Starting phenix.real_space_refine
on Fri Dec  8 13:32:54 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y15_33557/12_2023/7y15_33557_updated.pdb"
  }
  resolution = 2.9
  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=  -0.001 sd=   0.087
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      69      5.16       5
     C    5428      2.51       5
     N    1453      2.21       5
     O    1545      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   14": "OE1" <-> "OE2"
    Residue "A ASP  200": "OD1" <-> "OD2"
    Residue "B ASP  195": "OD1" <-> "OD2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B ASP  228": "OD1" <-> "OD2"
    Residue "C GLU   47": "OE1" <-> "OE2"
    Residue "R PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  109": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8495
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1654
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          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: "R"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2053
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 10, 'TRANS': 253}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 54
          Unusual residues: {'PLM': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.99, per 1000 atoms: 0.59
  Number of scatterers: 8495
  At special positions: 0
  Unit cell: (122.85, 84.375, 125.55, 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      69     16.00
     O    1545      8.00
     N    1453      7.00
     C    5428      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 164 " - pdb=" SG  CYS R 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  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: 3.26
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 12 sheets defined
      33.0% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 29
      removed outlier: 3.599A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 50
    Processing helix  chain 'A' and resid 208 through 211
      No H-bonds generated for 'chain 'A' and resid 208 through 211'
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 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 308
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 30 through 43
    Processing helix  chain 'C' and resid 56 through 58
      No H-bonds generated for 'chain 'C' and resid 56 through 58'
    Processing helix  chain 'R' and resid 23 through 52
    Processing helix  chain 'R' and resid 62 through 86
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 3.678A  pdb=" N   VAL R 127 " --> pdb=" O   ARG R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 141 through 164
      removed outlier: 4.497A  pdb=" N   PHE R 163 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 208
      Proline residue:  R 192  - end of helix
    Processing helix  chain 'R' and resid 217 through 233
    Processing helix  chain 'R' and resid 235 through 244
    Processing helix  chain 'R' and resid 254 through 276
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.344A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.616A  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: 3.535A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.739A  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: 6.978A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.712A  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: 6.715A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.036A  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: 6.954A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.130A  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: 6.713A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.110A  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: 6.567A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.806A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.546A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.659A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 143 through 148
      removed outlier: 3.664A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'S' and resid 213 through 219
      removed outlier: 3.602A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.488A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1131 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: 2.53

  Time building geometry restraints manager: 3.48 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: 2712
        1.34 -     1.46: 2133
        1.46 -     1.58: 3726
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 8671
  Sorted by residual:
  bond pdb=" C1  PLM R 403 "
       pdb=" C2  PLM R 403 "
    ideal  model  delta    sigma   weight residual
    1.542  1.508  0.034 2.00e-02 2.50e+03 2.82e+00
  bond pdb=" C1  PLM R 401 "
       pdb=" C2  PLM R 401 "
    ideal  model  delta    sigma   weight residual
    1.542  1.509  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" C1  PLM R 402 "
       pdb=" C2  PLM R 402 "
    ideal  model  delta    sigma   weight residual
    1.542  1.510  0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" CA  ASP B 205 "
       pdb=" C   ASP B 205 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.017 1.80e-02 3.09e+03 8.61e-01
  bond pdb=" CB  CYS S  96 "
       pdb=" SG  CYS S  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.782  0.026 3.30e-02 9.18e+02 6.15e-01
  ... (remaining 8666 not shown)

  Histogram of bond angle deviations from ideal:
       98.24 -   105.40: 120
      105.40 -   112.55: 4627
      112.55 -   119.71: 2703
      119.71 -   126.86: 4181
      126.86 -   134.02: 120
  Bond angle restraints: 11751
  Sorted by residual:
  angle pdb=" CA  LEU R  52 "
