Starting phenix.real_space_refine
on Fri Aug 22 20:56:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcp_29940/08_2025/8gcp_29940.cif"
  }
  resolution = 3.1
  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=   0.035
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: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5047      2.51       5
     N    1340      2.21       5
     O    1477      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 7921
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1548
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 204
          Unresolved non-hydrogen angles: 246
          Unresolved non-hydrogen dihedrals: 171
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE%COO:plan': 1}
          Unresolved non-hydrogen planarities: 107
    Chain: "B"
      Number of atoms: 2476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2476
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "C"
      Number of atoms: 362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 362
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "E"
      Number of atoms: 1614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1614
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 188
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 97
    Chain: "R"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 1896
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 233
          Unresolved non-hydrogen angles: 293
          Unresolved non-hydrogen dihedrals: 189
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 122
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.07, per 1000 atoms: 0.26
  Number of scatterers: 7921
  At special positions: 0
  Unit cell: (90.95, 119.85, 124.95, 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      57     16.00
     O    1477      8.00
     N    1340      7.00
     C    5047      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R  92 " - pdb=" SG  CYS R 170 " distance=2.05

  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: 0.69
  Conformation dependent library (CDL) restraints added in 457.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2072

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 14 sheets defined
      33.5% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 3.527A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.541A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.716A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.604A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.143A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   CYS A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 282 through 286'
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.787A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASP A 309 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 341
      removed outlier: 3.980A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 352
      removed outlier: 3.587A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 24
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 4.157A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 43
      removed outlier: 3.831A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.521A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 45
      removed outlier: 3.975A  pdb=" N   GLY R  34 " --> pdb=" O   PHE R  30 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN R  35 " --> pdb=" O   GLY R  31 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU R  36 " --> pdb=" O   VAL R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 52 through 82
      removed outlier: 4.375A  pdb=" N   THR R  56 " --> pdb=" O   THR R  52 " (cutoff:3.500A)
      Proline residue:  R  74  - end of helix
    Processing helix  chain 'R' and resid 91 through 113
      removed outlier: 3.983A  pdb=" N   PHE R  97 " --> pdb=" O   GLU R  93 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE R 102 " --> pdb=" O   ILE R  98 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 115 through 123
      removed outlier: 3.596A  pdb=" N   ILE R 121 " --> pdb=" O   ARG R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 131
      removed outlier: 3.655A  pdb=" N   VAL R 131 " --> pdb=" O   TYR R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 152
    Processing helix  chain 'R' and resid 152 through 157
      removed outlier: 3.645A  pdb=" N   MET R 156 " --> pdb=" O   ALA R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 218
