Starting phenix.real_space_refine
on Wed Feb 12 12:56:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxv_36714/02_2025/8jxv_36714.cif"
  }
  resolution = 3.21
  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=   0.016 sd=   0.078
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     Cl      1      4.86       5
     C    5111      2.51       5
     N    1307      2.21       5
     O    1464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7935
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1550
          Classifications: {'peptide': 204}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 201}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "C"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2293
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 300}
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 46
    Chain: "D"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 227
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 27}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1749
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "R"
      Number of atoms: 2093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2093
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 8, 'TRANS': 257}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 70
    Chain: "R"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'VBU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.07, per 1000 atoms: 0.64
  Number of scatterers: 7935
  At special positions: 0
  Unit cell: (83.6, 118.8, 129.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      52     16.00
     O    1464      8.00
     N    1307      7.00
     C    5111      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  87 " - pdb=" SG  CYS R 164 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      34.0% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 31
    Processing helix  chain 'B' and resid 212 through 216
    Processing helix  chain 'B' and resid 242 through 255
    Processing helix  chain 'B' and resid 256 through 260
    Processing helix  chain 'B' and resid 270 through 281
      removed outlier: 3.763A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LYS B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 295 through 309
      removed outlier: 3.697A  pdb=" N   ALA B 299 " --> pdb=" O   THR B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 348
    Processing helix  chain 'D' and resid 32 through 44
      removed outlier: 3.522A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.550A  pdb=" N   SER E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.680A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 15 through 43
      removed outlier: 4.002A  pdb=" N   VAL R  36 " --> pdb=" O   GLY R  32 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASP R  43 " --> pdb=" O   ALA R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 63
      removed outlier: 3.980A  pdb=" N   PHE R  63 " --> pdb=" O   ILE R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 78
      Proline residue:  R  74  - end of helix
    Processing helix  chain 'R' and resid 83 through 118
      removed outlier: 4.748A  pdb=" N   PHE R  89 " --> pdb=" O   GLU R  85 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL R 116 " --> pdb=" O   ARG R 112 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASN R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 148
      removed outlier: 4.324A  pdb=" N   TRP R 140 " --> pdb=" O   MET R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 151
      No H-bonds generated for 'chain 'R' and resid 149 through 151'
    Processing helix  chain 'R' and resid 155 through 159
      removed outlier: 3.670A  pdb=" N   ASP R 159 " --> pdb=" O   SER R 156 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 170
    Processing helix  chain 'R' and resid 171 through 181
      removed outlier: 3.570A  pdb=" N   LEU R 175 " --> pdb=" O   GLU R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 203
    Processing helix  chain 'R' and resid 294 through 329
      Proline residue:  R 318  - end of helix
      removed outlier: 4.206A  pdb=" N   TYR R 329 " --> pdb=" O   VAL R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 337 through 349
      removed outlier: 3.642A  pdb=" N   ARG R 341 " --> pdb=" O   SER R 337 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   TRP R 348 " --> pdb=" O   PHE R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 349 through 362
      removed outlier: 4.113A  pdb=" N   VAL R 353 " --> pdb=" O   PHE R 349 " (cutoff:3.500A)
      Proline residue:  R 355  - end of helix
      removed outlier: 4.129A  pdb=" N   TYR R 358 " --> pdb=" O   ASN R 354 " (cutoff:3.500A)
      Proline residue:  R 359  - end of helix
      removed outlier: 3.968A  pdb=" N   HIS R 362 " --> pdb=" O   TYR R 358 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 372
      removed outlier: 3.857A  pdb=" N   ILE R 372 " --> pdb=" O   ALA R 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191
      removed outlier: 6.489A  pdb=" N   VAL B  34 " --> pdb=" O   LYS B 197 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   PHE B 199 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA B 220 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ILE B 264 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   HIS B 322 " --> pdb=" O   ILE B 264 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU B 266 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.863A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.762A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.939A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151
      removed outlier: 3.753A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER C 160 " --> pdb=" O   CYS C 148 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.681A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.492A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 277
      removed outlier: 4.250A  pdb=" N   CYS C 294 " --> pdb=" O   LEU C 308 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.862A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 147 through 149
      removed outlier: 3.732A  pdb=" N   VAL E 148 " --> pdb=" O   LYS E 245 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU E 247 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU E 179 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   LEU E 188 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149
      removed outlier: 3.732A  pdb=" N   VAL E 148 " --> pdb=" O   LYS E 245 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU E 247 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLN E 232 " --> pdb=" O   THR E 239 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   THR E 239 " --> pdb=" O   GLN E 232 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 161

    373 hydrogen bonds defined for protein.