        pdb=" CB  LEU R  52 "
        pdb=" CG  LEU R  52 "
      ideal   model   delta    sigma   weight residual
     116.30  126.13   -9.83 3.50e+00 8.16e-02 7.89e+00
  angle pdb=" N   LEU B 308 "
        pdb=" CA  LEU B 308 "
        pdb=" C   LEU B 308 "
      ideal   model   delta    sigma   weight residual
     114.04  110.76    3.28 1.24e+00 6.50e-01 6.99e+00
  angle pdb=" CA  TRP R 144 "
        pdb=" CB  TRP R 144 "
        pdb=" CG  TRP R 144 "
      ideal   model   delta    sigma   weight residual
     113.60  118.31   -4.71 1.90e+00 2.77e-01 6.15e+00
  angle pdb=" O1  PLM R 401 "
        pdb=" C1  PLM R 401 "
        pdb=" O2  PLM R 401 "
      ideal   model   delta    sigma   weight residual
     126.37  118.94    7.43 3.00e+00 1.11e-01 6.13e+00
  angle pdb=" O1  PLM R 402 "
        pdb=" C1  PLM R 402 "
        pdb=" O2  PLM R 402 "
      ideal   model   delta    sigma   weight residual
     126.37  118.95    7.42 3.00e+00 1.11e-01 6.12e+00
  ... (remaining 11746 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4450
       17.69 -    35.38: 515
       35.38 -    53.07: 132
       53.07 -    70.76: 29
       70.76 -    88.45: 3
  Dihedral angle restraints: 5129
    sinusoidal: 1910
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS R 164 "
           pdb=" SG  CYS R 164 "
           pdb=" SG  CYS R 175 "
           pdb=" CB  CYS R 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -29.61  -56.39     1      1.00e+01 1.00e-02 4.29e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  LEU B  51 "
           pdb=" C   LEU B  51 "
           pdb=" N   ARG B  52 "
           pdb=" CA  ARG B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.38  -18.62     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5126 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 918
       0.032 -    0.064: 294
       0.064 -    0.096: 95
       0.096 -    0.128: 45
       0.128 -    0.160: 5
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  TRP R 144 "
            pdb=" N   TRP R 144 "
            pdb=" C   TRP R 144 "
            pdb=" CB  TRP R 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1467
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 235 "    0.033 5.00e-02 4.00e+02   5.04e-02 4.06e+00
        pdb=" N   PRO R 236 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 236 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 187 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   MET R 187 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET R 187 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY R 188 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 230 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   PHE R 230 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   PHE R 230 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU R 231 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1464 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1830
        2.78 -     3.31: 7744
        3.31 -     3.84: 14470
        3.84 -     4.37: 17093
        4.37 -     4.90: 29933
  Nonbonded interactions: 71070
  Sorted by model distance:
  nonbonded pdb=" O   THR R 191 "
            pdb=" OG1 THR R 195 "
     model   vdw
     2.248 2.440
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.282 2.440
  nonbonded pdb=" NE  ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.301 2.520
  nonbonded pdb=" OD1 ASP R  72 "
            pdb=" OG  SER R 269 "
     model   vdw
     2.303 2.440
  nonbonded pdb=" OH  TYR R 109 "
            pdb=" O   SER R 234 "
     model   vdw
     2.309 2.440
  ... (remaining 71065 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          7.310
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     27.080
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
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   0.034   8671  Z= 0.169
  Angle     :  0.563   9.830  11751  Z= 0.277
  Chirality :  0.039   0.160   1357
  Planarity :  0.003   0.050   1467
  Dihedral  : 16.240  88.452   3041
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.22 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.26 (0.26), residues: 1093
  helix:  2.64 (0.28), residues: 374
  sheet:  0.54 (0.32), residues: 255
  loop : -0.51 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP R 144 
   HIS   0.008   0.001   HIS B 183 
   PHE   0.015   0.001   PHE R 202 
   TYR   0.012   0.001   TYR S 178 
   ARG   0.004   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.971 
Fit side-chains
  outliers start: 24
  outliers final: 21
  residues processed: 130
  average time/residue: 1.1368
  time to fit residues: 158.2610
Evaluate side-chains
  126 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.952 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 20
  residues processed: 2
  average time/residue: 0.1043
  time to fit residues: 1.6716
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8671  Z= 0.172
  Angle     :  0.480   9.252  11751  Z= 0.247
  Chirality :  0.039   0.156   1357
  Planarity :  0.003   0.051   1467
  Dihedral  :  5.707  59.656   1236
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.88 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.33 (0.26), residues: 1093
  helix:  2.83 (0.27), residues: 374
  sheet:  0.48 (0.31), residues: 262
  loop : -0.53 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 144 
   HIS   0.005   0.001   HIS B 183 
   PHE   0.014   0.001   PHE R 202 
   TYR   0.012   0.001   TYR S 178 
   ARG   0.001   0.000   ARG S 168 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 108
  time to evaluate  : 0.984 
Fit side-chains
  outliers start: 43
  outliers final: 25
