Starting phenix.real_space_refine
on Fri Aug 22 22:46:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxw_36715/08_2025/8jxw_36715_neut.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.118
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
     S      57      5.16       5
     Cl      1      4.86       5
     C    5390      2.51       5
     N    1374      2.21       5
     O    1567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8389
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1727
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 217}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 2432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2432
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 181
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 13, 'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 118
    Chain: "D"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 363
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1691
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 49
    Chain: "R"
      Number of atoms: 2153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2153
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 9, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "R"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'VCF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.77, per 1000 atoms: 0.21
  Number of scatterers: 8389
  At special positions: 0
  Unit cell: (91.3, 121, 129.8, 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)
     Cl      1     17.00
     S      57     16.00
     O    1567      8.00
     N    1374      7.00
     C    5390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R  87 " - pdb=" SG  CYS R 164 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 314.8 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      38.1% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 30
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.931A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 3.525A  pdb=" N   GLU B 216 " --> pdb=" O   HIS B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 232
      removed outlier: 4.508A  pdb=" N   ASP B 231 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 232 " --> pdb=" O   ASP B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 228 through 232'
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.796A  pdb=" N   ALA B 245 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN B 255 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
      removed outlier: 4.097A  pdb=" N   THR B 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 278
      removed outlier: 3.624A  pdb=" N   PHE B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 295 through 309
      removed outlier: 3.885A  pdb=" N   ALA B 299 " --> pdb=" O   THR B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 351
      removed outlier: 4.094A  pdb=" N   VAL B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   CYS B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 25
      removed outlier: 3.862A  pdb=" N   CYS C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 24
      removed outlier: 3.658A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.574A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.763A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.505A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'R' and resid 14 through 43
      removed outlier: 4.124A  pdb=" N   LEU R  18 " --> pdb=" O   THR R  14 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA R  19 " --> pdb=" O   ARG R  15 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE R  20 " --> pdb=" O   VAL R  16 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE R  21 " --> pdb=" O   THR R  17 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP R  43 " --> pdb=" O   ALA R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 67
      removed outlier: 3.693A  pdb=" N   VAL R  64 " --> pdb=" O   SER R  60 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 78
      removed outlier: 3.843A  pdb=" N   LEU R  71 " --> pdb=" O   ILE R  67 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR R  72 " --> pdb=" O   SER R  68 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE R  73 " --> pdb=" O   ILE R  69 " (cutoff:3.500A)
      Proline residue:  R  74  - end of helix
    Processing helix  chain 'R' and resid 83 through 118
      removed outlier: 3.862A  pdb=" N   VAL R 116 " --> pdb=" O   ARG R 112 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 124
      removed outlier: 3.650A  pdb=" N   TYR R 122 " --> pdb=" O   ASN R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 154
      removed outlier: 3.974A  pdb=" N   ASN R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
    Processing helix  chain 'R' and resid 166 through 170
      removed outlier: 3.752A  pdb=" N   PHE R 169 " --> pdb=" O   PRO R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 203
      removed outlier: 3.823A  pdb=" N   LEU R 175 " --> pdb=" O   GLU R 171 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ILE R 185 " --> pdb=" O   LEU R 181 " (cutoff:3.500A)
      Proline residue:  R 186  - end of helix
    Processing helix  chain 'R' and resid 294 through 330
      Proline residue:  R 318  - end of helix
