Starting phenix.real_space_refine
on Wed Feb  4 13:19:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ruc_24702/02_2026/7ruc_24702.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      64      5.16       5
     C    6835      2.51       5
     N    1832      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10766
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2417
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 18, 'TRANS': 287}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2412
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 18, 'TRANS': 286}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2175
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
    Chain: "D"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 340
          Classifications: {'peptide': 43}
          Link IDs: {'PTRANS': 8, 'TRANS': 34}
    Chain: "F"
      Number of atoms: 2175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2175
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
    Chain: "G"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 790
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 12, 'TRANS': 87}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 392
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 47}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1952  SG  CYS A 283      54.155  67.467  98.552  1.00142.37           S
  ATOM   1975  SG  CYS A 286      55.590  69.741  96.078  1.00127.85           S
  ATOM   4364  SG  CYS B 283      53.181  71.227  98.454  1.00138.48           S
  ATOM   4387  SG  CYS B 286      51.745  68.778  96.011  1.00126.91           S

  Time building chain proxies: 2.01, per 1000 atoms: 0.19
  Number of scatterers: 10766
  At special positions: 0
  Unit cell: (108.9, 125.4, 113.025, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      64     16.00
     P       6     15.00
     Mg      2     11.99
     O    2026      8.00
     N    1832      7.00
     C    6835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 356.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 283 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 283 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A 286 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 286 "
      Number of angles added : 6


  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2554

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 2 sheets defined
      70.2% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 28
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.592A  pdb=" N   ALA A  57 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
    Processing helix  chain 'A' and resid 116 through 132
      removed outlier: 4.296A  pdb=" N   ALA A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 152
    Processing helix  chain 'A' and resid 163 through 187
      Proline residue:  A 174  - end of helix
    Processing helix  chain 'A' and resid 210 through 232
      removed outlier: 3.686A  pdb=" N   LEU A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      Proline residue:  A 221  - end of helix
    Processing helix  chain 'A' and resid 245 through 263
    Processing helix  chain 'A' and resid 283 through 304
    Processing helix  chain 'A' and resid 321 through 334
      removed outlier: 3.897A  pdb=" N   GLN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 332 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 333 " --> pdb=" O   SER A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 28
    Processing helix  chain 'B' and resid 43 through 57
      removed outlier: 3.517A  pdb=" N   ALA B  57 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 78
    Processing helix  chain 'B' and resid 116 through 131
      removed outlier: 4.975A  pdb=" N   GLY B 122 " --> pdb=" O   MET B 118 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 135 through 152
    Processing helix  chain 'B' and resid 163 through 190
      removed outlier: 3.531A  pdb=" N   THR B 167 " --> pdb=" O   PRO B 163 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
    Processing helix  chain 'B' and resid 211 through 232
      removed outlier: 4.251A  pdb=" N   LYS B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      Proline residue:  B 221  - end of helix
    Processing helix  chain 'B' and resid 245 through 263
    Processing helix  chain 'B' and resid 283 through 304
    Processing helix  chain 'B' and resid 321 through 334
      removed outlier: 4.003A  pdb=" N   GLN B 331 " --> pdb=" O   THR B 327 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU B 332 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU B 333 " --> pdb=" O   SER B 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 37
      removed outlier: 3.941A  pdb=" N   GLN C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 56
    Processing helix  chain 'C' and resid 58 through 76
    Processing helix  chain 'C' and resid 78 through 96
    Processing helix  chain 'C' and resid 101 through 115
    Processing helix  chain 'C' and resid 120 through 133
    Processing helix  chain 'C' and resid 142 through 156
    Processing helix  chain 'C' and resid 158 through 169
    Processing helix  chain 'C' and resid 171 through 186
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 191 through 206
      removed outlier: 4.126A  pdb=" N   VAL C 196 " --> pdb=" O   VAL C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 223
    Processing helix  chain 'C' and resid 234 through 250
    Processing helix  chain 'C' and resid 251 through 262
    Processing helix  chain 'C' and resid 262 through 267
    Processing helix  chain 'C' and resid 270 through 285
      removed outlier: 3.902A  pdb=" N   GLU C 274 " --> pdb=" O   PRO C 270 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY C 285 " --> pdb=" O   GLN C 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1009 through 1014
      removed outlier: 4.370A  pdb=" N   ALA D1013 " --> pdb=" O   PRO D1009 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL D1014 " --> pdb=" O   TRP D1010 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1009 through 1014'