  residues processed: 138
  average time/residue: 1.1372
  time to fit residues: 168.3899
Evaluate side-chains
  131 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.885 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 21
  residues processed: 5
  average time/residue: 1.0638
  time to fit residues: 6.9018
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0370
   chunk 106 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.0433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8671  Z= 0.136
  Angle     :  0.450   7.085  11751  Z= 0.233
  Chirality :  0.038   0.156   1357
  Planarity :  0.003   0.050   1467
  Dihedral  :  5.326  58.682   1236
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.11 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.46 (0.26), residues: 1093
  helix:  2.94 (0.27), residues: 374
  sheet:  0.49 (0.31), residues: 270
  loop : -0.43 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP R 144 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.013   0.001   PHE R 202 
   TYR   0.010   0.001   TYR S 178 
   ARG   0.003   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 108
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
  outliers start: 35
  outliers final: 27
  residues processed: 133
  average time/residue: 1.1414
  time to fit residues: 162.7714
Evaluate side-chains
  130 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.964 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 23
  residues processed: 5
  average time/residue: 1.0254
  time to fit residues: 6.7353
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 98 optimal weight:    0.0470
   chunk 104 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.6084

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.0448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8671  Z= 0.258
  Angle     :  0.523   8.224  11751  Z= 0.269
  Chirality :  0.041   0.153   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.654  54.649   1236
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 20.00 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.37 (0.26), residues: 1093
  helix:  2.85 (0.28), residues: 374
  sheet:  0.44 (0.30), residues: 279
  loop : -0.49 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP R 144 
   HIS   0.004   0.001   HIS B 183 
   PHE   0.015   0.002   PHE R 202 
   TYR   0.015   0.001   TYR S 178 
   ARG   0.002   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 107
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
  outliers start: 41
  outliers final: 28
  residues processed: 139
  average time/residue: 1.0746
  time to fit residues: 160.4146
Evaluate side-chains
  133 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.911 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 26
  residues processed: 3
  average time/residue: 0.6651
  time to fit residues: 3.5176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 259 GLN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.0602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8671  Z= 0.277
  Angle     :  0.545   7.952  11751  Z= 0.281
  Chirality :  0.041   0.159   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.874  57.524   1236
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 21.46 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.26), residues: 1093
  helix:  2.77 (0.27), residues: 374
  sheet:  0.47 (0.31), residues: 270
  loop : -0.54 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP R 144 
   HIS   0.006   0.001   HIS B 183 
   PHE   0.014   0.002   PHE R 202 
   TYR   0.017   0.001   TYR S 178 
   ARG   0.003   0.000   ARG S 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 107
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
  outliers start: 44
  outliers final: 30
  residues processed: 139
  average time/residue: 1.1756
  time to fit residues: 174.5891
Evaluate side-chains
  132 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 30
  outliers final: 27
  residues processed: 4
  average time/residue: 0.5689
  time to fit residues: 3.9280
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0870
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0270
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.3620

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
B 237 ASN
S 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.0583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8671  Z= 0.226
  Angle     :  0.516   8.408  11751  Z= 0.266
  Chirality :  0.040   0.150   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.671  53.156   1236
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 22.70 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.33 (0.26), residues: 1093
  helix:  2.79 (0.27), residues: 375
  sheet:  0.48 (0.31), residues: 270
  loop : -0.53 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP R 144 
   HIS   0.006   0.001   HIS B 183 
   PHE   0.015   0.001   PHE R 202 
   TYR   0.014   0.001   TYR S 178 
   ARG   0.005   0.000   ARG R 206 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 109
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
  outliers start: 40
  outliers final: 29
  residues processed: 141
  average time/residue: 1.1154
  time to fit residues: 168.6156
Evaluate side-chains
  135 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.940 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 27
  residues processed: 3
  average time/residue: 0.6650
  time to fit residues: 3.4929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0970
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.0519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8671  Z= 0.151
  Angle     :  0.475   7.672  11751  Z= 0.247