      removed outlier: 4.336A  pdb=" N   SER R 185 " --> pdb=" O   HIS R 181 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU R 211 " --> pdb=" O   CYS R 207 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ARG R 212 " --> pdb=" O   GLY R 208 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET R 213 " --> pdb=" O   ALA R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 298
      removed outlier: 3.834A  pdb=" N   LEU R 274 " --> pdb=" O   MET R 270 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU R 279 " --> pdb=" O   ILE R 275 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 311 through 318
    Processing helix  chain 'R' and resid 319 through 324
      removed outlier: 3.509A  pdb=" N   ILE R 323 " --> pdb=" O   SER R 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.536A  pdb=" N   VAL A  34 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.831A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.907A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.049A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.765A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.557A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277
      removed outlier: 6.411A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.776A  pdb=" N   VAL E  12 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 50
      removed outlier: 3.722A  pdb=" N   TYR E  50 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR E  59 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195
      removed outlier: 6.729A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 162 through 163
      removed outlier: 3.539A  pdb=" N   ARG R 162 " --> pdb=" O   PHE R 171 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE R 171 " --> pdb=" O   ARG R 162 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    365 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1310
        1.31 -     1.44: 2213
        1.44 -     1.57: 4472
        1.57 -     1.70: 2
        1.70 -     1.82: 79
  Bond restraints: 8076
  Sorted by residual:
  bond pdb=" C13 P2E R 501 "
       pdb=" C14 P2E R 501 "
    ideal  model  delta    sigma   weight residual
    1.329  1.530 -0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C5  P2E R 501 "
       pdb=" C6  P2E R 501 "
    ideal  model  delta    sigma   weight residual
    1.333  1.527 -0.194 2.00e-02 2.50e+03 9.39e+01
  bond pdb=" C   CYS R  59 "
       pdb=" N   GLY R  60 "
    ideal  model  delta    sigma   weight residual
    1.334  1.228  0.106 1.32e-02 5.74e+03 6.41e+01
  bond pdb=" N   HIS B 311 "
       pdb=" CA  HIS B 311 "
    ideal  model  delta    sigma   weight residual
    1.453  1.519 -0.066 1.31e-02 5.83e+03 2.57e+01
  bond pdb=" CA  VAL B 307 "
       pdb=" C   VAL B 307 "
    ideal  model  delta    sigma   weight residual
    1.523  1.462  0.061 1.27e-02 6.20e+03 2.33e+01
  ... (remaining 8071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 10633
        2.90 -     5.81: 313
        5.81 -     8.71: 61
        8.71 -    11.61: 16
       11.61 -    14.52: 5
  Bond angle restraints: 11028
  Sorted by residual:
  angle pdb=" C   GLN R 299 "
        pdb=" N   PRO R 300 "
        pdb=" CA  PRO R 300 "
      ideal   model   delta    sigma   weight residual
     120.51  130.47   -9.96 1.26e+00 6.30e-01 6.25e+01
  angle pdb=" N   PHE R 217 "
        pdb=" CA  PHE R 217 "
        pdb=" C   PHE R 217 "
      ideal   model   delta    sigma   weight residual
     112.90  123.12  -10.22 1.31e+00 5.83e-01 6.09e+01
  angle pdb=" N   SER R 307 "
        pdb=" CA  SER R 307 "
        pdb=" C   SER R 307 "
      ideal   model   delta    sigma   weight residual
     112.92  122.34   -9.42 1.23e+00 6.61e-01 5.87e+01
  angle pdb=" N   LEU R 302 "
        pdb=" CA  LEU R 302 "
        pdb=" C   LEU R 302 "
      ideal   model   delta    sigma   weight residual
     108.56  121.01  -12.45 1.74e+00 3.30e-01 5.12e+01
  angle pdb=" N   ALA C  56 "
        pdb=" CA  ALA C  56 "
        pdb=" C   ALA C  56 "
      ideal   model   delta    sigma   weight residual
     112.38  121.07   -8.69 1.22e+00 6.72e-01 5.07e+01
  ... (remaining 11023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4270
       17.73 -    35.45: 370
       35.45 -    53.18: 61
       53.18 -    70.91: 5
       70.91 -    88.63: 4
  Dihedral angle restraints: 4710
    sinusoidal: 1503
      harmonic: 3207
  Sorted by residual:
  dihedral pdb=" CA  LEU A 268 "
           pdb=" C   LEU A 268 "
           pdb=" N   ASN A 269 "
           pdb=" CA  ASN A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.64  -25.36     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" C   ALA C  56 "
           pdb=" N   ALA C  56 "
           pdb=" CA  ALA C  56 "