      removed outlier: 3.829A  pdb=" N   TYR R 329 " --> pdb=" O   VAL R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 362
      removed outlier: 4.080A  pdb=" N   ARG R 341 " --> pdb=" O   SER R 337 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TRP R 348 " --> pdb=" O   PHE R 344 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASN R 350 " --> pdb=" O   LEU R 346 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   SER R 351 " --> pdb=" O   GLN R 347 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   PHE R 352 " --> pdb=" O   TRP R 348 " (cutoff:3.500A)
      Proline residue:  R 355  - end of helix
      removed outlier: 3.665A  pdb=" N   TYR R 358 " --> pdb=" O   ASN R 354 " (cutoff:3.500A)
      Proline residue:  R 359  - end of helix
      removed outlier: 3.679A  pdb=" N   HIS R 362 " --> pdb=" O   TYR R 358 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 372
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191
      removed outlier: 3.775A  pdb=" N   ALA B 220 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.673A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 7.043A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.955A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153
      removed outlier: 3.739A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   CYS C 166 " --> pdb=" O   THR C 179 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   THR C 179 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   LEU C 168 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.855A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.899A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.118A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11
      removed outlier: 6.123A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143
    Processing sheet with id=AB3, first strand: chain 'E' and resid 148 through 149
      removed outlier: 3.596A  pdb=" N   GLU E 247 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU E 179 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   LEU E 188 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1146 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.91

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2652
        1.34 -     1.46: 2161
        1.46 -     1.58: 3684
        1.58 -     1.70: 1
        1.70 -     1.83: 83
  Bond restraints: 8581
  Sorted by residual:
  bond pdb=" C08 VCF R 401 "
       pdb=" N05 VCF R 401 "
    ideal  model  delta    sigma   weight residual
    1.358  1.488 -0.130 2.00e-02 2.50e+03 4.21e+01
  bond pdb=" C08 VCF R 401 "
       pdb=" C23 VCF R 401 "
    ideal  model  delta    sigma   weight residual
    1.485  1.550 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" N   VAL B 233 "
       pdb=" CA  VAL B 233 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.25e-02 6.40e+03 8.39e+00
  bond pdb=" N   THR R  14 "
       pdb=" CA  THR R  14 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.26e-02 6.30e+03 6.51e+00
  bond pdb=" N   SER R  13 "
       pdb=" CA  SER R  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.14e-02 7.69e+03 6.35e+00
  ... (remaining 8576 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11276
        1.91 -     3.82: 335
        3.82 -     5.73: 54
        5.73 -     7.64: 16
        7.64 -     9.55: 7
  Bond angle restraints: 11688
  Sorted by residual:
  angle pdb=" CA  PRO R 355 "
        pdb=" N   PRO R 355 "
        pdb=" CD  PRO R 355 "
      ideal   model   delta    sigma   weight residual
     112.00  102.45    9.55 1.40e+00 5.10e-01 4.66e+01
  angle pdb=" CA  PRO C  39 "
        pdb=" N   PRO C  39 "
        pdb=" CD  PRO C  39 "
      ideal   model   delta    sigma   weight residual
     112.00  102.87    9.13 1.40e+00 5.10e-01 4.25e+01
  angle pdb=" N   ALA E  92 "
        pdb=" CA  ALA E  92 "
        pdb=" C   ALA E  92 "
      ideal   model   delta    sigma   weight residual
     107.88  113.70   -5.82 1.41e+00 5.03e-01 1.70e+01
  angle pdb=" CG  ARG C 314 "
        pdb=" CD  ARG C 314 "
        pdb=" NE  ARG C 314 "
      ideal   model   delta    sigma   weight residual
     112.00  120.22   -8.22 2.20e+00 2.07e-01 1.40e+01
  angle pdb=" N   GLY C 319 "
        pdb=" CA  GLY C 319 "
        pdb=" C   GLY C 319 "
      ideal   model   delta    sigma   weight residual
     110.87  116.17   -5.30 1.54e+00 4.22e-01 1.18e+01
  ... (remaining 11683 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.99: 4384
       13.99 -    27.98: 447
       27.98 -    41.96: 118
       41.96 -    55.95: 26
       55.95 -    69.94: 12
  Dihedral angle restraints: 4987
    sinusoidal: 1767
      harmonic: 3220
  Sorted by residual:
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 230 "
           pdb=" CB  CYS E 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.07  -45.07     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CA  ILE R  67 "
           pdb=" C   ILE R  67 "
           pdb=" N   SER R  68 "
           pdb=" CA  SER R  68 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  GLU R 182 "
           pdb=" C   GLU R 182 "
           pdb=" N   PHE R 183 "
           pdb=" CA  PHE R 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.83  -23.17     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 4984 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 833
       0.039 -    0.078: 382
       0.078 -    0.118: 103
