Starting phenix.real_space_refine
on Mon Apr 28 17:54:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcp_29940/04_2025/8gcp_29940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcp_29940/04_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_29940/04_2025/8gcp_29940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcp_29940/04_2025/8gcp_29940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcp_29940/04_2025/8gcp_29940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcp_29940/04_2025/8gcp_29940.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'TYR:plan': 2, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4}
          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: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          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, 'GLU:plan': 4, 'ARG:plan': 1, '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, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5}
          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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6}
          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: 5.27, per 1000 atoms: 0.67
  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: 2.05
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.17
  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: 2.20

  Time building geometry restraints manager: 2.45 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.380
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.400
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (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
 TRP   0.072   0.004   TRP R 174 
 HIS   0.017   0.003   HIS B 311 
 PHE   0.029   0.003   PHE A 196 
 TYR   0.027   0.003   TYR B 105 
 ARG   0.009   0.001   ARG E  18 

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

*********************** 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  : 0.799 
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: 0.8002 (m)
  outliers start: 5
  outliers final: 1
  residues processed: 144
  average time/residue: 0.1980
  time to fit residues: 38.4624
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  : 0.797 
-------------------------------------------------------------------------------
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 91 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    0.4980
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.169447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.135278 restraints weight = 11024.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.18
r_work: 0.3408 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8078  Z= 0.136
  Angle     :  0.609  12.145  11032  Z= 0.317
  Chirality :  0.042   0.170   1324
  Planarity :  0.004   0.056   1403
  Dihedral  :  6.581  83.950   1202
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  9.83 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.25), residues: 1086
  helix:  0.40 (0.28), residues: 348
  sheet: -0.31 (0.34), residues: 249
  loop : -2.13 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 174 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.013   0.002   PHE A 336 
 TYR   0.013   0.001   TYR R 144 
 ARG   0.005   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  365)
  hydrogen bonds       : angle       4.34676 ( 1035)
  SS BOND              : bond        0.00715 (    2)
  SS BOND              : angle       0.97874 (    4)
  covalent geometry    : bond        0.00299 ( 8076)
  covalent geometry    : angle       0.60878 (11028)

*********************** 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
  161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 150
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8780 (tp) cc_final: 0.8520 (tt)
REVERT: B   52 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7995 (mtt-85)
REVERT: B  124 TYR cc_start: 0.8620 (m-80) cc_final: 0.8162 (m-80)
REVERT: B  129 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7332 (mmm-85)
REVERT: B  209 LYS cc_start: 0.8743 (mttm) cc_final: 0.7229 (mtmt)
REVERT: B  228 ASP cc_start: 0.8034 (p0) cc_final: 0.7828 (p0)
  outliers start: 11
  outliers final: 6
  residues processed: 151
  average time/residue: 0.2081
  time to fit residues: 42.0616
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 140
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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 6 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 79 optimal weight:   10.0000
   chunk 82 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.168674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134646 restraints weight = 11182.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.25
r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.2086

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= 0.146
  Angle     :  0.589  10.013  11032  Z= 0.305
  Chirality :  0.042   0.147   1324
  Planarity :  0.004   0.048   1403
  Dihedral  :  6.193  82.291   1202
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.61 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.26), residues: 1086
  helix:  1.03 (0.30), residues: 349
  sheet: -0.09 (0.34), residues: 242
  loop : -2.06 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 174 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.019   0.002   PHE E  29 
 TYR   0.015   0.001   TYR B 105 
 ARG   0.004   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  365)
  hydrogen bonds       : angle       4.17849 ( 1035)
  SS BOND              : bond        0.00680 (    2)
  SS BOND              : angle       0.87201 (    4)
  covalent geometry    : bond        0.00339 ( 8076)
  covalent geometry    : angle       0.58907 (11028)

*********************** 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  : 0.882 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8767 (tp) cc_final: 0.8497 (tt)
REVERT: B   52 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7991 (mtt-85)
REVERT: B  129 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7246 (mmm-85)
REVERT: B  209 LYS cc_start: 0.8752 (mttm) cc_final: 0.7256 (mtmt)
REVERT: B  228 ASP cc_start: 0.8024 (p0) cc_final: 0.7811 (p0)
REVERT: B  268 ASN cc_start: 0.7540 (m110) cc_final: 0.7250 (m-40)
  outliers start: 11
  outliers final: 7
  residues processed: 149
  average time/residue: 0.2191
  time to fit residues: 44.6135
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  : 0.915 
-------------------------------------------------------------------------------
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 93 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0020
   chunk 78 optimal weight:    0.0030
   chunk 59 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0370
   overall best weight:    0.2676

