 20
  residues processed: 6
  average time/residue: 0.4551
  time to fit residues: 4.5006
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.0070
   chunk 55 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0970
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 38 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
B  36 ASN
B  91 HIS
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8671  Z= 0.132
  Angle     :  0.488  11.212  11760  Z= 0.250
  Chirality :  0.039   0.237   1328
  Planarity :  0.004   0.049   1462
  Dihedral  :  4.681  29.054   1233
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer Outliers :  3.33 %
  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:  0.57 (0.26), residues: 1031
  helix:  2.04 (0.26), residues: 382
  sheet: -0.08 (0.32), residues: 223
  loop : -0.89 (0.29), residues: 426

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 21
  residues processed: 145
  average time/residue: 0.9838
  time to fit residues: 153.9777
Evaluate side-chains
  132 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.030 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 18
  residues processed: 6
  average time/residue: 0.1566
  time to fit residues: 2.7166
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
G  44 HIS
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8671  Z= 0.210
  Angle     :  0.523   7.471  11760  Z= 0.271
  Chirality :  0.041   0.138   1328
  Planarity :  0.004   0.084   1462
  Dihedral  :  4.820  30.575   1233
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer Outliers :  3.55 %
  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:  0.56 (0.26), residues: 1031
  helix:  1.96 (0.26), residues: 383
  sheet: -0.10 (0.32), residues: 234
  loop : -0.85 (0.30), residues: 414

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 32
  outliers final: 24
  residues processed: 135
  average time/residue: 0.9589
  time to fit residues: 140.9032
Evaluate side-chains
  128 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.899 
Switching outliers to nearest non-outliers
  outliers start: 24
  outliers final: 22
  residues processed: 5
  average time/residue: 0.1952
  time to fit residues: 2.6162
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 54 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 27 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8671  Z= 0.167
  Angle     :  0.521  10.046  11760  Z= 0.268
  Chirality :  0.041   0.261   1328
  Planarity :  0.004   0.070   1462
  Dihedral  :  4.760  39.460   1233
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer Outliers :  3.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.62 (0.26), residues: 1031
  helix:  2.11 (0.26), residues: 385
  sheet: -0.22 (0.31), residues: 237
  loop : -0.82 (0.30), residues: 409

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 28
  residues processed: 123
  average time/residue: 1.0179
  time to fit residues: 135.6694
Evaluate side-chains
  129 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 23
  residues processed: 9
  average time/residue: 0.4887
  time to fit residues: 6.4433
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.0470
   chunk 66 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 92 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0470
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.120   8671  Z= 0.216
  Angle     :  0.531   9.826  11760  Z= 0.277
  Chirality :  0.040   0.243   1328
  Planarity :  0.005   0.101   1462
  Dihedral  :  4.699  37.596   1233
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer Outliers :  3.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.65 (0.26), residues: 1031
  helix:  2.14 (0.26), residues: 385
  sheet: -0.18 (0.32), residues: 230
  loop : -0.81 (0.30), residues: 416

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 25
  residues processed: 122
  average time/residue: 1.0048
  time to fit residues: 132.4796
Evaluate side-chains
  123 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 21
  residues processed: 7
  average time/residue: 0.4097
  time to fit residues: 4.6248
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0770
   chunk 33 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.9944

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
G  44 HIS
** N  82 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 = 0.4218 r_free = 0.4218 target = 0.188132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.142233 restraints weight = 8410.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.32
r_work: 0.3567 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work: 0.3538 rms_B_bonded: 2.13 restraints_weight: 0.1250
r_work: 0.3523 rms_B_bonded: 2.21 restraints_weight: 0.0625
r_work: 0.3506 rms_B_bonded: 2.32 restraints_weight: 0.0312
r_work: 0.3489 rms_B_bonded: 2.46 restraints_weight: 0.0156
r_work: 0.3470 rms_B_bonded: 2.65 restraints_weight: 0.0078
r_work: 0.3449 rms_B_bonded: 2.87 restraints_weight: 0.0039
r_work: 0.3427 rms_B_bonded: 3.14 restraints_weight: 0.0020
r_work: 0.3402 rms_B_bonded: 3.46 restraints_weight: 0.0010
r_work: 0.3375 rms_B_bonded: 3.83 restraints_weight: 0.0005
r_work: 0.3345 rms_B_bonded: 4.28 restraints_weight: 0.0002
r_work: 0.3312 rms_B_bonded: 4.79 restraints_weight: 0.0001
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.086   8671  Z= 0.305
  Angle     :  0.598   9.611  11760  Z= 0.312
  Chirality :  0.044   0.244   1328
  Planarity :  0.005   0.085   1462
  Dihedral  :  5.197  37.804   1233
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer Outliers :  3.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    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:  0.47 (0.26), residues: 1031
  helix:  1.83 (0.26), residues: 387
  sheet: -0.20 (0.33), residues: 235
  loop : -0.82 (0.31), residues: 409

===============================================================================
Job complete
usr+sys time: 3038.56 seconds
wall clock time: 54 minutes 43.91 seconds (3283.91 seconds total)