  Chirality :  0.039   0.151   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.295  55.361   1236
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.15 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.40 (0.26), residues: 1093
  helix:  2.90 (0.27), residues: 376
  sheet:  0.47 (0.31), residues: 274
  loop : -0.51 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 144 
   HIS   0.005   0.001   HIS B 183 
   PHE   0.015   0.001   PHE R 202 
   TYR   0.011   0.001   TYR S 178 
   ARG   0.006   0.000   ARG R 206 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 107
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
  outliers start: 36
  outliers final: 28
  residues processed: 135
  average time/residue: 1.0426
  time to fit residues: 151.2775
Evaluate side-chains
  132 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.893 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 27
  residues processed: 2
  average time/residue: 0.8023
  time to fit residues: 2.9948
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.0653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8671  Z= 0.257
  Angle     :  0.545   9.329  11751  Z= 0.278
  Chirality :  0.041   0.173   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.612  56.381   1236
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.82 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.34 (0.26), residues: 1093
  helix:  2.79 (0.27), residues: 375
  sheet:  0.51 (0.31), residues: 270
  loop : -0.52 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP R 144 
   HIS   0.004   0.001   HIS B 183 
   PHE   0.016   0.001   PHE R 202 
   TYR   0.016   0.001   TYR S 178 
   ARG   0.004   0.000   ARG R 206 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 29
  residues processed: 136
  average time/residue: 1.2517
  time to fit residues: 181.5310
Evaluate side-chains
  135 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 1.003 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 27
  residues processed: 3
  average time/residue: 0.6647
  time to fit residues: 3.5700
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 97 optimal weight:    0.2980
   chunk 99 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0980
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
S 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8671  Z= 0.167
  Angle     :  0.502   9.200  11751  Z= 0.255
  Chirality :  0.039   0.152   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.293  59.625   1236
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.38 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: 1093
  helix:  2.87 (0.27), residues: 376
  sheet:  0.49 (0.31), residues: 274
  loop : -0.52 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 144 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.015   0.001   PHE R 202 
   TYR   0.012   0.001   TYR S 178 
   ARG   0.004   0.000   ARG S 206 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 26
  residues processed: 132
  average time/residue: 1.0989
  time to fit residues: 155.7224
Evaluate side-chains
  131 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.939 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 26
  residues processed: 1
  average time/residue: 0.1279
  time to fit residues: 1.5420
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 85 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
S 130 GLN
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.0646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8671  Z= 0.213
  Angle     :  0.510   8.567  11751  Z= 0.264
  Chirality :  0.040   0.147   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.420  58.895   1236
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.49 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.37 (0.26), residues: 1093
  helix:  2.85 (0.27), residues: 376
  sheet:  0.49 (0.30), residues: 277
  loop : -0.53 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP R 144 
   HIS   0.004   0.001   HIS A 188 
   PHE   0.017   0.001   PHE R 202 
   TYR   0.013   0.001   TYR S 178 
   ARG   0.004   0.000   ARG S 206 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 26
  residues processed: 132
  average time/residue: 1.1943
  time to fit residues: 168.4243
Evaluate side-chains
  132 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.952 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 26
  residues processed: 1
  average time/residue: 0.1243
  time to fit residues: 1.5136
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 10 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
S 130 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.175001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135598 restraints weight = 9247.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.89
r_work: 0.3291 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.0622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8671  Z= 0.155
  Angle     :  0.502  10.811  11751  Z= 0.254
  Chirality :  0.039   0.152   1357
  Planarity :  0.003   0.049   1467
  Dihedral  :  5.174  56.173   1236
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.49 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.41 (0.26), residues: 1093
  helix:  2.88 (0.27), residues: 376
  sheet:  0.55 (0.31), residues: 272
  loop : -0.53 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 144 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.017   0.001   PHE R 202 
   TYR   0.011   0.001   TYR S 178 
   ARG   0.004   0.000   ARG S 206 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3355.26 seconds
wall clock time: 60 minutes 26.87 seconds (3626.87 seconds total)