    1026 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: 2.32

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2491
        1.34 -     1.46: 2032
        1.46 -     1.58: 3522
        1.58 -     1.70: 2
        1.70 -     1.82: 74
  Bond restraints: 8121
  Sorted by residual:
  bond pdb=" C10 VBU R 401 "
       pdb=" N02 VBU R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.618 -0.267 2.00e-02 2.50e+03 1.79e+02
  bond pdb=" C10 VBU R 401 "
       pdb=" C11 VBU R 401 "
    ideal  model  delta    sigma   weight residual
    1.486  1.624 -0.138 2.00e-02 2.50e+03 4.78e+01
  bond pdb=" C14 VBU R 401 "
       pdb=" N04 VBU R 401 "
    ideal  model  delta    sigma   weight residual
    1.377  1.481 -0.104 2.00e-02 2.50e+03 2.72e+01
  bond pdb=" C07 VBU R 401 "
       pdb=" N02 VBU R 401 "
    ideal  model  delta    sigma   weight residual
    1.453  1.543 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C06 VBU R 401 "
       pdb=" N02 VBU R 401 "
    ideal  model  delta    sigma   weight residual
    1.458  1.534 -0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 8116 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 10862
        2.54 -     5.08: 161
        5.08 -     7.61: 21
        7.61 -    10.15: 6
       10.15 -    12.69: 4
  Bond angle restraints: 11054
  Sorted by residual:
  angle pdb=" C08 VBU R 401 "
        pdb=" N03 VBU R 401 "
        pdb=" C09 VBU R 401 "
      ideal   model   delta    sigma   weight residual
     113.13  100.44   12.69 3.00e+00 1.11e-01 1.79e+01
  angle pdb=" C10 VBU R 401 "
        pdb=" N04 VBU R 401 "
        pdb=" C14 VBU R 401 "
      ideal   model   delta    sigma   weight residual
     123.92  135.64  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" C13 VBU R 401 "
        pdb=" N05 VBU R 401 "
        pdb=" C15 VBU R 401 "
      ideal   model   delta    sigma   weight residual
     112.77  124.09  -11.32 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" N   VAL R 153 "
        pdb=" CA  VAL R 153 "
        pdb=" C   VAL R 153 "
      ideal   model   delta    sigma   weight residual
     112.80  108.89    3.91 1.15e+00 7.56e-01 1.15e+01
  angle pdb=" C19 VBU R 401 "
        pdb=" C14 VBU R 401 "
        pdb=" N04 VBU R 401 "
      ideal   model   delta    sigma   weight residual
     117.94  127.49   -9.55 3.00e+00 1.11e-01 1.01e+01
  ... (remaining 11049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 4278
       16.79 -    33.57: 344
       33.57 -    50.36: 71
       50.36 -    67.15: 10
       67.15 -    83.93: 3
  Dihedral angle restraints: 4706
    sinusoidal: 1690
      harmonic: 3016
  Sorted by residual:
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 230 "
           pdb=" CB  CYS E 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.04  -45.04     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CA  PHE E  80 "
           pdb=" C   PHE E  80 "
           pdb=" N   LEU E  81 "
           pdb=" CA  LEU E  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.54   19.46     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  ARG E 192 "
           pdb=" C   ARG E 192 "
           pdb=" N   MET E 193 "
           pdb=" CA  MET E 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.08   18.92     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 805
       0.038 -    0.076: 332
       0.076 -    0.114: 110
       0.114 -    0.153: 24
       0.153 -    0.191: 4
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  PRO R 186 "
            pdb=" N   PRO R 186 "
            pdb=" C   PRO R 186 "
            pdb=" CB  PRO R 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.10e-01
  chirality pdb=" CA  TRP R 316 "
            pdb=" N   TRP R 316 "
            pdb=" C   TRP R 316 "
            pdb=" CB  TRP R 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  TYR C  59 "
            pdb=" N   TYR C  59 "
            pdb=" C   TYR C  59 "
            pdb=" CB  TYR C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 306 "   -0.014 2.00e-02 2.50e+03   2.89e-02 8.37e+00
        pdb=" C   GLY C 306 "    0.050 2.00e-02 2.50e+03
        pdb=" O   GLY C 306 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL C 307 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 332 "   -0.019 2.00e-02 2.50e+03   1.64e-02 6.73e+00
        pdb=" CG  TRP C 332 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 332 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 332 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 332 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 332 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 332 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 332 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 354 "    0.041 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO R 355 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO R 355 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 355 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 87
        2.63 -     3.20: 7208
        3.20 -     3.77: 11921
        3.77 -     4.33: 16091
        4.33 -     4.90: 27251
  Nonbonded interactions: 62558
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 275 "
            pdb=" O   SER C 316 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" O   ARG E  67 "
            pdb=" OG1 THR E  84 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG1 THR C 274 "
            pdb=" O   VAL C 315 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   CYS C 103 "
