Starting phenix.real_space_refine
on Fri Dec  8 16:13:56 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/12_2023/8w8b_37351_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.152
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5613      2.51       5
     N    1459      2.21       5
     O    1598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   28": "OE1" <-> "OE2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "A GLU  318": "OE1" <-> "OE2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B GLU  260": "OE1" <-> "OE2"
    Residue "E GLU    6": "OE1" <-> "OE2"
    Residue "E GLU   42": "OE1" <-> "OE2"
    Residue "E GLU   46": "OE1" <-> "OE2"
    Residue "E GLU  222": "OE1" <-> "OE2"
    Residue "E GLU  234": "OE1" <-> "OE2"
    Residue "G GLU   58": "OE1" <-> "OE2"
    Residue "R TYR  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8734
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1751
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2513
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1756
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 10, 'TRANS': 217}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 347
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 4, 'TRANS': 40}
    Chain: "R"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2197
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 170
          Unusual residues: {'CLR': 5, 'PLM': 1, 'UJL': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 5.16, per 1000 atoms: 0.59
  Number of scatterers: 8734
  At special positions: 0
  Unit cell: (86.52, 115.36, 128.544, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1598      8.00
     N    1459      7.00
     C    5613      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.53
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      36.7% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.585A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 46 through 54
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 4.021A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 351
      removed outlier: 3.692A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 4.457A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'E' and resid 53 through 55
      No H-bonds generated for 'chain 'E' and resid 53 through 55'
    Processing helix  chain 'E' and resid 88 through 90
      No H-bonds generated for 'chain 'E' and resid 88 through 90'
    Processing helix  chain 'E' and resid 221 through 223
      No H-bonds generated for 'chain 'E' and resid 221 through 223'
    Processing helix  chain 'G' and resid 19 through 24
      removed outlier: 4.465A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 36 through 63
    Processing helix  chain 'R' and resid 65 through 67
      No H-bonds generated for 'chain 'R' and resid 65 through 67'
    Processing helix  chain 'R' and resid 70 through 99
      removed outlier: 4.402A  pdb=" N   LEU R  90 " --> pdb=" O   SER R  86 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 105 through 139
    Processing helix  chain 'R' and resid 141 through 146
    Processing helix  chain 'R' and resid 150 through 173
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 193 through 203
    Processing helix  chain 'R' and resid 205 through 227
    Processing helix  chain 'R' and resid 326 through 371
      Proline residue:  R 360  - end of helix
      Proline residue:  R 369  - end of helix
    Processing helix  chain 'R' and resid 379 through 400
      removed outlier: 3.800A  pdb=" N   ASN R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   SER R 393 " --> pdb=" O   GLY R 389 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   LEU R 394 " --> pdb=" O   TYR R 390 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
    Processing helix  chain 'R' and resid 405 through 414
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.676A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   GLY A  40 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.960A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.782A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.662A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.604A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.659A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.381A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.600A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=  J, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.030A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=  L, first strand: chain 'E' and resid 146 through 148
      removed outlier: 7.000A  pdb=" N   LYS E 244 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 3.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2760
        1.34 -     1.46: 1943
        1.46 -     1.58: 4132
        1.58 -     1.69: 1
        1.69 -     1.81: 90
  Bond restraints: 8926
  Sorted by residual:
  bond pdb=" C3  UJL R 507 "
       pdb=" O1  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.460  1.421  0.039 2.00e-02 2.50e+03 3.84e+00
  bond pdb=" C6  UJL R 507 "
       pdb=" C9  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.428  1.390  0.038 2.00e-02 2.50e+03 3.60e+00
  bond pdb=" N   TYR R  35 "
       pdb=" CA  TYR R  35 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
  bond pdb=" N   GLN G  18 "
       pdb=" CA  GLN G  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   THR A   4 "