           pdb=" CB  ALA C  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.80   11.20     0      2.50e+00 1.60e-01 2.01e+01
  dihedral pdb=" CA  CYS A 286 "
           pdb=" C   CYS A 286 "
           pdb=" N   TYR A 287 "
           pdb=" CA  TYR A 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.47   21.53     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 4707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1225
       0.120 -    0.240: 78
       0.240 -    0.360: 13
       0.360 -    0.480: 7
       0.480 -    0.600: 1
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CA  ALA C  56 "
            pdb=" N   ALA C  56 "
            pdb=" C   ALA C  56 "
            pdb=" CB  ALA C  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.88    0.60 2.00e-01 2.50e+01 9.00e+00
  chirality pdb=" CA  PHE R 217 "
            pdb=" N   PHE R 217 "
            pdb=" C   PHE R 217 "
            pdb=" CB  PHE R 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.65e+00
  chirality pdb=" CA  MET E 192 "
            pdb=" N   MET E 192 "
            pdb=" C   MET E 192 "
            pdb=" CB  MET E 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 1321 not shown)

  Planarity restraints: 1403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C4  P2E R 501 "    0.153 2.00e-02 2.50e+03   3.20e-01 1.02e+03
        pdb=" C5  P2E R 501 "   -0.424 2.00e-02 2.50e+03
        pdb=" C6  P2E R 501 "    0.427 2.00e-02 2.50e+03
        pdb=" C7  P2E R 501 "   -0.156 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 174 "   -0.031 2.00e-02 2.50e+03   2.69e-02 1.80e+01
        pdb=" CG  TRP R 174 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 174 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 174 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 174 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 174 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 174 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 174 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 174 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 174 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.066 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO E 236 "   -0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.052 5.00e-02 4.00e+02
  ... (remaining 1400 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1723
        2.77 -     3.31: 6848
        3.31 -     3.84: 12533
        3.84 -     4.37: 14162
        4.37 -     4.90: 25231
  Nonbonded interactions: 60497
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  64 "
            pdb=" OH  TYR R 144 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   THR E 243 "
            pdb=" CG2 THR E 243 "
     model   vdw
     2.294 3.460
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.312 3.040
  ... (remaining 60492 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.130
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
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      :  0.011   0.201   8078  Z= 0.568
  Angle     :  1.266  14.515  11032  Z= 0.724
  Chirality :  0.077   0.600   1324
  Planarity :  0.012   0.320   1403
  Dihedral  : 13.822  88.634   2632
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  2.02 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.24), residues: 1086
  helix: -1.49 (0.25), residues: 355
  sheet: -0.16 (0.34), residues: 244
  loop : -2.40 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  18 
 TYR   0.027   0.003   TYR B 105 
 PHE   0.029   0.003   PHE A 196 
 TRP   0.072   0.004   TRP R 174 
 HIS   0.017   0.003   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.01084 ( 8076)
  covalent geometry    : angle       1.26448 (11028)
  SS BOND              : bond        0.01673 (    2)
  SS BOND              : angle       3.30016 (    4)
  hydrogen bonds       : bond        0.14745 (  365)
  hydrogen bonds       : angle       6.48991 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  270 LYS cc_start: 0.7003 (pttm) cc_final: 0.6784 (pttm)
REVERT: B  209 LYS cc_start: 0.8645 (mttm) cc_final: 0.7098 (mtmt)
REVERT: B  228 ASP cc_start: 0.7436 (p0) cc_final: 0.7222 (p0)
REVERT: E   83 MET cc_start: 0.6809 (mtm) cc_final: 0.6396 (mtm)
REVERT: E  243 THR cc_start: 0.8296 (t) cc_final: 0.8001 (m)
  outliers start: 5
  outliers final: 1
  residues processed: 144
  average time/residue: 0.0901
  time to fit residues: 17.5076
Evaluate side-chains
  124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  110 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 331 ASN
B 220 GLN