            pdb=" NH1 ARG C 150 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG1 THR C  86 "
            pdb=" OD1 ASN C  88 "
     model   vdw
     2.241 3.040
  ... (remaining 62553 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:             1.520
  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:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.110
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
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      :  0.007   0.267   8121  Z= 0.413
  Angle     :  0.827  12.690  11054  Z= 0.431
  Chirality :  0.046   0.191   1275
  Planarity :  0.004   0.061   1379
  Dihedral  : 13.108  83.932   2752
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.75 (0.26), residues: 1016
  helix:  1.11 (0.30), residues: 302
  sheet: -0.28 (0.33), residues: 243
  loop : -1.71 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP C 332 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.021   0.002   PHE C 234 
 TYR   0.012   0.002   TYR E  95 
 ARG   0.006   0.001   ARG B  32 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.857 
Fit side-chains
REVERT: C  332 TRP cc_start: 0.6650 (m-10) cc_final: 0.6368 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1991
  time to fit residues: 32.1934
Evaluate side-chains
  106 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0970
   chunk 52 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
E  39 GLN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.149018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.126620 restraints weight = 13197.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 2.44
r_work: 0.3844 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.1111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8121  Z= 0.174
  Angle     :  0.625  11.150  11054  Z= 0.322
  Chirality :  0.042   0.152   1275
  Planarity :  0.004   0.045   1379
  Dihedral  :  5.012  19.193   1123
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  7.26 %
    Favored  : 92.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.33 (0.26), residues: 1016
  helix:  1.66 (0.30), residues: 297
  sheet: -0.29 (0.31), residues: 279
  loop : -1.51 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 345 
 HIS   0.002   0.001   HIS C 311 
 PHE   0.015   0.002   PHE R 168 
 TYR   0.011   0.001   TYR R 329 
 ARG   0.002   0.000   ARG E  98 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.886 
Fit side-chains
REVERT: C  264 TYR cc_start: 0.5785 (m-10) cc_final: 0.5545 (m-10)
REVERT: E   98 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6564 (mtm110)
  outliers start: 4
  outliers final: 3
  residues processed: 121
  average time/residue: 0.2021
  time to fit residues: 33.3745
Evaluate side-chains
  113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 143 GLN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.148298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.125564 restraints weight = 13368.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 2.25
r_work: 0.3853 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8121  Z= 0.199
  Angle     :  0.611  10.714  11054  Z= 0.313
  Chirality :  0.042   0.145   1275
  Planarity :  0.004   0.043   1379
  Dihedral  :  4.831  17.783   1123
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.81 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.19 (0.26), residues: 1016
  helix:  1.80 (0.30), residues: 298
  sheet: -0.18 (0.32), residues: 261
  loop : -1.42 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 345 
 HIS   0.003   0.001   HIS C 142 
 PHE   0.024   0.002   PHE E  29 
 TYR   0.009   0.001   TYR R 329 
 ARG   0.005   0.000   ARG E  67 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.871 
Fit side-chains
REVERT: C  264 TYR cc_start: 0.5871 (m-10) cc_final: 0.5630 (m-10)
REVERT: E   98 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6673 (mtm110)
REVERT: E  177 TRP cc_start: 0.6077 (m100) cc_final: 0.5505 (m100)
REVERT: R  150 MET cc_start: 0.8370 (tpp) cc_final: 0.7752 (mmt)
REVERT: R  322 PHE cc_start: 0.7437 (t80) cc_final: 0.7232 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 119
  average time/residue: 0.1912
  time to fit residues: 31.4945
Evaluate side-chains
  110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  338 VAL
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 84 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 66 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 95 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.144408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.121714 restraints weight = 13218.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 2.40
r_work: 0.3771 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8121  Z= 0.367
  Angle     :  0.714  11.363  11054  Z= 0.365
  Chirality :  0.045   0.173   1275
  Planarity :  0.005   0.056   1379
  Dihedral  :  5.128  19.533   1123
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.32 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1016
  helix:  1.56 (0.30), residues: 293
  sheet: -0.16 (0.33), residues: 245
  loop : -1.47 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  99 
 HIS   0.004   0.001   HIS C 142 
 PHE   0.023   0.003   PHE R 180 
 TYR   0.024   0.002   TYR E  60 
 ARG   0.007   0.001   ARG E  67 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.863 
Fit side-chains
REVERT: B  266 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6183 (tp)
REVERT: C  327 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7164 (p)
  outliers start: 13