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.172431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.139197 restraints weight = 11055.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.24
r_work: 0.3444 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8078  Z= 0.088
  Angle     :  0.502   8.287  11032  Z= 0.260
  Chirality :  0.040   0.132   1324
  Planarity :  0.003   0.047   1403
  Dihedral  :  5.657  80.385   1202
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.36 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.26), residues: 1086
  helix:  1.37 (0.30), residues: 354
  sheet:  0.24 (0.34), residues: 241
  loop : -1.92 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.018   0.001   PHE E  29 
 TYR   0.007   0.001   TYR E 102 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02818 (  365)
  hydrogen bonds       : angle       3.80324 ( 1035)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       0.55575 (    4)
  covalent geometry    : bond        0.00189 ( 8076)
  covalent geometry    : angle       0.50247 (11028)

*********************** 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
  148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8795 (tp) cc_final: 0.8445 (tt)
REVERT: A  197 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7790 (ptpt)
REVERT: B  127 LYS cc_start: 0.8470 (mttt) cc_final: 0.8158 (mttp)
REVERT: B  134 ARG cc_start: 0.8150 (ptt-90) cc_final: 0.7933 (ptt-90)
REVERT: B  209 LYS cc_start: 0.8604 (mttm) cc_final: 0.7217 (mtmt)
REVERT: B  268 ASN cc_start: 0.7549 (m110) cc_final: 0.7254 (m-40)
REVERT: E   83 MET cc_start: 0.6927 (mtm) cc_final: 0.6423 (mtm)
REVERT: R   27 MET cc_start: 0.4927 (mtt) cc_final: 0.4720 (mtt)
  outliers start: 9
  outliers final: 4
  residues processed: 143
  average time/residue: 0.2097
  time to fit residues: 39.8367
Evaluate side-chains
  137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain R residue  110 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 60 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 64 optimal weight:    0.0980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
B 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.169122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.134290 restraints weight = 10998.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.14
r_work: 0.3406 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8078  Z= 0.129
  Angle     :  0.546   7.726  11032  Z= 0.282
  Chirality :  0.042   0.147   1324
  Planarity :  0.003   0.040   1403
  Dihedral  :  5.683  83.820   1202
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.26), residues: 1086
  helix:  1.55 (0.30), residues: 355
  sheet:  0.21 (0.34), residues: 249
  loop : -1.84 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E 167 
 PHE   0.019   0.002   PHE E  29 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.004   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  365)
  hydrogen bonds       : angle       3.87936 ( 1035)
  SS BOND              : bond        0.00620 (    2)
  SS BOND              : angle       0.77715 (    4)
  covalent geometry    : bond        0.00300 ( 8076)
  covalent geometry    : angle       0.54570 (11028)

*********************** 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
  156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.8790 (tp) cc_final: 0.8523 (tt)
REVERT: A  197 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7836 (ptpt)
REVERT: A  225 VAL cc_start: 0.7922 (t) cc_final: 0.7718 (t)
REVERT: A  270 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6844 (pttm)
REVERT: B   50 THR cc_start: 0.8338 (m) cc_final: 0.8068 (m)
REVERT: B  209 LYS cc_start: 0.8706 (mttm) cc_final: 0.7208 (mtmt)
REVERT: B  268 ASN cc_start: 0.7598 (m110) cc_final: 0.7300 (m-40)
REVERT: E   83 MET cc_start: 0.6995 (mtm) cc_final: 0.6450 (mtm)
REVERT: R   27 MET cc_start: 0.4900 (mtt) cc_final: 0.4696 (mtt)
REVERT: R  140 LEU cc_start: 0.4389 (mp) cc_final: 0.4106 (mt)
  outliers start: 21
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2153
  time to fit residues: 41.0760
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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   86 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  172 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   chunk 99 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0570
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.170267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.136543 restraints weight = 10914.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 1.93
r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8078  Z= 0.110
  Angle     :  0.519   6.852  11032  Z= 0.269
  Chirality :  0.042   0.235   1324
  Planarity :  0.003   0.039   1403
  Dihedral  :  5.496  87.446   1200
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.98 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.27), residues: 1086
  helix:  1.65 (0.30), residues: 361
  sheet:  0.28 (0.34), residues: 248
  loop : -1.74 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.020   0.001   PHE E  29 
 TYR   0.008   0.001   TYR E 173 
 ARG   0.004   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03085 (  365)
  hydrogen bonds       : angle       3.80316 ( 1035)
  SS BOND              : bond        0.00552 (    2)
  SS BOND              : angle       0.66365 (    4)
  covalent geometry    : bond        0.00252 ( 8076)
  covalent geometry    : angle       0.51901 (11028)