R 214 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.167866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133199 restraints weight = 11256.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.40
r_work: 0.3385 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8078  Z= 0.140
  Angle     :  0.618  12.401  11032  Z= 0.321
  Chirality :  0.043   0.171   1324
  Planarity :  0.005   0.056   1403
  Dihedral  :  6.616  84.111   1202
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.42 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.25), residues: 1086
  helix:  0.41 (0.29), residues: 348
  sheet: -0.32 (0.34), residues: 249
  loop : -2.14 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.013   0.001   TYR R 144 
 PHE   0.013   0.002   PHE B 234 
 TRP   0.014   0.001   TRP R 174 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8076)
  covalent geometry    : angle       0.61770 (11028)
  SS BOND              : bond        0.00739 (    2)
  SS BOND              : angle       1.00746 (    4)
  hydrogen bonds       : bond        0.04060 (  365)
  hydrogen bonds       : angle       4.37370 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8814 (tp) cc_final: 0.8553 (tt)
REVERT: B   52 ARG cc_start: 0.8188 (mtt90) cc_final: 0.7973 (mtt-85)
REVERT: B  124 TYR cc_start: 0.8625 (m-80) cc_final: 0.8144 (m-80)
REVERT: B  129 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7481 (mmm-85)
REVERT: B  209 LYS cc_start: 0.8746 (mttm) cc_final: 0.7239 (mtmt)
REVERT: B  228 ASP cc_start: 0.8073 (p0) cc_final: 0.7862 (p0)
  outliers start: 11
  outliers final: 6
  residues processed: 150
  average time/residue: 0.0998
  time to fit residues: 20.1564
Evaluate side-chains
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   27 MET
Chi-restraints excluded: chain R residue  110 ILE
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 71 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0870
   chunk 78 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.168669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.133377 restraints weight = 11004.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.99
r_work: 0.3390 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8078  Z= 0.143
  Angle     :  0.585   9.802  11032  Z= 0.304
  Chirality :  0.042   0.146   1324
  Planarity :  0.004   0.048   1403
  Dihedral  :  6.173  82.194   1202
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.34 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.26), residues: 1086
  helix:  1.05 (0.30), residues: 350
  sheet: -0.09 (0.34), residues: 242
  loop : -2.05 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 134 
 TYR   0.016   0.001   TYR B 105 
 PHE   0.017   0.002   PHE E  29 
 TRP   0.010   0.001   TRP R 174 
 HIS   0.006   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8076)
  covalent geometry    : angle       0.58481 (11028)
  SS BOND              : bond        0.00671 (    2)
  SS BOND              : angle       0.87892 (    4)
  hydrogen bonds       : bond        0.03841 (  365)
  hydrogen bonds       : angle       4.17209 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8763 (tp) cc_final: 0.8493 (tt)
REVERT: B   52 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7943 (mtt-85)
REVERT: B  209 LYS cc_start: 0.8748 (mttm) cc_final: 0.7256 (mtmt)
REVERT: B  228 ASP cc_start: 0.8026 (p0) cc_final: 0.7791 (p0)
REVERT: B  268 ASN cc_start: 0.7543 (m110) cc_final: 0.7257 (m-40)
  outliers start: 11
  outliers final: 7
  residues processed: 149
  average time/residue: 0.0928
  time to fit residues: 18.4260
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain R residue  110 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.170502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135137 restraints weight = 11249.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.41
r_work: 0.3420 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8078  Z= 0.100
  Angle     :  0.520   8.154  11032  Z= 0.270
  Chirality :  0.041   0.137   1324
  Planarity :  0.003   0.043   1403
  Dihedral  :  5.758  81.289   1202
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 17.63 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.26), residues: 1086
  helix:  1.37 (0.30), residues: 354
  sheet:  0.15 (0.34), residues: 244
  loop : -1.95 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 191 
 TYR   0.008   0.001   TYR E 102 
 PHE   0.018   0.001   PHE E  29 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8076)
  covalent geometry    : angle       0.51977 (11028)
  SS BOND              : bond        0.00553 (    2)
  SS BOND              : angle       0.64021 (    4)
  hydrogen bonds       : bond        0.03093 (  365)