       pdb=" CA  THR A   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.96e+00
  ... (remaining 8921 not shown)

  Histogram of bond angle deviations from ideal:
       99.33 -   106.26: 196
      106.26 -   113.20: 4949
      113.20 -   120.13: 3075
      120.13 -   127.07: 3790
      127.07 -   134.00: 100
  Bond angle restraints: 12110
  Sorted by residual:
  angle pdb=" N   ARG A 242 "
        pdb=" CA  ARG A 242 "
        pdb=" C   ARG A 242 "
      ideal   model   delta    sigma   weight residual
     112.89  108.28    4.61 1.24e+00 6.50e-01 1.38e+01
  angle pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
        pdb=" CB  THR B 128 "
      ideal   model   delta    sigma   weight residual
     109.97  115.34   -5.37 1.47e+00 4.63e-01 1.33e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     113.21  109.45    3.76 1.15e+00 7.56e-01 1.07e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.69  114.17   -4.48 1.44e+00 4.82e-01 9.69e+00
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" CB  SER B 245 "
      ideal   model   delta    sigma   weight residual
     110.87  107.18    3.69 1.51e+00 4.39e-01 5.96e+00
  ... (remaining 12105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4986
       17.94 -    35.87: 408
       35.87 -    53.80: 105
       53.80 -    71.74: 23
       71.74 -    89.67: 7
  Dihedral angle restraints: 5529
    sinusoidal: 2356
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  LEU B 117 "
           pdb=" C   LEU B 117 "
           pdb=" N   ASP B 118 "
           pdb=" CA  ASP B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.30   17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CG  ARG G  62 "
           pdb=" CD  ARG G  62 "
           pdb=" NE  ARG G  62 "
           pdb=" CZ  ARG G  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.43   48.57     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 5526 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1070
       0.040 -    0.080: 221
       0.080 -    0.120: 80
       0.120 -    0.159: 13
       0.159 -    0.199: 2
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  THR B 128 "
            pdb=" N   THR B 128 "
            pdb=" C   THR B 128 "
            pdb=" CB  THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" C3  UJL R 507 "
            pdb=" C2  UJL R 507 "
            pdb=" C9  UJL R 507 "
            pdb=" O1  UJL R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.32   -0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CB  VAL R  98 "
            pdb=" CA  VAL R  98 "
            pdb=" CG1 VAL R  98 "
            pdb=" CG2 VAL R  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  62 "    0.172 9.50e-02 1.11e+02   7.74e-02 4.24e+00
        pdb=" NE  ARG G  62 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  62 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  62 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  62 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO E 236 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "    0.112 9.50e-02 1.11e+02   5.02e-02 1.84e+00
        pdb=" NE  ARG B 219 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 113
        2.63 -     3.20: 7811
        3.20 -     3.77: 13243
        3.77 -     4.33: 19418
        4.33 -     4.90: 32920
  Nonbonded interactions: 73505
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.063 2.440
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.182 2.440
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.200 2.440
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.207 2.440
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.232 2.440
  ... (remaining 73500 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:             0.000
  Extract box with map and model:          4.060
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     27.540
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
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      :  0.003   0.039   8926  Z= 0.202
  Angle     :  0.532   5.368  12110  Z= 0.306
  Chirality :  0.040   0.199   1386
  Planarity :  0.004   0.077   1492
  Dihedral  : 14.539  89.673   3483
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.72 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1076
  helix:  2.56 (0.27), residues: 375
  sheet:  0.50 (0.31), residues: 275
  loop : -0.32 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP E  47 
   HIS   0.003   0.001   HIS A 213 
   PHE   0.020   0.001   PHE B 292 
   TYR   0.010   0.001   TYR E 190 
   ARG   0.013   0.001   ARG G  62 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 1.044 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 112
  average time/residue: 1.3220
  time to fit residues: 157.6617
Evaluate side-chains
  99 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.974 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 2
  residues processed: 1
  average time/residue: 0.0803
  time to fit residues: 1.5020
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN
R  72 ASN
R 408 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8926  Z= 0.169
  Angle     :  0.504   8.187  12110  Z= 0.267
  Chirality :  0.041   0.139   1386
  Planarity :  0.003   0.047   1492
  Dihedral  :  5.425  57.917   1531
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.96 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1076
  helix:  2.78 (0.27), residues: 374
  sheet:  0.78 (0.31), residues: 270