       0.118 -    0.157: 38
       0.157 -    0.196: 3
  Chirality restraints: 1359
  Sorted by residual:
  chirality pdb=" CA  PRO R 355 "
            pdb=" N   PRO R 355 "
            pdb=" C   PRO R 355 "
            pdb=" CB  PRO R 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CA  VAL R  16 "
            pdb=" N   VAL R  16 "
            pdb=" C   VAL R  16 "
            pdb=" CB  VAL R  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CA  VAL B 233 "
            pdb=" N   VAL B 233 "
            pdb=" C   VAL B 233 "
            pdb=" CB  VAL B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.49e-01
  ... (remaining 1356 not shown)

  Planarity restraints: 1465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 354 "    0.068 5.00e-02 4.00e+02   9.69e-02 1.50e+01
        pdb=" N   PRO R 355 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO R 355 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO R 355 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  38 "   -0.063 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO C  39 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO C  39 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C  39 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  48 "   -0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO D  49 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1462 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 81
        2.65 -     3.22: 7412
        3.22 -     3.78: 11784
        3.78 -     4.34: 15846
        4.34 -     4.90: 27557
  Nonbonded interactions: 62680
  Sorted by model distance:
  nonbonded pdb=" O   HIS C  54 "
            pdb=" OG  SER C 334 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" OG  SER C 331 "
            pdb=" OD1 ASP C 333 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OD1 ASP C 247 "
            pdb=" OG1 THR C 249 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   ASP C 163 "
            pdb=" OG1 THR C 164 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG  SER R 179 "
            pdb=" OG  SER R 320 "
     model   vdw
     2.243 3.040
  ... (remaining 62675 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
========== 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
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:             1.220
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.840
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.130   8583  Z= 0.280
  Angle     :  0.822   9.553  11692  Z= 0.463
  Chirality :  0.048   0.196   1359
  Planarity :  0.006   0.097   1465
  Dihedral  : 13.111  69.938   2901
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  1.03 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.24), residues: 1088
  helix:  1.24 (0.26), residues: 374
  sheet:  0.09 (0.30), residues: 280
  loop : -2.25 (0.25), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 314 
 TYR   0.014   0.002   TYR R 329 
 PHE   0.017   0.002   PHE R 349 
 TRP   0.029   0.002   TRP B 211 
 HIS   0.010   0.002   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 8581)
  covalent geometry    : angle       0.82236 (11688)
  SS BOND              : bond        0.01023 (    2)
  SS BOND              : angle       0.56854 (    4)
  hydrogen bonds       : bond        0.13928 (  411)
  hydrogen bonds       : angle       5.63327 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.287 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8642 (mtt) cc_final: 0.8392 (mtt)
  outliers start: 7
  outliers final: 4
  residues processed: 119
  average time/residue: 0.0779
  time to fit residues: 12.7420
Evaluate side-chains
  98 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  293 ASN
Chi-restraints excluded: chain R residue   14 THR
Chi-restraints excluded: chain R residue   15 ARG
Chi-restraints excluded: chain R residue   16 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
C 119 ASN
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  33 ASN
R 147 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.177477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125154 restraints weight = 10034.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.76
r_work: 0.3365 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8583  Z= 0.140
  Angle     :  0.592   7.450  11692  Z= 0.314
  Chirality :  0.043   0.147   1359
  Planarity :  0.004   0.050   1465
  Dihedral  :  5.701  54.809   1197
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  7.34 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.25), residues: 1088
  helix:  2.04 (0.27), residues: 375
  sheet:  0.26 (0.31), residues: 278
  loop : -1.87 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 304 
 TYR   0.014   0.001   TYR R 329 
 PHE   0.020   0.002   PHE R 322 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.005   0.001   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8581)
  covalent geometry    : angle       0.59247 (11688)
  SS BOND              : bond        0.00624 (    2)
  SS BOND              : angle       0.42036 (    4)
  hydrogen bonds       : bond        0.06308 (  411)
  hydrogen bonds       : angle       4.37065 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.361 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8740 (mtt) cc_final: 0.8503 (mtt)