  hydrogen bonds       : angle       3.89492 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8794 (tp) cc_final: 0.8472 (tt)
REVERT: A  197 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7823 (ptpt)
REVERT: B   50 THR cc_start: 0.8351 (m) cc_final: 0.8130 (m)
REVERT: B  124 TYR cc_start: 0.8611 (m-80) cc_final: 0.8392 (m-80)
REVERT: B  127 LYS cc_start: 0.8478 (mttt) cc_final: 0.8224 (mttp)
REVERT: B  209 LYS cc_start: 0.8681 (mttm) cc_final: 0.7326 (mtmt)
REVERT: B  268 ASN cc_start: 0.7583 (m110) cc_final: 0.7294 (m-40)
REVERT: E    6 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6511 (pt0)
REVERT: E   83 MET cc_start: 0.6991 (mtm) cc_final: 0.6421 (mtm)
  outliers start: 11
  outliers final: 5
  residues processed: 142
  average time/residue: 0.0830
  time to fit residues: 15.8770
Evaluate side-chains
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 133
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain R residue  110 ILE
Chi-restraints excluded: chain R residue  113 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0670
   chunk 14 optimal weight:    0.0970
   chunk 77 optimal weight:    0.2980
   chunk 85 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 70 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.173211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138175 restraints weight = 11071.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 2.15
r_work: 0.3483 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8078  Z= 0.086
  Angle     :  0.498   8.886  11032  Z= 0.255
  Chirality :  0.040   0.134   1324
  Planarity :  0.003   0.039   1403
  Dihedral  :  5.448  85.374   1202
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.90 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.27), residues: 1086
  helix:  1.61 (0.30), residues: 360
  sheet:  0.28 (0.34), residues: 244
  loop : -1.77 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 191 
 TYR   0.010   0.001   TYR R  94 
 PHE   0.019   0.001   PHE E  29 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 8076)
  covalent geometry    : angle       0.49845 (11028)
  SS BOND              : bond        0.00437 (    2)
  SS BOND              : angle       0.57409 (    4)
  hydrogen bonds       : bond        0.02716 (  365)
  hydrogen bonds       : angle       3.70730 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.8059 (ptpt) cc_final: 0.7772 (ptpt)
REVERT: A  225 VAL cc_start: 0.7867 (t) cc_final: 0.7645 (t)
REVERT: B  209 LYS cc_start: 0.8625 (mttm) cc_final: 0.7295 (mtmt)
REVERT: B  268 ASN cc_start: 0.7543 (m110) cc_final: 0.7260 (m-40)
REVERT: E   83 MET cc_start: 0.6963 (mtm) cc_final: 0.6492 (mtm)
  outliers start: 20
  outliers final: 11
  residues processed: 143
  average time/residue: 0.1035
  time to fit residues: 19.7338
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  175 THR
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  218 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 87 optimal weight:   20.0000
   chunk 27 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0770
   chunk 84 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.170389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.136074 restraints weight = 10979.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.23
r_work: 0.3438 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8078  Z= 0.112
  Angle     :  0.518   7.623  11032  Z= 0.268
  Chirality :  0.041   0.149   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  5.460  87.950   1200
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.71 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.06 (0.27), residues: 1086
  helix:  1.74 (0.30), residues: 361
  sheet:  0.25 (0.34), residues: 250
  loop : -1.68 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 191 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.016   0.001   PHE E  29 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8076)
  covalent geometry    : angle       0.51834 (11028)
  SS BOND              : bond        0.00557 (    2)
  SS BOND              : angle       0.64697 (    4)
  hydrogen bonds       : bond        0.03055 (  365)
  hydrogen bonds       : angle       3.76434 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7827 (ptpt)
REVERT: B   50 THR cc_start: 0.8340 (m) cc_final: 0.8106 (m)
REVERT: B  209 LYS cc_start: 0.8708 (mttm) cc_final: 0.7365 (mtmt)
REVERT: B  268 ASN cc_start: 0.7560 (m110) cc_final: 0.7255 (m-40)
REVERT: E   83 MET cc_start: 0.7029 (mtm) cc_final: 0.6547 (mtm)
  outliers start: 17
  outliers final: 10
  residues processed: 136
  average time/residue: 0.0976