  loop : -0.25 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.002   0.001   HIS B  91 
   PHE   0.012   0.001   PHE R 362 
   TYR   0.011   0.001   TYR E 190 
   ARG   0.006   0.000   ARG G  62 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.050 
Fit side-chains
  outliers start: 16
  outliers final: 3
  residues processed: 104
  average time/residue: 1.1363
  time to fit residues: 127.0793
Evaluate side-chains
  96 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 2
  residues processed: 1
  average time/residue: 0.1229
  time to fit residues: 1.5244
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8926  Z= 0.184
  Angle     :  0.488   6.519  12110  Z= 0.259
  Chirality :  0.041   0.139   1386
  Planarity :  0.003   0.042   1492
  Dihedral  :  5.287  57.249   1531
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.39 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1076
  helix:  2.82 (0.27), residues: 374
  sheet:  0.77 (0.30), residues: 270
  loop : -0.25 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP B  82 
   HIS   0.002   0.001   HIS A 213 
   PHE   0.010   0.001   PHE R 362 
   TYR   0.011   0.001   TYR E 190 
   ARG   0.005   0.000   ARG B 219 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.971 
Fit side-chains
  outliers start: 24
  outliers final: 10
  residues processed: 119
  average time/residue: 1.2336
  time to fit residues: 156.8194
Evaluate side-chains
  99 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 8
  residues processed: 2
  average time/residue: 0.6445
  time to fit residues: 2.6630
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 96 optimal weight:    0.8980
   chunk 102 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 85 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8926  Z= 0.284
  Angle     :  0.537   7.145  12110  Z= 0.283
  Chirality :  0.042   0.143   1386
  Planarity :  0.004   0.044   1492
  Dihedral  :  5.682  53.337   1531
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.25 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1076
  helix:  2.65 (0.27), residues: 373
  sheet:  0.66 (0.30), residues: 264
  loop : -0.43 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 213 
   PHE   0.013   0.002   PHE A 196 
   TYR   0.013   0.001   TYR R 198 
   ARG   0.007   0.000   ARG B 219 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.896 
Fit side-chains
  outliers start: 29
  outliers final: 13
  residues processed: 120
  average time/residue: 1.1119
  time to fit residues: 143.3119
Evaluate side-chains
  109 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.947 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 9
  residues processed: 4
  average time/residue: 0.3608
  time to fit residues: 3.0287
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:    0.4980
   chunk 87 optimal weight:    0.8980
   chunk 70 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN
R  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8926  Z= 0.151
  Angle     :  0.469   6.506  12110  Z= 0.249
  Chirality :  0.040   0.133   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  5.287  49.462   1531
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.86 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1076
  helix:  2.82 (0.27), residues: 374
  sheet:  0.68 (0.30), residues: 266
  loop : -0.32 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.001   0.001   HIS B 142 
   PHE   0.010   0.001   PHE R 362 
   TYR   0.010   0.001   TYR E 190 
   ARG   0.006   0.000   ARG B 134 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.991 
Fit side-chains
  outliers start: 18
  outliers final: 10
  residues processed: 116
  average time/residue: 1.2766
  time to fit residues: 157.9226
Evaluate side-chains
  102 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 9
  residues processed: 1
  average time/residue: 0.0796
  time to fit residues: 1.4638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8926  Z= 0.205
  Angle     :  0.497   7.012  12110  Z= 0.262
  Chirality :  0.041   0.139   1386
  Planarity :  0.003   0.040   1492
  Dihedral  :  5.383  48.713   1531
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.40 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1076
  helix:  2.73 (0.27), residues: 376
  sheet:  0.56 (0.30), residues: 268
  loop : -0.27 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP B  82 
   HIS   0.002   0.001   HIS B  91 
   PHE   0.011   0.001   PHE A 196 
   TYR   0.012   0.001   TYR E 190 
   ARG   0.004   0.000   ARG B 219 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.993 
Fit side-chains
  outliers start: 24
  outliers final: 14
  residues processed: 110
  average time/residue: 1.2926
  time to fit residues: 151.8638
Evaluate side-chains
  106 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.182 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 11
  residues processed: 3
  average time/residue: 0.2384
  time to fit residues: 2.6231
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    0.0050
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0370
   chunk 63 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5874

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8926  Z= 0.145
  Angle     :  0.464   6.477  12110  Z= 0.246
  Chirality :  0.040   0.133   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  5.111  49.218   1531
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.72 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1076