    Processing helix  chain 'D' and resid 1015 through 1017
      No H-bonds generated for 'chain 'D' and resid 1015 through 1017'
    Processing helix  chain 'D' and resid 1018 through 1030
      removed outlier: 3.745A  pdb=" N   ILE D1022 " --> pdb=" O   TRP D1018 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN D1023 " --> pdb=" O   VAL D1019 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN D1024 " --> pdb=" O   PRO D1020 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1039 through 1044
    Processing helix  chain 'F' and resid 21 through 37
    Processing helix  chain 'F' and resid 38 through 57
    Processing helix  chain 'F' and resid 58 through 77
    Processing helix  chain 'F' and resid 78 through 97
    Processing helix  chain 'F' and resid 101 through 115
    Processing helix  chain 'F' and resid 119 through 133
      removed outlier: 4.081A  pdb=" N   VAL F 123 " --> pdb=" O   SER F 119 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 142 through 156
      removed outlier: 3.535A  pdb=" N   HIS F 146 " --> pdb=" O   HIS F 142 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 158 through 169
    Processing helix  chain 'F' and resid 172 through 187
    Processing helix  chain 'F' and resid 188 through 190
      No H-bonds generated for 'chain 'F' and resid 188 through 190'
    Processing helix  chain 'F' and resid 191 through 206
      removed outlier: 3.798A  pdb=" N   VAL F 196 " --> pdb=" O   VAL F 192 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU F 206 " --> pdb=" O   GLN F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 223
      removed outlier: 3.586A  pdb=" N   ALA F 212 " --> pdb=" O   ASN F 208 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 234 through 248
    Processing helix  chain 'F' and resid 251 through 262
    Processing helix  chain 'F' and resid 262 through 267
    Processing helix  chain 'F' and resid 269 through 284
      removed outlier: 4.289A  pdb=" N   ASN F 273 " --> pdb=" O   ASP F 269 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   GLU F 274 " --> pdb=" O   PRO F 270 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1017 through 1032
      removed outlier: 4.732A  pdb=" N   ILE G1021 " --> pdb=" O   GLU G1017 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG G1030 " --> pdb=" O   ILE G1026 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS G1031 " --> pdb=" O   GLN G1027 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1039 through 1044
    Processing helix  chain 'G' and resid 1062 through 1075
    Processing helix  chain 'G' and resid 1081 through 1089
      removed outlier: 3.841A  pdb=" N   LEU G1085 " --> pdb=" O   SER G1081 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 1092 through 1111
      removed outlier: 4.357A  pdb=" N   TYR G1098 " --> pdb=" O   VAL G1094 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ARG G1099 " --> pdb=" O   GLN G1095 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLN G1111 " --> pdb=" O   GLN G1107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 107
      removed outlier: 4.329A  pdb=" N   VAL H 102 " --> pdb=" O   LEU H  98 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ARG H 105 " --> pdb=" O   LYS H 101 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   HIS H 106 " --> pdb=" O   VAL H 102 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 130
    Processing helix  chain 'H' and resid 133 through 140
      removed outlier: 3.551A  pdb=" N   ARG H 137 " --> pdb=" O   ASP H 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.470A  pdb=" N   VAL A  62 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   MET A  97 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE A  64 " --> pdb=" O   MET A  97 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU A  63 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ASP A 160 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   ILE A  65 " --> pdb=" O   ASP A 160 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   TRP A  33 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ILE A 239 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   PHE A  35 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   VAL A 241 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   ILE A 243 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 10.241A  pdb=" N   ASN A 268 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   PHE A 238 " --> pdb=" O   ASN A 268 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   ILE A 270 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   CYS A 240 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   ASN A 272 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   CYS A 242 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LEU A 274 " --> pdb=" O   CYS A 242 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ILE A 269 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   LEU A 312 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87
      removed outlier: 6.555A  pdb=" N   VAL B  62 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   MET B  97 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE B  64 " --> pdb=" O   MET B  97 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   TRP B  33 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ILE B 239 " --> pdb=" O   TRP B  33 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   PHE B  35 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   VAL B 241 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   GLY B  37 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   ASN B 268 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   CYS B 240 " --> pdb=" O   ASN B 268 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ILE B 269 " --> pdb=" O   VAL B 310 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   LEU B 312 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B 271 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)

    651 hydrogen bonds defined for protein.