*********************** 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
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7873 (ptpt)
REVERT: A  225 VAL cc_start: 0.7931 (t) cc_final: 0.7712 (t)
REVERT: A  270 LYS cc_start: 0.6964 (pttm) cc_final: 0.6757 (pttm)
REVERT: B   50 THR cc_start: 0.8250 (m) cc_final: 0.8020 (m)
REVERT: B  209 LYS cc_start: 0.8679 (mttm) cc_final: 0.7330 (mtmt)
REVERT: B  268 ASN cc_start: 0.7532 (m110) cc_final: 0.7238 (m-40)
REVERT: E   83 MET cc_start: 0.6967 (mtm) cc_final: 0.6466 (mtm)
  outliers start: 13
  outliers final: 8
  residues processed: 138
  average time/residue: 0.2282
  time to fit residues: 41.4997
Evaluate side-chains
  136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  172 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0170
   chunk 26 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0870
   chunk 103 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.171598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137880 restraints weight = 11012.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.01
r_work: 0.3462 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2989

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= 0.092
  Angle     :  0.497   7.963  11032  Z= 0.258
  Chirality :  0.041   0.208   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  5.228  88.387   1200
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 19.92 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.27), residues: 1086
  helix:  1.86 (0.30), residues: 356
  sheet:  0.32 (0.34), residues: 250
  loop : -1.66 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.001   PHE E  29 
 TYR   0.009   0.001   TYR E 173 
 ARG   0.003   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02732 (  365)
  hydrogen bonds       : angle       3.65351 ( 1035)
  SS BOND              : bond        0.00462 (    2)
  SS BOND              : angle       0.58529 (    4)
  covalent geometry    : bond        0.00203 ( 8076)
  covalent geometry    : angle       0.49739 (11028)

*********************** 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
  147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7757 (ptpt)
REVERT: A  225 VAL cc_start: 0.7940 (t) cc_final: 0.7710 (t)
REVERT: A  270 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6699 (pttm)
REVERT: B   50 THR cc_start: 0.8188 (m) cc_final: 0.7983 (m)
REVERT: B  209 LYS cc_start: 0.8623 (mttm) cc_final: 0.7320 (mtmt)
REVERT: B  268 ASN cc_start: 0.7585 (m110) cc_final: 0.7302 (m-40)
REVERT: B  280 LYS cc_start: 0.8495 (tttp) cc_final: 0.8078 (mtpt)
REVERT: E   83 MET cc_start: 0.6982 (mtm) cc_final: 0.6523 (mtm)
REVERT: R  140 LEU cc_start: 0.4687 (mp) cc_final: 0.4113 (mp)
  outliers start: 10
  outliers final: 8
  residues processed: 142
  average time/residue: 0.2139
  time to fit residues: 40.4019
Evaluate side-chains
  141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  270 LYS
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 E residue  172 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.0570
   chunk 16 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 104 optimal weight:   30.0000
   chunk 8 optimal weight:    0.5980
   chunk 107 optimal weight:    0.0030
   chunk 100 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.4108

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.172530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.139866 restraints weight = 10953.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.93
r_work: 0.3484 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3146

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= 0.089
  Angle     :  0.492   7.344  11032  Z= 0.255
  Chirality :  0.041   0.209   1324
  Planarity :  0.003   0.037   1403
  Dihedral  :  4.988  83.570   1200
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 20.46 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.27), residues: 1086
  helix:  2.13 (0.30), residues: 350
  sheet:  0.39 (0.34), residues: 252
  loop : -1.65 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE E  29 
 TYR   0.009   0.001   TYR E 173 
 ARG   0.004   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02688 (  365)
  hydrogen bonds       : angle       3.61842 ( 1035)
  SS BOND              : bond        0.00451 (    2)
  SS BOND              : angle       0.50722 (    4)
  covalent geometry    : bond        0.00195 ( 8076)
  covalent geometry    : angle       0.49238 (11028)

*********************** 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
  156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8045 (ptpt) cc_final: 0.7777 (ptpt)
REVERT: A  225 VAL cc_start: 0.7929 (t) cc_final: 0.7693 (t)
REVERT: B  209 LYS cc_start: 0.8634 (mttm) cc_final: 0.7275 (mtmt)
REVERT: B  268 ASN cc_start: 0.7559 (m110) cc_final: 0.7242 (m-40)
REVERT: B  280 LYS cc_start: 0.8505 (tttp) cc_final: 0.8083 (mtpt)
REVERT: E   83 MET cc_start: 0.6949 (mtm) cc_final: 0.6490 (mtm)
REVERT: R  140 LEU cc_start: 0.4434 (mp) cc_final: 0.3867 (mp)
  outliers start: 16
  outliers final: 14
  residues processed: 145
  average time/residue: 0.2158
  time to fit residues: 41.3916
Evaluate side-chains
  153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  195 HIS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  353 LEU
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  172 THR
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 35 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0370
   chunk 63 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 331 ASN
R 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.167902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.132799 restraints weight = 11009.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.14
r_work: 0.3420 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8078  Z= 0.174
  Angle     :  0.585   7.293  11032  Z= 0.303
  Chirality :  0.044   0.215   1324
  Planarity :  0.003   0.039   1403
  Dihedral  :  5.259  79.264   1200
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.59 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.26), residues: 1086
  helix:  1.98 (0.30), residues: 354
  sheet:  0.28 (0.33), residues: 253
  loop : -1.70 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 211 
 HIS   0.005   0.001   HIS E 167 
 PHE   0.021   0.002   PHE A 196 
 TYR   0.016   0.002   TYR B 105 
 ARG   0.006   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  365)
  hydrogen bonds       : angle       3.92345 ( 1035)
  SS BOND              : bond        0.00801 (    2)
  SS BOND              : angle       1.04280 (    4)
  covalent geometry    : bond        0.00412 ( 8076)
  covalent geometry    : angle       0.58456 (11028)