  helix:  2.81 (0.27), residues: 376
  sheet:  0.67 (0.31), residues: 257
  loop : -0.22 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.001   0.000   HIS E  35 
   PHE   0.010   0.001   PHE R 362 
   TYR   0.011   0.001   TYR E 190 
   ARG   0.004   0.000   ARG B 219 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 1.035 
Fit side-chains
  outliers start: 19
  outliers final: 13
  residues processed: 117
  average time/residue: 1.3061
  time to fit residues: 162.8584
Evaluate side-chains
  108 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.938 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 11
  residues processed: 2
  average time/residue: 0.8150
  time to fit residues: 3.0412
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 69 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 89 optimal weight:    0.2980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8926  Z= 0.244
  Angle     :  0.516   7.311  12110  Z= 0.271
  Chirality :  0.041   0.138   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.412  51.656   1531
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.15 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1076
  helix:  2.70 (0.27), residues: 376
  sheet:  0.47 (0.30), residues: 275
  loop : -0.21 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP E  47 
   HIS   0.002   0.001   HIS B 311 
   PHE   0.012   0.001   PHE A 196 
   TYR   0.016   0.001   TYR B  59 
   ARG   0.005   0.000   ARG G  62 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 13
  residues processed: 110
  average time/residue: 1.2487
  time to fit residues: 146.8372
Evaluate side-chains
  109 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.961 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 11
  residues processed: 2
  average time/residue: 0.1536
  time to fit residues: 1.7833
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0570
   chunk 57 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN
** R  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8926  Z= 0.162
  Angle     :  0.486   6.463  12110  Z= 0.256
  Chirality :  0.040   0.132   1386
  Planarity :  0.003   0.037   1492
  Dihedral  :  5.197  51.955   1531
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.90 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1076
  helix:  2.75 (0.27), residues: 376
  sheet:  0.62 (0.30), residues: 265
  loop : -0.16 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.002   0.001   HIS E  35 
   PHE   0.009   0.001   PHE R 362 
   TYR   0.012   0.001   TYR B  59 
   ARG   0.005   0.000   ARG G  62 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.968 
Fit side-chains
  outliers start: 15
  outliers final: 11
  residues processed: 108
  average time/residue: 1.3184
  time to fit residues: 151.6373
Evaluate side-chains
  104 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 10
  residues processed: 1
  average time/residue: 1.4457
  time to fit residues: 2.7826
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 105 optimal weight:    0.2980
   chunk 97 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8926  Z= 0.169
  Angle     :  0.497   6.796  12110  Z= 0.260
  Chirality :  0.040   0.131   1386
  Planarity :  0.003   0.037   1492
  Dihedral  :  5.184  53.811   1531
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 19.23 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1076
  helix:  2.74 (0.27), residues: 376
  sheet:  0.57 (0.30), residues: 266
  loop : -0.16 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.002   0.001   HIS B 311 
   PHE   0.009   0.001   PHE R 362 
   TYR   0.013   0.001   TYR B  59 
   ARG   0.006   0.000   ARG G  62 

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 1.031 
Fit side-chains
  outliers start: 12
  outliers final: 11
  residues processed: 107
  average time/residue: 1.2911
  time to fit residues: 147.8890
Evaluate side-chains
  106 residues out of total 932 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.926 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 10
  residues processed: 1
  average time/residue: 0.0899
  time to fit residues: 1.5836
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    0.0570
   chunk 77 optimal weight:    0.1980
   chunk 12 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0170
   chunk 84 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0010
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.1142

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.153626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.118028 restraints weight = 9717.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.75
r_work: 0.3096 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8926  Z= 0.111
  Angle     :  0.455   6.569  12110  Z= 0.240
  Chirality :  0.039   0.133   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  4.752  55.516   1531
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.55 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.26), residues: 1076
  helix:  2.88 (0.27), residues: 376
  sheet:  0.64 (0.31), residues: 267
  loop : -0.05 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP B  82 
   HIS   0.002   0.000   HIS E  35 
   PHE   0.008   0.001   PHE A 189 
   TYR   0.009   0.001   TYR E 190 
   ARG   0.004   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3291.19 seconds
wall clock time: 59 minutes 27.46 seconds (3567.46 seconds total)