    1947 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.04 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: 3527
        1.34 -     1.46: 1966
        1.46 -     1.58: 5393
        1.58 -     1.69: 6
        1.69 -     1.81: 106
  Bond restraints: 10998
  Sorted by residual:
  bond pdb=" C   LEU A 314 "
       pdb=" N   LEU A 315 "
    ideal  model  delta    sigma   weight residual
    1.330  1.303  0.027 1.47e-02 4.63e+03 3.26e+00
  bond pdb=" CA  PRO B 163 "
       pdb=" C   PRO B 163 "
    ideal  model  delta    sigma   weight residual
    1.525  1.514  0.012 9.70e-03 1.06e+04 1.49e+00
  bond pdb=" O3B ATP B 402 "
       pdb=" PB  ATP B 402 "
    ideal  model  delta    sigma   weight residual
    1.592  1.562  0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" C1' ATP B 402 "
       pdb=" C2' ATP B 402 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 8.73e-01
  bond pdb=" C1' ATP A 401 "
       pdb=" C2' ATP A 401 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 8.51e-01
  ... (remaining 10993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 14537
        1.40 -     2.79: 248
        2.79 -     4.19: 83
        4.19 -     5.59: 6
        5.59 -     6.98: 8
  Bond angle restraints: 14882
  Sorted by residual:
  angle pdb=" N   ASP B 116 "
        pdb=" CA  ASP B 116 "
        pdb=" C   ASP B 116 "
      ideal   model   delta    sigma   weight residual
     112.97  110.05    2.92 1.06e+00 8.90e-01 7.61e+00
  angle pdb=" N   SER G1097 "
        pdb=" CA  SER G1097 "
        pdb=" C   SER G1097 "
      ideal   model   delta    sigma   weight residual
     111.75  108.44    3.31 1.28e+00 6.10e-01 6.68e+00
  angle pdb=" C2' ATP A 401 "
        pdb=" C3' ATP A 401 "
        pdb=" O3' ATP A 401 "
      ideal   model   delta    sigma   weight residual
     111.83  105.10    6.73 2.67e+00 1.40e-01 6.35e+00
  angle pdb=" C1' ATP A 401 "
        pdb=" C2' ATP A 401 "
        pdb=" O2' ATP A 401 "
      ideal   model   delta    sigma   weight residual
     110.58  103.60    6.98 2.79e+00 1.28e-01 6.25e+00
  angle pdb=" C2' ATP B 402 "
        pdb=" C3' ATP B 402 "
        pdb=" O3' ATP B 402 "
      ideal   model   delta    sigma   weight residual
     111.83  105.29    6.54 2.67e+00 1.40e-01 6.01e+00
  ... (remaining 14877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 6045
       17.61 -    35.21: 567
       35.21 -    52.82: 114
       52.82 -    70.43: 28
       70.43 -    88.04: 12
  Dihedral angle restraints: 6766
    sinusoidal: 2838
      harmonic: 3928
  Sorted by residual:
  dihedral pdb=" CA  LEU A 303 "
           pdb=" C   LEU A 303 "
           pdb=" N   TYR A 304 "
           pdb=" CA  TYR A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.63  -16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CB  GLU F 181 "
           pdb=" CG  GLU F 181 "
           pdb=" CD  GLU F 181 "
           pdb=" OE1 GLU F 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.04  -88.04     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CG  ARG B 263 "
           pdb=" CD  ARG B 263 "
           pdb=" NE  ARG B 263 "
           pdb=" CZ  ARG B 263 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.99   44.01     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 6763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1462
       0.060 -    0.120: 157
       0.120 -    0.180: 12
       0.180 -    0.240: 2
       0.240 -    0.300: 4
  Chirality restraints: 1637
  Sorted by residual:
  chirality pdb=" C2' ATP A 401 "
            pdb=" C1' ATP A 401 "
            pdb=" C3' ATP A 401 "
            pdb=" O2' ATP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" C2' ATP B 402 "
            pdb=" C1' ATP B 402 "
            pdb=" C3' ATP B 402 "
            pdb=" O2' ATP B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" C3' ATP A 401 "
            pdb=" C2' ATP A 401 "
            pdb=" C4' ATP A 401 "
            pdb=" O3' ATP A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.93    0.29 2.00e-01 2.50e+01 2.13e+00
  ... (remaining 1634 not shown)

  Planarity restraints: 1922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO F 230 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO F 231 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO F 231 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO F 231 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 122 "   -0.132 9.50e-02 1.11e+02   5.95e-02 2.76e+00
        pdb=" NE  ARG C 122 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 122 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 122 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 122 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 197 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   ALA C 197 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ALA C 197 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLN C 198 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1919 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.40: 48
        2.40 -     3.02: 7471
        3.02 -     3.65: 17099
        3.65 -     4.27: 24908
        4.27 -     4.90: 41551
  Nonbonded interactions: 91077
  Sorted by model distance:
  nonbonded pdb=" O2B ATP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.772 2.170
  nonbonded pdb=" O2G ATP A 401 "
            pdb="MG    MG A 402 "
     model   vdw
     1.780 2.170
  nonbonded pdb=" O2G ATP B 402 "
            pdb="MG    MG B 403 "
     model   vdw
     1.856 2.170
  nonbonded pdb=" O2B ATP B 402 "
            pdb="MG    MG B 403 "
     model   vdw
     1.858 2.170
  nonbonded pdb=" OG1 THR B  45 "
            pdb="MG    MG B 403 "
     model   vdw