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1932
  time to fit residues: 30.5076
Evaluate side-chains
  110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  338 VAL
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 79 optimal weight:    0.2980
   chunk 86 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
C 125 ASN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.148581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.126222 restraints weight = 13201.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 2.25
r_work: 0.3854 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8121  Z= 0.177
  Angle     :  0.594  10.361  11054  Z= 0.305
  Chirality :  0.042   0.148   1275
  Planarity :  0.004   0.047   1379
  Dihedral  :  4.726  16.894   1123
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.01 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: 1016
  helix:  1.96 (0.30), residues: 299
  sheet: -0.06 (0.33), residues: 258
  loop : -1.30 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 345 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.024   0.002   PHE R 180 
 TYR   0.011   0.001   TYR R 319 
 ARG   0.006   0.000   ARG E  98 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.867 
Fit side-chains
REVERT: B  266 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6189 (tt)
REVERT: C   61 MET cc_start: 0.7314 (ppp) cc_final: 0.7084 (tmm)
REVERT: C  264 TYR cc_start: 0.6120 (m-10) cc_final: 0.5813 (m-10)
REVERT: C  327 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7093 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1943
  time to fit residues: 31.6787
Evaluate side-chains
  113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 79 optimal weight:    0.4980
   chunk 38 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.148542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.126000 restraints weight = 13221.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 2.22
r_work: 0.3858 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8121  Z= 0.183
  Angle     :  0.596  10.131  11054  Z= 0.305
  Chirality :  0.041   0.145   1275
  Planarity :  0.004   0.046   1379
  Dihedral  :  4.603  17.042   1123
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.38 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: 1016
  helix:  1.90 (0.30), residues: 305
  sheet:  0.02 (0.32), residues: 267
  loop : -1.15 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 345 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.023   0.002   PHE R 180 
 TYR   0.009   0.001   TYR R  72 
 ARG   0.012   0.000   ARG E  98 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.865 
Fit side-chains
REVERT: B    4 THR cc_start: 0.6906 (OUTLIER) cc_final: 0.6606 (m)
REVERT: B  266 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6192 (tt)
REVERT: C  264 TYR cc_start: 0.6095 (m-10) cc_final: 0.5800 (m-10)
REVERT: C  327 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7201 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 114
  average time/residue: 0.1945
  time to fit residues: 30.6753
Evaluate side-chains
  113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue  193 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.146872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.123824 restraints weight = 13285.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 2.24
r_work: 0.3828 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8121  Z= 0.251
  Angle     :  0.634  10.384  11054  Z= 0.324
  Chirality :  0.042   0.150   1275
  Planarity :  0.004   0.050   1379
  Dihedral  :  4.710  16.957   1123
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.62 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.10 (0.27), residues: 1016
  helix:  1.86 (0.30), residues: 301
  sheet:  0.07 (0.33), residues: 262
  loop : -1.19 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 332 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.022   0.002   PHE R 180 
 TYR   0.011   0.002   TYR E 102 
 ARG   0.006   0.000   ARG E  98 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.845 
Fit side-chains
REVERT: B    4 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.6645 (m)
REVERT: B  243 MET cc_start: 0.5602 (mmp) cc_final: 0.5320 (mmt)
REVERT: B  266 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6277 (tt)
REVERT: C  264 TYR cc_start: 0.6198 (m-10) cc_final: 0.5942 (m-10)
REVERT: C  327 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7054 (p)
REVERT: E  177 TRP cc_start: 0.6108 (m100) cc_final: 0.5544 (m100)
  outliers start: 23
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1941
  time to fit residues: 31.8530
Evaluate side-chains
  119 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain E residue  193 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  338 VAL
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0020
   chunk 100 optimal weight:    0.2980
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0270
   chunk 73 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    0.4046

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

Flipped N/Q/H residues before XYZ refinement:
C 119 ASN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.150632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.128902 restraints weight = 13548.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.19
r_work: 0.3891 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8121  Z= 0.160
  Angle     :  0.592   9.951  11054  Z= 0.300
  Chirality :  0.041   0.178   1275