REVERT: R   33 ASN cc_start: 0.6806 (m-40) cc_final: 0.6552 (m-40)
  outliers start: 14
  outliers final: 11
  residues processed: 115
  average time/residue: 0.0946
  time to fit residues: 15.0674
Evaluate side-chains
  117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   15 ARG
Chi-restraints excluded: chain R residue   16 VAL
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0040
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.180244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.127445 restraints weight = 10004.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.79
r_work: 0.3387 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8583  Z= 0.115
  Angle     :  0.535   7.659  11692  Z= 0.282
  Chirality :  0.041   0.141   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.877  47.590   1194
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.17 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.26), residues: 1088
  helix:  2.33 (0.27), residues: 380
  sheet:  0.44 (0.31), residues: 280
  loop : -1.56 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 304 
 TYR   0.009   0.001   TYR C 124 
 PHE   0.013   0.001   PHE R 168 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8581)
  covalent geometry    : angle       0.53506 (11688)
  SS BOND              : bond        0.00808 (    2)
  SS BOND              : angle       0.47990 (    4)
  hydrogen bonds       : bond        0.05323 (  411)
  hydrogen bonds       : angle       4.00813 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.323 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8722 (mtt) cc_final: 0.8507 (mtt)
REVERT: C  237 ASN cc_start: 0.8700 (t0) cc_final: 0.8434 (t0)
REVERT: D   48 ASP cc_start: 0.8309 (t70) cc_final: 0.8052 (t70)
REVERT: R   33 ASN cc_start: 0.6656 (m-40) cc_final: 0.6394 (m-40)
  outliers start: 18
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0944
  time to fit residues: 14.9418
Evaluate side-chains
  116 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 106 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.181058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.128173 restraints weight = 10146.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.80
r_work: 0.3395 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8583  Z= 0.108
  Angle     :  0.517   7.656  11692  Z= 0.271
  Chirality :  0.041   0.139   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.280  24.382   1189
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  9.40 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.26), residues: 1088
  helix:  2.55 (0.27), residues: 380
  sheet:  0.49 (0.31), residues: 280
  loop : -1.41 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 304 
 TYR   0.012   0.001   TYR R 329 
 PHE   0.012   0.001   PHE R 168 
 TRP   0.016   0.001   TRP R 172 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8581)
  covalent geometry    : angle       0.51705 (11688)
  SS BOND              : bond        0.00695 (    2)
  SS BOND              : angle       0.32273 (    4)
  hydrogen bonds       : bond        0.05038 (  411)
  hydrogen bonds       : angle       3.88441 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8709 (mtt) cc_final: 0.8490 (mtt)
REVERT: C  237 ASN cc_start: 0.8670 (t0) cc_final: 0.8403 (t0)
REVERT: C  262 MET cc_start: 0.7961 (mtp) cc_final: 0.7735 (ttm)
REVERT: D   48 ASP cc_start: 0.8420 (t70) cc_final: 0.8166 (t70)
REVERT: R   30 MET cc_start: 0.7548 (ptm) cc_final: 0.7321 (ptp)
  outliers start: 20
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0956
  time to fit residues: 15.1420
Evaluate side-chains
  117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0270
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
C 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.180201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.127690 restraints weight = 10036.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.75
r_work: 0.3387 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8583  Z= 0.117
  Angle     :  0.527   7.715  11692  Z= 0.275
  Chirality :  0.041   0.135   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.231  23.623   1189
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 10.67 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1088
  helix:  2.45 (0.27), residues: 387
  sheet:  0.51 (0.31), residues: 277
  loop : -1.34 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.011   0.001   TYR E 191 
 PHE   0.012   0.001   PHE R 168 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8581)
  covalent geometry    : angle       0.52657 (11688)
  SS BOND              : bond        0.00758 (    2)
  SS BOND              : angle       0.35269 (    4)
  hydrogen bonds       : bond        0.05277 (  411)
  hydrogen bonds       : angle       3.88872 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.325 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8665 (mtt) cc_final: 0.8457 (mtt)
REVERT: C  262 MET cc_start: 0.8003 (mtp) cc_final: 0.7674 (ttm)
REVERT: D   48 ASP cc_start: 0.8423 (t70) cc_final: 0.8151 (t70)
REVERT: R   30 MET cc_start: 0.7548 (ptm) cc_final: 0.7307 (ptp)
  outliers start: 22
  outliers final: 21
  residues processed: 111
  average time/residue: 0.1096
  time to fit residues: 16.4249
Evaluate side-chains
  122 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue   60 SER