  time to fit residues: 17.8239
Evaluate side-chains
  138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  175 THR
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  218 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.169873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.134943 restraints weight = 10988.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.13
r_work: 0.3422 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8078  Z= 0.118
  Angle     :  0.522   7.869  11032  Z= 0.271
  Chirality :  0.041   0.138   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  5.349  87.587   1200
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.05 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.27), residues: 1086
  helix:  1.84 (0.30), residues: 360
  sheet:  0.26 (0.34), residues: 254
  loop : -1.68 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 191 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.014   0.001   PHE B 292 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8076)
  covalent geometry    : angle       0.52200 (11028)
  SS BOND              : bond        0.00598 (    2)
  SS BOND              : angle       0.76674 (    4)
  hydrogen bonds       : bond        0.03132 (  365)
  hydrogen bonds       : angle       3.78876 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7824 (ptpt)
REVERT: B  209 LYS cc_start: 0.8712 (mttm) cc_final: 0.7378 (mtmt)
REVERT: B  268 ASN cc_start: 0.7557 (m110) cc_final: 0.7270 (m-40)
REVERT: E   83 MET cc_start: 0.6986 (mtm) cc_final: 0.6473 (mtm)
REVERT: R  126 PHE cc_start: 0.7032 (t80) cc_final: 0.6791 (t80)
REVERT: R  140 LEU cc_start: 0.4483 (mp) cc_final: 0.3909 (mp)
  outliers start: 16
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0976
  time to fit residues: 17.9066
Evaluate side-chains
  141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  175 THR
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  218 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0470
   chunk 90 optimal weight:    0.0010
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.3684

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.171890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.137888 restraints weight = 11032.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.26
r_work: 0.3458 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8078  Z= 0.087
  Angle     :  0.496   8.935  11032  Z= 0.255
  Chirality :  0.040   0.141   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  5.011  83.206   1200
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.46 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.27), residues: 1086
  helix:  2.16 (0.30), residues: 348
  sheet:  0.35 (0.34), residues: 252
  loop : -1.60 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 191 
 TYR   0.010   0.001   TYR R  94 
 PHE   0.014   0.001   PHE E  29 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 8076)
  covalent geometry    : angle       0.49565 (11028)
  SS BOND              : bond        0.00470 (    2)
  SS BOND              : angle       0.55853 (    4)
  hydrogen bonds       : bond        0.02629 (  365)
  hydrogen bonds       : angle       3.65345 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7812 (ptpt)
REVERT: B   50 THR cc_start: 0.8342 (m) cc_final: 0.8079 (m)
REVERT: B  209 LYS cc_start: 0.8663 (mttm) cc_final: 0.7351 (mtmt)
REVERT: B  268 ASN cc_start: 0.7550 (m110) cc_final: 0.7259 (m-40)
REVERT: B  280 LYS cc_start: 0.8525 (tttp) cc_final: 0.8111 (mtpt)
REVERT: E   83 MET cc_start: 0.6955 (mtm) cc_final: 0.6494 (mtm)
REVERT: R  140 LEU cc_start: 0.4530 (mp) cc_final: 0.3932 (mp)
  outliers start: 14
  outliers final: 12
  residues processed: 141
  average time/residue: 0.1028
  time to fit residues: 19.3097
Evaluate side-chains
  149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain R residue  175 THR
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  218 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0030
   chunk 79 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0970
   overall best weight:    0.3566

-------------------------------------------------------------------------------
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 = 0.171954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.137783 restraints weight = 10996.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.22
r_work: 0.3460 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8078  Z= 0.086
  Angle     :  0.487   8.280  11032  Z= 0.251
  Chirality :  0.040   0.140   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  4.802  77.728   1200