*********************** 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
  159 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.265 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7771 (ptpt)
REVERT: A  225 VAL cc_start: 0.8052 (t) cc_final: 0.7818 (t)
REVERT: B  209 LYS cc_start: 0.8762 (mttm) cc_final: 0.7340 (mtmt)
REVERT: B  268 ASN cc_start: 0.7552 (m110) cc_final: 0.7261 (m-40)
REVERT: R  126 PHE cc_start: 0.7050 (t80) cc_final: 0.6822 (t80)
REVERT: R  140 LEU cc_start: 0.4517 (mp) cc_final: 0.3902 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 147
  average time/residue: 0.2071
  time to fit residues: 41.1586
Evaluate side-chains
  153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  341 ASP
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  172 THR
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain R residue  114 SER
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 99 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 11 optimal weight:    0.3980
   chunk 84 optimal weight:    0.7980
   chunk 87 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0170
   chunk 20 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0000
   chunk 78 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.3822

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.172239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.139334 restraints weight = 10854.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.45
r_work: 0.3451 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3245

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= 0.090
  Angle     :  0.501   8.490  11032  Z= 0.259
  Chirality :  0.041   0.209   1324
  Planarity :  0.003   0.036   1403
  Dihedral  :  4.883  72.585   1200
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 21.13 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.27), residues: 1086
  helix:  2.25 (0.30), residues: 348
  sheet:  0.41 (0.34), residues: 252
  loop : -1.57 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.015   0.001   PHE E  29 
 TYR   0.012   0.001   TYR E 173 
 ARG   0.002   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02705 (  365)
  hydrogen bonds       : angle       3.67237 ( 1035)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       0.58714 (    4)
  covalent geometry    : bond        0.00195 ( 8076)
  covalent geometry    : angle       0.50086 (11028)

********************** 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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A  197 LYS cc_start: 0.8009 (ptpt) cc_final: 0.7808 (ptpt)
REVERT: A  225 VAL cc_start: 0.7978 (t) cc_final: 0.7740 (t)
REVERT: B  209 LYS cc_start: 0.8670 (mttm) cc_final: 0.7218 (mtmt)
REVERT: B  268 ASN cc_start: 0.7549 (m110) cc_final: 0.7251 (m-40)
REVERT: R  126 PHE cc_start: 0.7022 (t80) cc_final: 0.6785 (t80)
REVERT: R  140 LEU cc_start: 0.4590 (mp) cc_final: 0.3986 (mp)
  outliers start: 11
  outliers final: 9
  residues processed: 142
  average time/residue: 0.2261
  time to fit residues: 42.0016
Evaluate side-chains
  145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain E residue  172 THR
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 52 optimal weight:    0.0010
   chunk 76 optimal weight:    1.9990
   chunk 92 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0670
   chunk 70 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.0130

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.169411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.134288 restraints weight = 11022.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.18
r_work: 0.3434 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8078  Z= 0.138
  Angle     :  0.547   8.667  11032  Z= 0.284
  Chirality :  0.043   0.213   1324
  Planarity :  0.003   0.038   1403
  Dihedral  :  4.982  66.043   1200
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 21.53 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 1086
  helix:  2.22 (0.30), residues: 348
  sheet:  0.43 (0.34), residues: 252
  loop : -1.61 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.004   0.001   HIS E 167 
 PHE   0.015   0.002   PHE E  29 
 TYR   0.010   0.001   TYR B 105 
 ARG   0.005   0.000   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  365)
  hydrogen bonds       : angle       3.82645 ( 1035)
  SS BOND              : bond        0.00713 (    2)
  SS BOND              : angle       0.94170 (    4)
  covalent geometry    : bond        0.00325 ( 8076)
  covalent geometry    : angle       0.54683 (11028)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5374.64 seconds
wall clock time: 92 minutes 21.46 seconds (5541.46 seconds total)