     1.962 2.170
  ... (remaining 91072 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 16 through 190 or resid 210 through 339))
  selection = (chain 'B' and resid 16 through 339)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}

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 group one per residue
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:             3.770
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.060
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
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      :  0.009   0.837  11003  Z= 0.817
  Angle     :  0.541   8.052  14888  Z= 0.283
  Chirality :  0.040   0.300   1637
  Planarity :  0.004   0.060   1922
  Dihedral  : 14.647  88.037   4212
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.24), residues: 1324
  helix:  1.87 (0.18), residues: 861
  sheet:  0.70 (0.63), residues: 67
  loop :  0.08 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 122 
 TYR   0.024   0.001   TYR G1098 
 PHE   0.018   0.001   PHE B 173 
 TRP   0.014   0.001   TRP H  96 
 HIS   0.005   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10998)
  covalent geometry    : angle       0.53281 (14882)
  hydrogen bonds       : bond        0.13371 (  651)
  hydrogen bonds       : angle       6.01354 ( 1947)
  metal coordination   : bond        0.01379 (    4)
  metal coordination   : angle       4.71418 (    6)
  Misc. bond           : bond        0.83728 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8479 (tppt)
REVERT: A   91 TYR cc_start: 0.8539 (m-80) cc_final: 0.7911 (m-80)
REVERT: A  118 MET cc_start: 0.1844 (tpp) cc_final: 0.0711 (tmm)
REVERT: A  140 MET cc_start: 0.6098 (mtm) cc_final: 0.5891 (mtm)
REVERT: A  258 GLU cc_start: 0.7352 (tp30) cc_final: 0.7030 (tp30)
REVERT: A  323 ASP cc_start: 0.7994 (p0) cc_final: 0.7428 (t0)
REVERT: B  140 MET cc_start: 0.6634 (mmp) cc_final: 0.6324 (mmm)
REVERT: B  146 MET cc_start: 0.8080 (mtp) cc_final: 0.7871 (mtm)
REVERT: C   91 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: C  102 ASP cc_start: 0.7543 (t70) cc_final: 0.7095 (t0)
REVERT: C  156 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7596 (mt-10)
REVERT: C  158 ASN cc_start: 0.7802 (t0) cc_final: 0.6970 (t0)
REVERT: C  208 ASN cc_start: 0.8714 (t0) cc_final: 0.8273 (t0)
REVERT: C  209 LYS cc_start: 0.8882 (ptpt) cc_final: 0.8203 (ttpp)
REVERT: C  226 ILE cc_start: 0.7488 (mm) cc_final: 0.7169 (mt)
REVERT: C  228 ASP cc_start: 0.7013 (t0) cc_final: 0.6802 (t0)
REVERT: D 1043 LEU cc_start: 0.8196 (mm) cc_final: 0.7879 (mm)
REVERT: F  208 ASN cc_start: 0.8184 (t0) cc_final: 0.7886 (t0)
REVERT: G 1026 ILE cc_start: 0.7819 (mt) cc_final: 0.7008 (mt)
REVERT: G 1030 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7498 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0901
  time to fit residues: 25.1186
Evaluate side-chains
  141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  54 GLN
A  68 ASN
A 326 ASN
B  54 GLN
C 281 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.140459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102001 restraints weight = 20416.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102506 restraints weight = 11820.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103110 restraints weight = 8787.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.103536 restraints weight = 7905.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.103710 restraints weight = 7649.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11003  Z= 0.161
  Angle     :  0.595   6.567  14888  Z= 0.310
  Chirality :  0.042   0.150   1637
  Planarity :  0.005   0.051   1922
  Dihedral  :  8.437  88.170   1513
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  5.74 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.24), residues: 1324
  helix:  1.99 (0.18), residues: 882
  sheet:  0.63 (0.62), residues: 67
  loop :  0.15 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 122 
 TYR   0.015   0.002   TYR G1042 
 PHE   0.019   0.002   PHE C 255 
 TRP   0.012   0.001   TRP D1018 
 HIS   0.005   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10998)
  covalent geometry    : angle       0.59113 (14882)
  hydrogen bonds       : bond        0.04482 (  651)
  hydrogen bonds       : angle       4.49497 ( 1947)
  metal coordination   : bond        0.00741 (    4)
  metal coordination   : angle       3.54693 (    6)
  Misc. bond           : bond        0.00080 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2032 (tpp) cc_final: 0.0847 (tmm)
REVERT: B  264 ILE cc_start: 0.9459 (mm) cc_final: 0.9178 (mt)
REVERT: C  158 ASN cc_start: 0.8501 (t0) cc_final: 0.8116 (t0)
REVERT: C  208 ASN cc_start: 0.8958 (t0) cc_final: 0.8549 (t0)
REVERT: C  226 ILE cc_start: 0.8099 (mm) cc_final: 0.7722 (mt)
REVERT: C  255 PHE cc_start: 0.8321 (t80) cc_final: 0.8075 (t80)
REVERT: D 1027 GLN cc_start: 0.8245 (mm110) cc_final: 0.7679 (tm-30)
REVERT: D 1042 TYR cc_start: 0.7560 (t80) cc_final: 0.7291 (t80)
REVERT: D 1043 LEU cc_start: 0.8240 (mm) cc_final: 0.7820 (tt)
REVERT: F  271 MET cc_start: 0.8251 (mpp) cc_final: 0.8018 (mpp)
REVERT: G 1030 ARG cc_start: 0.7678 (mpp80) cc_final: 0.7398 (ptm160)
  outliers start: 13
  outliers final: 7
  residues processed: 166
  average time/residue: 0.0717
  time to fit residues: 18.0887
Evaluate side-chains
  137 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   60 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 11 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 326 ASN
** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 261 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 = 0.3959 r_free = 0.3959 target = 0.140835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101817 restraints weight = 20361.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.103870 restraints weight = 10430.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.104240 restraints weight = 7743.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.104531 restraints weight = 7253.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.104650 restraints weight = 7027.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11003  Z= 0.139
  Angle     :  0.541   6.816  14888  Z= 0.280
  Chirality :  0.040   0.191   1637
  Planarity :  0.005   0.055   1922
  Dihedral  :  7.944  88.985   1513
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.17 %
    Favored  : 91.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.24), residues: 1324
  helix:  1.98 (0.18), residues: 886
  sheet:  0.41 (0.60), residues: 72
  loop :  0.26 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 122 
 TYR   0.027   0.002   TYR C 275 
 PHE   0.014   0.001   PHE C 188 
 TRP   0.011   0.001   TRP D1018 
 HIS   0.004   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10998)
  covalent geometry    : angle       0.53589 (14882)
  hydrogen bonds       : bond        0.04063 (  651)
  hydrogen bonds       : angle       4.29497 ( 1947)
  metal coordination   : bond        0.00874 (    4)
  metal coordination   : angle       3.84343 (    6)
  Misc. bond           : bond        0.00176 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2078 (tpp) cc_final: 0.0825 (tmm)
REVERT: A  147 ARG cc_start: 0.7046 (ttm110) cc_final: 0.6806 (mtt-85)
REVERT: A  297 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9117 (mp)
REVERT: B  264 ILE cc_start: 0.9443 (mm) cc_final: 0.9206 (mt)
REVERT: C  158 ASN cc_start: 0.8476 (t0) cc_final: 0.8090 (t0)
REVERT: C  208 ASN cc_start: 0.8922 (t0) cc_final: 0.8587 (t0)
REVERT: C  226 ILE cc_start: 0.8097 (mm) cc_final: 0.7727 (mt)
REVERT: C  239 PHE cc_start: 0.8326 (t80) cc_final: 0.8121 (t80)
REVERT: C  255 PHE cc_start: 0.8440 (t80) cc_final: 0.8016 (t80)
REVERT: D 1043 LEU cc_start: 0.8274 (mm) cc_final: 0.7851 (tt)
REVERT: F  208 ASN cc_start: 0.8140 (t0) cc_final: 0.7907 (t0)
REVERT: F  269 ASP cc_start: 0.7776 (t0) cc_final: 0.6338 (t0)
REVERT: F  271 MET cc_start: 0.8195 (mpp) cc_final: 0.7766 (mpp)
REVERT: G 1030 ARG cc_start: 0.7753 (mpp80) cc_final: 0.7187 (ptp-170)
REVERT: G 1042 TYR cc_start: 0.7431 (t80) cc_final: 0.7065 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 164
  average time/residue: 0.0765
  time to fit residues: 19.2535
Evaluate side-chains
  154 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain F residue  233 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 99 optimal weight:    0.3980
   chunk 61 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 326 ASN
B 331 GLN
** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.140735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.101080 restraints weight = 20587.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103336 restraints weight = 11390.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103451 restraints weight = 7469.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103992 restraints weight = 8250.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.103937 restraints weight = 6758.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11003  Z= 0.145
  Angle     :  0.540   6.297  14888  Z= 0.280
  Chirality :  0.040   0.153   1637
  Planarity :  0.005   0.051   1922
  Dihedral  :  7.490  81.981   1513
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.44 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.23), residues: 1324
  helix:  1.95 (0.18), residues: 883
  sheet:  0.42 (0.59), residues: 72
  loop :  0.21 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 179 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.016   0.001   PHE C 188 
 TRP   0.030   0.002   TRP F 241 
 HIS   0.003   0.001   HIS C 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10998)
  covalent geometry    : angle       0.53536 (14882)
  hydrogen bonds       : bond        0.03926 (  651)
  hydrogen bonds       : angle       4.24165 ( 1947)
  metal coordination   : bond        0.00864 (    4)
  metal coordination   : angle       3.72304 (    6)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.1973 (tpp) cc_final: 0.0735 (tmm)
REVERT: B   23 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7878 (ttpt)
REVERT: B  264 ILE cc_start: 0.9440 (mm) cc_final: 0.9227 (mt)
REVERT: C  158 ASN cc_start: 0.8440 (t0) cc_final: 0.8042 (t0)
REVERT: C  208 ASN cc_start: 0.8902 (t0) cc_final: 0.8588 (t0)
REVERT: C  226 ILE cc_start: 0.8103 (mm) cc_final: 0.7729 (mt)
REVERT: C  239 PHE cc_start: 0.8377 (t80) cc_final: 0.8174 (t80)
REVERT: D 1043 LEU cc_start: 0.8245 (mm) cc_final: 0.7805 (tt)
REVERT: F  269 ASP cc_start: 0.7817 (t0) cc_final: 0.6799 (t0)
REVERT: F  271 MET cc_start: 0.8149 (mpp) cc_final: 0.7734 (mpp)
  outliers start: 22
  outliers final: 16
  residues processed: 170
  average time/residue: 0.0834
  time to fit residues: 21.2005
Evaluate side-chains
  160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  281 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 130 optimal weight:    9.9990
   chunk 7 optimal weight:    0.5980
   chunk 131 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 326 ASN
B  68 ASN
B 308 HIS
** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G1027 GLN
H 106 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.138827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.096338 restraints weight = 20283.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099397 restraints weight = 10559.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.101276 restraints weight = 7239.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102101 restraints weight = 5882.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.102821 restraints weight = 5327.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11003  Z= 0.195
  Angle     :  0.588  12.720  14888  Z= 0.301
  Chirality :  0.042   0.353   1637
  Planarity :  0.005   0.050   1922
  Dihedral  :  7.278  76.912   1513
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.30 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.23), residues: 1324
  helix:  1.82 (0.17), residues: 886
  sheet: -0.14 (0.54), residues: 83
  loop :  0.26 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 179 
 TYR   0.018   0.002   TYR G1042 
 PHE   0.015   0.002   PHE C 188 
 TRP   0.050   0.002   TRP F 241 
 HIS   0.005   0.001   HIS F 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10998)
  covalent geometry    : angle       0.58345 (14882)
  hydrogen bonds       : bond        0.04097 (  651)
  hydrogen bonds       : angle       4.30277 ( 1947)
  metal coordination   : bond        0.01129 (    4)
  metal coordination   : angle       3.68285 (    6)
  Misc. bond           : bond        0.00143 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2190 (tpp) cc_final: 0.0932 (tmm)
REVERT: A  127 GLN cc_start: 0.6088 (pt0) cc_final: 0.5687 (mm110)
REVERT: B  264 ILE cc_start: 0.9453 (mm) cc_final: 0.9246 (mt)
REVERT: C  158 ASN cc_start: 0.8472 (t0) cc_final: 0.8085 (t0)
REVERT: C  208 ASN cc_start: 0.8876 (t0) cc_final: 0.8591 (t0)
REVERT: C  226 ILE cc_start: 0.8145 (mm) cc_final: 0.7751 (mt)
REVERT: C  239 PHE cc_start: 0.8434 (t80) cc_final: 0.8225 (t80)
REVERT: D 1043 LEU cc_start: 0.8211 (mm) cc_final: 0.7833 (tt)
REVERT: F  269 ASP cc_start: 0.7885 (t0) cc_final: 0.6778 (t0)
REVERT: F  271 MET cc_start: 0.7967 (mpp) cc_final: 0.7579 (mpp)
  outliers start: 26
  outliers final: 20
  residues processed: 166
  average time/residue: 0.0737
  time to fit residues: 19.1980
Evaluate side-chains
  158 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  281 GLN
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain G residue 1089 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 120 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 326 ASN
** F 261 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 = 0.3941 r_free = 0.3941 target = 0.139362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.096886 restraints weight = 20368.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.099981 restraints weight = 10517.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.101807 restraints weight = 7270.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.102862 restraints weight = 5907.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103308 restraints weight = 5309.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11003  Z= 0.158
  Angle     :  0.566   8.843  14888  Z= 0.289
  Chirality :  0.041   0.189   1637
  Planarity :  0.005   0.054   1922
  Dihedral  :  7.015  69.360   1513
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.90 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.24), residues: 1324
  helix:  1.80 (0.17), residues: 887
  sheet: -0.17 (0.54), residues: 83
  loop :  0.29 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 179 
 TYR   0.013   0.002   TYR A 250 
 PHE   0.015   0.001   PHE C 188 
 TRP   0.056   0.002   TRP F 241 
 HIS   0.004   0.001   HIS F 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10998)
  covalent geometry    : angle       0.56147 (14882)
  hydrogen bonds       : bond        0.03912 (  651)
  hydrogen bonds       : angle       4.24446 ( 1947)
  metal coordination   : bond        0.00914 (    4)
  metal coordination   : angle       3.72374 (    6)
  Misc. bond           : bond        0.00123 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2023 (tpp) cc_final: 0.0789 (tmm)
REVERT: A  127 GLN cc_start: 0.6196 (pt0) cc_final: 0.5752 (mm110)
REVERT: B   71 HIS cc_start: 0.7645 (m-70) cc_final: 0.7330 (m-70)
REVERT: B  171 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8559 (mp)
REVERT: B  264 ILE cc_start: 0.9446 (mm) cc_final: 0.9230 (mt)
REVERT: C  158 ASN cc_start: 0.8458 (t0) cc_final: 0.8074 (t0)
REVERT: C  203 PHE cc_start: 0.8161 (m-80) cc_final: 0.7936 (m-80)
REVERT: C  226 ILE cc_start: 0.8199 (mm) cc_final: 0.7820 (mt)
REVERT: C  239 PHE cc_start: 0.8413 (t80) cc_final: 0.8213 (t80)
REVERT: D 1043 LEU cc_start: 0.8194 (mm) cc_final: 0.7613 (tt)
REVERT: F  194 MET cc_start: 0.7724 (ttp) cc_final: 0.7354 (ttp)
  outliers start: 26
  outliers final: 19
  residues processed: 165
  average time/residue: 0.0739
  time to fit residues: 18.9723
Evaluate side-chains
  163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  281 GLN
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain G residue 1019 VAL
Chi-restraints excluded: chain G residue 1089 LEU
Chi-restraints excluded: chain G residue 1100 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 238 ASN
** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G1027 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.137238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.094382 restraints weight = 20355.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.097385 restraints weight = 10318.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.099277 restraints weight = 7049.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.100369 restraints weight = 5717.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100606 restraints weight = 5117.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11003  Z= 0.242
  Angle     :  0.622  10.112  14888  Z= 0.322