Chi-restraints excluded: chain R residue  151 ILE
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   chunk 93 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    1.5144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.175513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122324 restraints weight = 10039.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.77
r_work: 0.3331 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8583  Z= 0.173
  Angle     :  0.601   7.951  11692  Z= 0.317
  Chirality :  0.043   0.136   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.506  22.599   1189
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 11.47 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1088
  helix:  2.48 (0.27), residues: 380
  sheet:  0.32 (0.32), residues: 271
  loop : -1.40 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  72 
 TYR   0.016   0.002   TYR C 105 
 PHE   0.015   0.002   PHE B 189 
 TRP   0.014   0.002   TRP R 172 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8581)
  covalent geometry    : angle       0.60147 (11688)
  SS BOND              : bond        0.00957 (    2)
  SS BOND              : angle       0.48794 (    4)
  hydrogen bonds       : bond        0.06943 (  411)
  hydrogen bonds       : angle       4.15362 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: C   76 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7597 (m-30)
REVERT: C  101 MET cc_start: 0.8750 (mtt) cc_final: 0.8548 (mtt)
REVERT: C  262 MET cc_start: 0.8058 (mtp) cc_final: 0.7397 (mtt)
  outliers start: 26
  outliers final: 23
  residues processed: 113
  average time/residue: 0.1045
  time to fit residues: 15.7794
Evaluate side-chains
  121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue   60 SER
Chi-restraints excluded: chain R residue  151 ILE
Chi-restraints excluded: chain R residue  182 GLU
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  362 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.177528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.124406 restraints weight = 10163.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.79
r_work: 0.3347 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8583  Z= 0.138
  Angle     :  0.557   7.724  11692  Z= 0.293
  Chirality :  0.042   0.135   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.383  23.344   1189
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 12.27 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.26), residues: 1088
  helix:  2.51 (0.27), residues: 382
  sheet:  0.31 (0.31), residues: 272
  loop : -1.34 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  24 
 TYR   0.012   0.001   TYR E 191 
 PHE   0.013   0.001   PHE C 199 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8581)
  covalent geometry    : angle       0.55680 (11688)
  SS BOND              : bond        0.00858 (    2)
  SS BOND              : angle       0.43584 (    4)
  hydrogen bonds       : bond        0.06042 (  411)
  hydrogen bonds       : angle       4.01052 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: C  101 MET cc_start: 0.8681 (mtt) cc_final: 0.8473 (mtt)
REVERT: C  234 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7800 (t80)
REVERT: C  262 MET cc_start: 0.7921 (mtp) cc_final: 0.7300 (mtt)
REVERT: R  367 LYS cc_start: 0.7704 (ttpp) cc_final: 0.7466 (tttt)
  outliers start: 25
  outliers final: 24
  residues processed: 110
  average time/residue: 0.0980
  time to fit residues: 14.7603
Evaluate side-chains
  122 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue  151 ILE
Chi-restraints excluded: chain R residue  182 GLU
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  362 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    0.0770
   chunk 89 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0060
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.5154

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.181325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.128763 restraints weight = 10018.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.77
r_work: 0.3400 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8583  Z= 0.104
  Angle     :  0.511   7.666  11692  Z= 0.267
  Chirality :  0.040   0.134   1359
  Planarity :  0.004   0.041   1465
  Dihedral  :  4.128  23.591   1189
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.73 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 1088
  helix:  2.54 (0.27), residues: 388
  sheet:  0.41 (0.31), residues: 280
  loop : -1.31 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  24 
 TYR   0.009   0.001   TYR E 191 
 PHE   0.011   0.001   PHE R 168 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8581)
  covalent geometry    : angle       0.51100 (11688)
  SS BOND              : bond        0.00698 (    2)
  SS BOND              : angle       0.36776 (    4)
  hydrogen bonds       : bond        0.04711 (  411)
  hydrogen bonds       : angle       3.79260 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.257 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8615 (mtt) cc_final: 0.8394 (mtt)
REVERT: C  130 GLU cc_start: 0.7626 (mp0) cc_final: 0.7349 (mm-30)
REVERT: C  262 MET cc_start: 0.7916 (mtp) cc_final: 0.7276 (mtt)
REVERT: R   31 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8267 (tp)