  Planarity :  0.004   0.046   1379
  Dihedral  :  4.518  16.569   1123
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.83 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.26 (0.27), residues: 1016
  helix:  2.01 (0.31), residues: 304
  sheet:  0.22 (0.32), residues: 272
  loop : -1.18 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 332 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.025   0.002   PHE R 180 
 TYR   0.010   0.001   TYR R  72 
 ARG   0.008   0.000   ARG E  98 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.002 
Fit side-chains
REVERT: B    4 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6620 (m)
REVERT: B  266 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6261 (tt)
REVERT: C  125 ASN cc_start: 0.6771 (t0) cc_final: 0.6069 (p0)
REVERT: C  264 TYR cc_start: 0.6160 (m-10) cc_final: 0.5868 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1951
  time to fit residues: 31.5672
Evaluate side-chains
  113 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain E residue  193 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 66 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 101 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.149082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.127017 restraints weight = 13404.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 2.21
r_work: 0.3865 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8121  Z= 0.191
  Angle     :  0.609   9.764  11054  Z= 0.309
  Chirality :  0.042   0.146   1275
  Planarity :  0.004   0.046   1379
  Dihedral  :  4.517  16.983   1123
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.68 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.33 (0.27), residues: 1016
  helix:  2.15 (0.31), residues: 294
  sheet:  0.25 (0.33), residues: 261
  loop : -1.10 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 332 
 HIS   0.003   0.001   HIS C 142 
 PHE   0.025   0.002   PHE R 180 
 TYR   0.037   0.002   TYR E  60 
 ARG   0.002   0.000   ARG R 112 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.865 
Fit side-chains
REVERT: B    4 THR cc_start: 0.6904 (OUTLIER) cc_final: 0.6601 (m)
REVERT: B  266 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6221 (tt)
REVERT: C  125 ASN cc_start: 0.6833 (t0) cc_final: 0.6025 (p0)
REVERT: C  264 TYR cc_start: 0.6133 (m-10) cc_final: 0.5843 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1826
  time to fit residues: 28.7139
Evaluate side-chains
  116 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain E residue  193 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue   76 THR
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  117 SER
Chi-restraints excluded: chain R residue  338 VAL
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    0.0370
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0770
   chunk 18 optimal weight:    0.6980
   chunk 100 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.150805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.128181 restraints weight = 13287.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.27
r_work: 0.3874 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8121  Z= 0.157
  Angle     :  0.594   9.356  11054  Z= 0.301
  Chirality :  0.041   0.153   1275
  Planarity :  0.004   0.045   1379
  Dihedral  :  4.415  19.859   1123
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 18.40 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.45 (0.27), residues: 1016
  helix:  2.31 (0.30), residues: 297
  sheet:  0.27 (0.32), residues: 273
  loop : -1.10 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 345 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.025   0.002   PHE R 180 
 TYR   0.021   0.001   TYR E  60 
 ARG   0.003   0.000   ARG E  67 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: B    4 THR cc_start: 0.6878 (OUTLIER) cc_final: 0.6558 (m)
REVERT: B  266 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6145 (tt)
REVERT: C  125 ASN cc_start: 0.6585 (t0) cc_final: 0.5904 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 111
  average time/residue: 0.1927
  time to fit residues: 30.2888
Evaluate side-chains
  110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain E residue  193 MET
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   61 ASP
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  356 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 91 optimal weight:    0.2980
   chunk 29 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 59 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.150654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.127945 restraints weight = 13367.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 2.26
r_work: 0.3868 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8121  Z= 0.170
  Angle     :  0.599   9.671  11054  Z= 0.303
  Chirality :  0.041   0.144   1275
  Planarity :  0.004   0.045   1379
  Dihedral  :  4.377  18.235   1123
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.64 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.52 (0.27), residues: 1016
  helix:  2.32 (0.30), residues: 301
  sheet:  0.30 (0.32), residues: 272
  loop : -1.03 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 332 
 HIS   0.002   0.001   HIS C 142 
 PHE   0.030   0.002   PHE R 180 
 TYR   0.019   0.002   TYR E  60 
 ARG   0.003   0.000   ARG E  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5169.54 seconds
wall clock time: 91 minutes 55.50 seconds (5515.50 seconds total)