  Chirality :  0.043   0.146   1637
  Planarity :  0.005   0.061   1922
  Dihedral  :  7.111  73.567   1513
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.41 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.23), residues: 1324
  helix:  1.62 (0.17), residues: 885
  sheet: -0.37 (0.55), residues: 80
  loop :  0.14 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 122 
 TYR   0.015   0.002   TYR A 250 
 PHE   0.024   0.002   PHE F 232 
 TRP   0.052   0.003   TRP F 241 
 HIS   0.006   0.002   HIS F 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (10998)
  covalent geometry    : angle       0.61815 (14882)
  hydrogen bonds       : bond        0.04315 (  651)
  hydrogen bonds       : angle       4.36363 ( 1947)
  metal coordination   : bond        0.01273 (    4)
  metal coordination   : angle       3.55703 (    6)
  Misc. bond           : bond        0.00205 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2069 (tpp) cc_final: 0.0853 (tmm)
REVERT: A  125 MET cc_start: 0.4514 (tpt) cc_final: 0.4211 (ptt)
REVERT: A  127 GLN cc_start: 0.6113 (pt0) cc_final: 0.5689 (mm-40)
REVERT: C  158 ASN cc_start: 0.8484 (t0) cc_final: 0.8121 (t0)
REVERT: C  203 PHE cc_start: 0.8244 (m-80) cc_final: 0.8003 (m-80)
REVERT: C  226 ILE cc_start: 0.8215 (mm) cc_final: 0.7835 (mt)
REVERT: C  239 PHE cc_start: 0.8460 (t80) cc_final: 0.8254 (t80)
REVERT: D 1043 LEU cc_start: 0.8242 (mm) cc_final: 0.7838 (tt)
  outliers start: 31
  outliers final: 26
  residues processed: 166
  average time/residue: 0.0689
  time to fit residues: 17.8458
Evaluate side-chains
  159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  226 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain G residue 1014 VAL
Chi-restraints excluded: chain G residue 1019 VAL
Chi-restraints excluded: chain G residue 1089 LEU
Chi-restraints excluded: chain G residue 1100 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0010
   chunk 82 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 104 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 10 optimal weight:    0.2980
   chunk 99 optimal weight:    0.0000
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 GLN
** F 261 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 = 0.3960 r_free = 0.3960 target = 0.140840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103961 restraints weight = 20242.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.102281 restraints weight = 14146.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103157 restraints weight = 10046.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.103824 restraints weight = 8968.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.103995 restraints weight = 7660.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11003  Z= 0.121
  Angle     :  0.569  12.801  14888  Z= 0.290
  Chirality :  0.041   0.169   1637
  Planarity :  0.005   0.064   1922
  Dihedral  :  6.588  63.290   1513
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.67 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.24), residues: 1324
  helix:  1.85 (0.18), residues: 886
  sheet: -0.17 (0.55), residues: 83
  loop :  0.18 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 179 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.022   0.001   PHE F 232 
 TRP   0.048   0.002   TRP F 241 
 HIS   0.003   0.001   HIS F 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10998)
  covalent geometry    : angle       0.56553 (14882)
  hydrogen bonds       : bond        0.03728 (  651)
  hydrogen bonds       : angle       4.17628 ( 1947)
  metal coordination   : bond        0.00401 (    4)
  metal coordination   : angle       3.30244 (    6)
  Misc. bond           : bond        0.00090 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.1699 (tpp) cc_final: 0.0531 (tmm)
REVERT: A  127 GLN cc_start: 0.6093 (pt0) cc_final: 0.5629 (mm-40)
REVERT: C  158 ASN cc_start: 0.8439 (t0) cc_final: 0.8075 (t0)
REVERT: C  203 PHE cc_start: 0.8122 (m-80) cc_final: 0.7910 (m-80)
REVERT: C  226 ILE cc_start: 0.8125 (mm) cc_final: 0.7764 (mt)
  outliers start: 24
  outliers final: 18
  residues processed: 163
  average time/residue: 0.0737
  time to fit residues: 18.7034
Evaluate side-chains
  155 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain G residue 1019 VAL
Chi-restraints excluded: chain G residue 1089 LEU
Chi-restraints excluded: chain G residue 1100 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
F 261 GLN
G1027 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.139324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102302 restraints weight = 20142.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.100366 restraints weight = 15474.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101004 restraints weight = 12429.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101859 restraints weight = 10048.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.102207 restraints weight = 8320.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11003  Z= 0.158
  Angle     :  0.594  13.189  14888  Z= 0.304
  Chirality :  0.041   0.223   1637
  Planarity :  0.005   0.085   1922
  Dihedral  :  6.660  63.583   1513
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.43 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.24), residues: 1324
  helix:  1.81 (0.18), residues: 883
  sheet: -0.33 (0.55), residues: 85
  loop :  0.12 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG G1030 
 TYR   0.013   0.001   TYR B 250 
 PHE   0.022   0.001   PHE F 232 
 TRP   0.062   0.002   TRP F 241 
 HIS   0.004   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (10998)