REVERT: R  367 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7544 (tttt)
  outliers start: 21
  outliers final: 17
  residues processed: 110
  average time/residue: 0.0845
  time to fit residues: 12.7499
Evaluate side-chains
  118 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue   31 LEU
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  362 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0770
   chunk 45 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.9140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.179481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126700 restraints weight = 10079.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.77
r_work: 0.3375 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8583  Z= 0.127
  Angle     :  0.543   8.007  11692  Z= 0.284
  Chirality :  0.041   0.134   1359
  Planarity :  0.004   0.042   1465
  Dihedral  :  4.228  24.726   1189
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.84 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1088
  helix:  2.50 (0.27), residues: 389
  sheet:  0.29 (0.32), residues: 277
  loop : -1.25 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 304 
 TYR   0.012   0.001   TYR E 191 
 PHE   0.012   0.001   PHE B 189 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8581)
  covalent geometry    : angle       0.54347 (11688)
  SS BOND              : bond        0.00792 (    2)
  SS BOND              : angle       0.36686 (    4)
  hydrogen bonds       : bond        0.05361 (  411)
  hydrogen bonds       : angle       3.84739 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8647 (mtt) cc_final: 0.8434 (mtt)
REVERT: C  234 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7803 (t80)
REVERT: C  262 MET cc_start: 0.7875 (mtp) cc_final: 0.7290 (mtt)
  outliers start: 20
  outliers final: 18
  residues processed: 110
  average time/residue: 0.1070
  time to fit residues: 15.8630
Evaluate side-chains
  119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue   23 SER
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 73 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.180460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.127871 restraints weight = 10027.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.76
r_work: 0.3388 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8583  Z= 0.116
  Angle     :  0.530   7.595  11692  Z= 0.278
  Chirality :  0.041   0.134   1359
  Planarity :  0.004   0.042   1465
  Dihedral  :  4.163  23.867   1189
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.53 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.26), residues: 1088
  helix:  2.54 (0.27), residues: 390
  sheet:  0.41 (0.31), residues: 284
  loop : -1.23 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 304 
 TYR   0.010   0.001   TYR E 191 
 PHE   0.011   0.001   PHE B 189 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8581)
  covalent geometry    : angle       0.52991 (11688)
  SS BOND              : bond        0.00741 (    2)
  SS BOND              : angle       0.36025 (    4)
  hydrogen bonds       : bond        0.05104 (  411)
  hydrogen bonds       : angle       3.80441 ( 1146)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.282 
Fit side-chains
REVERT: C  101 MET cc_start: 0.8622 (mtt) cc_final: 0.8407 (mtt)
REVERT: C  130 GLU cc_start: 0.7681 (mp0) cc_final: 0.7389 (mm-30)
REVERT: C  262 MET cc_start: 0.7897 (mtp) cc_final: 0.7321 (mtt)
  outliers start: 18
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1026
  time to fit residues: 14.9158
Evaluate side-chains
  117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  276 GLU
Chi-restraints excluded: chain B residue  312 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  218 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  267 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  160 CYS
Chi-restraints excluded: chain E residue  196 LEU
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain R residue  314 VAL
Chi-restraints excluded: chain R residue  362 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.172061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.119163 restraints weight = 10101.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.73
r_work: 0.3281 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8583  Z= 0.268
  Angle     :  0.713  10.177  11692  Z= 0.376
  Chirality :  0.048   0.156   1359
  Planarity :  0.005   0.046   1465
  Dihedral  :  4.836  26.467   1189
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.07 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.26), residues: 1088
  helix:  2.17 (0.27), residues: 384
  sheet:  0.42 (0.32), residues: 265
  loop : -1.47 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 304 
 TYR   0.024   0.002   TYR C 105 
 PHE   0.018   0.002   PHE C 199 
 TRP   0.012   0.002   TRP E 111 
 HIS   0.007   0.002   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 ( 8581)
  covalent geometry    : angle       0.71270 (11688)
  SS BOND              : bond        0.01143 (    2)
  SS BOND              : angle       0.64452 (    4)
  hydrogen bonds       : bond        0.08513 (  411)
  hydrogen bonds       : angle       4.45534 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2104.11 seconds
wall clock time: 36 minutes 41.36 seconds (2201.36 seconds total)