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 21.13 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.27), residues: 1086
  helix:  2.24 (0.30), residues: 347
  sheet:  0.40 (0.34), residues: 253
  loop : -1.54 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 191 
 TYR   0.010   0.001   TYR E 173 
 PHE   0.013   0.001   PHE E  29 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 8076)
  covalent geometry    : angle       0.48722 (11028)
  SS BOND              : bond        0.00448 (    2)
  SS BOND              : angle       0.58575 (    4)
  hydrogen bonds       : bond        0.02562 (  365)
  hydrogen bonds       : angle       3.60384 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7735 (ptpt)
REVERT: A  270 LYS cc_start: 0.6656 (pttm) cc_final: 0.6439 (pttp)
REVERT: B  209 LYS cc_start: 0.8668 (mttm) cc_final: 0.7355 (mtmt)
REVERT: B  268 ASN cc_start: 0.7546 (m110) cc_final: 0.7267 (m-40)
REVERT: B  280 LYS cc_start: 0.8511 (tttp) cc_final: 0.8093 (mtpt)
REVERT: E   83 MET cc_start: 0.6931 (mtm) cc_final: 0.6483 (mtm)
REVERT: R  140 LEU cc_start: 0.4486 (mp) cc_final: 0.3898 (mp)
  outliers start: 13
  outliers final: 12
  residues processed: 141
  average time/residue: 0.0960
  time to fit residues: 18.3718
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain R residue  175 THR
Chi-restraints excluded: chain R residue  213 MET
Chi-restraints excluded: chain R residue  218 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0050
   chunk 18 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
R 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.171085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.136466 restraints weight = 11059.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.15
r_work: 0.3458 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8078  Z= 0.096
  Angle     :  0.499   8.308  11032  Z= 0.257
  Chirality :  0.041   0.142   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  4.737  71.252   1200
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.40 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.27), residues: 1086
  helix:  2.32 (0.30), residues: 347
  sheet:  0.46 (0.34), residues: 252
  loop : -1.55 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 191 
 TYR   0.008   0.001   TYR R  94 
 PHE   0.014   0.001   PHE B 292 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 8076)
  covalent geometry    : angle       0.49874 (11028)
  SS BOND              : bond        0.00492 (    2)
  SS BOND              : angle       0.59213 (    4)
  hydrogen bonds       : bond        0.02712 (  365)
  hydrogen bonds       : angle       3.62151 ( 1035)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7999 (ptpt) cc_final: 0.7753 (ptpt)
REVERT: B  209 LYS cc_start: 0.8711 (mttm) cc_final: 0.7276 (mtmt)
REVERT: B  268 ASN cc_start: 0.7567 (m110) cc_final: 0.7269 (m-40)
REVERT: E   83 MET cc_start: 0.6988 (mtm) cc_final: 0.6516 (mtm)
REVERT: R  140 LEU cc_start: 0.4405 (mp) cc_final: 0.3775 (mp)
  outliers start: 12
  outliers final: 10
  residues processed: 136
  average time/residue: 0.0948
  time to fit residues: 17.4188
Evaluate side-chains
  140 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain R residue  175 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 106 optimal weight:    0.4980
   chunk 100 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0040
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.170992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.136550 restraints weight = 10926.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.10
r_work: 0.3455 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8078  Z= 0.098
  Angle     :  0.494   7.383  11032  Z= 0.257
  Chirality :  0.041   0.142   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  4.648  63.528   1200
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.67 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.27), residues: 1086
  helix:  2.34 (0.30), residues: 347
  sheet:  0.51 (0.34), residues: 252
  loop : -1.53 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 191 
 TYR   0.012   0.001   TYR E 173 
 PHE   0.013   0.001   PHE B 292 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8076)
  covalent geometry    : angle       0.49419 (11028)
  SS BOND              : bond        0.00523 (    2)
  SS BOND              : angle       0.69775 (    4)
  hydrogen bonds       : bond        0.02748 (  365)
  hydrogen bonds       : angle       3.62506 ( 1035)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2796.05 seconds
wall clock time: 48 minutes 26.62 seconds (2906.62 seconds total)