  covalent geometry    : angle       0.59010 (14882)
  hydrogen bonds       : bond        0.03840 (  651)
  hydrogen bonds       : angle       4.22307 ( 1947)
  metal coordination   : bond        0.00773 (    4)
  metal coordination   : angle       3.59356 (    6)
  Misc. bond           : bond        0.00123 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.1738 (tpp) cc_final: 0.0534 (tmm)
REVERT: A  125 MET cc_start: 0.4908 (tpt) cc_final: 0.4420 (ptt)
REVERT: A  127 GLN cc_start: 0.6098 (pt0) cc_final: 0.5716 (mm110)
REVERT: C  158 ASN cc_start: 0.8459 (t0) cc_final: 0.8088 (t0)
REVERT: C  203 PHE cc_start: 0.8140 (m-80) cc_final: 0.7929 (m-80)
REVERT: C  226 ILE cc_start: 0.8142 (mm) cc_final: 0.7795 (mt)
REVERT: F  273 ASN cc_start: 0.8455 (m-40) cc_final: 0.7615 (t0)
  outliers start: 22
  outliers final: 19
  residues processed: 156
  average time/residue: 0.0759
  time to fit residues: 18.3537
Evaluate side-chains
  153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  244 LEU
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain G residue 1019 VAL
Chi-restraints excluded: chain G residue 1089 LEU
Chi-restraints excluded: chain G residue 1100 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 121 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 130 optimal weight:    9.9990
   chunk 72 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.138847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.096364 restraints weight = 20160.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099454 restraints weight = 10579.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101264 restraints weight = 7263.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.102113 restraints weight = 5935.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.102854 restraints weight = 5377.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11003  Z= 0.176
  Angle     :  0.608  14.086  14888  Z= 0.311
  Chirality :  0.042   0.220   1637
  Planarity :  0.005   0.069   1922
  Dihedral  :  6.576  64.555   1513
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.43 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.24), residues: 1324
  helix:  1.75 (0.18), residues: 882
  sheet: -0.13 (0.58), residues: 78
  loop :  0.11 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 122 
 TYR   0.014   0.002   TYR A 250 
 PHE   0.021   0.002   PHE F 232 
 TRP   0.061   0.002   TRP F 241 
 HIS   0.004   0.001   HIS C 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10998)
  covalent geometry    : angle       0.60453 (14882)
  hydrogen bonds       : bond        0.04007 (  651)
  hydrogen bonds       : angle       4.25573 ( 1947)
  metal coordination   : bond        0.01002 (    4)
  metal coordination   : angle       3.21620 (    6)
  Misc. bond           : bond        0.00136 (    1)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.2031 (tpp) cc_final: 0.0813 (tmm)
REVERT: A  127 GLN cc_start: 0.6163 (pt0) cc_final: 0.5811 (mm-40)
REVERT: C  158 ASN cc_start: 0.8440 (t0) cc_final: 0.8073 (t0)
REVERT: C  226 ILE cc_start: 0.8184 (mm) cc_final: 0.7838 (mt)
REVERT: F  194 MET cc_start: 0.7875 (ttp) cc_final: 0.7136 (ttp)
REVERT: F  272 TYR cc_start: 0.8542 (m-10) cc_final: 0.8220 (m-10)
REVERT: F  273 ASN cc_start: 0.8325 (m-40) cc_final: 0.7563 (t0)
  outliers start: 22
  outliers final: 20
  residues processed: 152
  average time/residue: 0.0748
  time to fit residues: 17.5139
Evaluate side-chains
  156 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  153 ASN
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain D residue 1046 MET
Chi-restraints excluded: chain F residue  126 VAL
Chi-restraints excluded: chain F residue  282 LEU
Chi-restraints excluded: chain G residue 1019 VAL
Chi-restraints excluded: chain G residue 1089 LEU
Chi-restraints excluded: chain G residue 1100 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.2980
   chunk 123 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 130 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 326 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.139126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100449 restraints weight = 20358.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.100512 restraints weight = 11750.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101951 restraints weight = 8523.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102119 restraints weight = 6941.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.102335 restraints weight = 6708.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11003  Z= 0.166
  Angle     :  0.602  14.887  14888  Z= 0.309
  Chirality :  0.042   0.199   1637
  Planarity :  0.005   0.067   1922
  Dihedral  :  6.586  63.614   1513
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.60 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.23), residues: 1324
  helix:  1.74 (0.18), residues: 884
  sheet: -0.19 (0.58), residues: 78
  loop :  0.10 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G1030 
 TYR   0.013   0.001   TYR A 250 
 PHE   0.018   0.001   PHE F 232 
 TRP   0.056   0.002   TRP F 241 
 HIS   0.005   0.001   HIS C 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (10998)
  covalent geometry    : angle       0.59828 (14882)
  hydrogen bonds       : bond        0.03921 (  651)
  hydrogen bonds       : angle       4.23340 ( 1947)
  metal coordination   : bond        0.00949 (    4)
  metal coordination   : angle       3.16400 (    6)
  Misc. bond           : bond        0.00134 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1836.77 seconds
wall clock time: 32 minutes 32.20 seconds (1952.20 seconds total)