Starting phenix.real_space_refine
on Wed Sep 17 09:25:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jhj_61484/09_2025/9jhj_61484.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.032 sd=   0.598
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      41      5.16       5
     C    5021      2.51       5
     N    1335      2.21       5
     O    1364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7761
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2085
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 13, 'TRANS': 279}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 233
          Unresolved non-hydrogen angles: 289
          Unresolved non-hydrogen dihedrals: 190
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 4, 'GLU:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 90
    Chain: "A"
      Number of atoms: 1567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1567
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 198
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 14, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 100
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2343
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 245
          Unresolved non-hydrogen angles: 307
          Unresolved non-hydrogen dihedrals: 195
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 8, 'ASP:plan': 19, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 192
    Chain: "C"
      Number of atoms: 312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 312
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 3, 'TRANS': 46}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "E"
      Number of atoms: 1414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1414
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 74}
          Link IDs: {'PTRANS': 10, 'TRANS': 200}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 248
          Unresolved non-hydrogen angles: 310
          Unresolved non-hydrogen dihedrals: 202
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 4, 'PHE:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 138
    Chain: "R"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'18C': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.28
  Number of scatterers: 7761
  At special positions: 0
  Unit cell: (89.91, 120.69, 130.41, 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      41     16.00
     O    1364      8.00
     N    1335      7.00
     C    5021      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 428.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2058

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 12 sheets defined
      39.1% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'R' and resid 26 through 54
      removed outlier: 3.994A  pdb=" N   LEU R  30 " --> pdb=" O   ARG R  26 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY R  52 " --> pdb=" O   ILE R  48 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG R  54 " --> pdb=" O   VAL R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 88
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 146
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 4.334A  pdb=" N   TRP R 150 " --> pdb=" O   ILE R 146 " (cutoff:3.500A)
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 210
      removed outlier: 3.830A  pdb=" N   PHE R 210 " --> pdb=" O   PHE R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 268 through 273
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 4.456A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      removed outlier: 3.850A  pdb=" N   ASN R 294 " --> pdb=" O   LEU R 290 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   SER R 295 " --> pdb=" O   ALA R 291 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   CYS R 296 " --> pdb=" O   PHE R 292 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 8 through 32
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.712A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 256
    Processing helix  chain 'A' and resid 257 through 260
      removed outlier: 3.912A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 257 through 260'
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 3.808A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 25
      removed outlier: 3.621A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.802A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 56
      removed outlier: 4.170A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.541A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.921A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.024A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.797A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.816A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.514A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.720A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.532A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 18
      removed outlier: 3.550A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASP E  73 " --> pdb=" O   THR E  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 46 through 49
      removed outlier: 5.130A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
      removed outlier: 3.646A  pdb=" N   PHE E 212 " --> pdb=" O   CYS E 159 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER E 206 " --> pdb=" O   THR E 213 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 175 through 178
      removed outlier: 3.995A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1218
        1.31 -     1.44: 2213
        1.44 -     1.56: 4433
        1.56 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 7922
  Sorted by residual:
  bond pdb=" C4  18C R 401 "
       pdb=" C5  18C R 401 "
    ideal  model  delta    sigma   weight residual
    1.329  1.461 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" C19 18C R 401 "
       pdb=" N2  18C R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.455 -0.111 2.00e-02 2.50e+03 3.11e+01
  bond pdb=" CA  ILE R 280 "
       pdb=" C   ILE R 280 "
    ideal  model  delta    sigma   weight residual
    1.522  1.461  0.061 1.38e-02 5.25e+03 1.96e+01
  bond pdb=" CA  LEU R 272 "
       pdb=" C   LEU R 272 "
    ideal  model  delta    sigma   weight residual
    1.525  1.480  0.045 1.02e-02 9.61e+03 1.96e+01
  bond pdb=" CA  ILE R 282 "
       pdb=" C   ILE R 282 "
    ideal  model  delta    sigma   weight residual
    1.520  1.468  0.052 1.26e-02 6.30e+03 1.68e+01
  ... (remaining 7917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 10659
        2.58 -     5.15: 129
        5.15 -     7.73: 22
        7.73 -    10.31: 5
       10.31 -    12.88: 3
  Bond angle restraints: 10818
  Sorted by residual:
  angle pdb=" N   ILE R 282 "
        pdb=" CA  ILE R 282 "
        pdb=" C   ILE R 282 "
      ideal   model   delta    sigma   weight residual
     113.00  103.47    9.53 1.30e+00 5.92e-01 5.38e+01
  angle pdb=" N   MET R 271 "
        pdb=" CA  MET R 271 "
        pdb=" C   MET R 271 "
      ideal   model   delta    sigma   weight residual
     113.72  104.54    9.18 1.30e+00 5.92e-01 4.98e+01
  angle pdb=" N   PHE R 180 "
        pdb=" CA  PHE R 180 "
        pdb=" C   PHE R 180 "
      ideal   model   delta    sigma   weight residual
     111.30  120.35   -9.05 1.36e+00 5.41e-01 4.43e+01
  angle pdb=" N   ALA R 181 "
        pdb=" CA  ALA R 181 "
        pdb=" C   ALA R 181 "
      ideal   model   delta    sigma   weight residual
     113.21  106.39    6.82 1.15e+00 7.56e-01 3.51e+01
  angle pdb=" N   THR B 181 "
        pdb=" CA  THR B 181 "
        pdb=" C   THR B 181 "
      ideal   model   delta    sigma   weight residual
     113.61  120.86   -7.25 1.50e+00 4.44e-01 2.34e+01
  ... (remaining 10813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 4153
       16.34 -    32.69: 312
       32.69 -    49.03: 61
       49.03 -    65.38: 19
       65.38 -    81.72: 5
  Dihedral angle restraints: 4550
    sinusoidal: 1377
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" N   PHE R 180 "
           pdb=" C   PHE R 180 "
           pdb=" CA  PHE R 180 "
           pdb=" CB  PHE R 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.83  -12.03     0      2.50e+00 1.60e-01 2.31e+01
  dihedral pdb=" C   PHE R 180 "
           pdb=" N   PHE R 180 "
           pdb=" CA  PHE R 180 "
           pdb=" CB  PHE R 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.60   12.00     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" CA  ILE E  51 "
           pdb=" C   ILE E  51 "
           pdb=" N   SER E  52 "
           pdb=" CA  SER E  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.72   22.28     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 4547 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1238
       0.099 -    0.197: 62
       0.197 -    0.296: 6
       0.296 -    0.394: 1
       0.394 -    0.493: 2
  Chirality restraints: 1309
  Sorted by residual:
  chirality pdb=" CA  PHE R 180 "
            pdb=" N   PHE R 180 "
            pdb=" C   PHE R 180 "
            pdb=" CB  PHE R 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.07e+00
  chirality pdb=" C3  18C R 401 "
            pdb=" C2  18C R 401 "
            pdb=" C4  18C R 401 "
            pdb=" O3  18C R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.24   -2.72    0.48 2.00e-01 2.50e+01 5.85e+00
  chirality pdb=" CA  GLU A  14 "
            pdb=" N   GLU A  14 "
            pdb=" C   GLU A  14 "
            pdb=" CB  GLU A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  ... (remaining 1306 not shown)

  Planarity restraints: 1357
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  18C R 401 "   -0.030 2.00e-02 2.50e+03   2.97e-02 8.79e+00
        pdb=" C4  18C R 401 "    0.030 2.00e-02 2.50e+03
        pdb=" C5  18C R 401 "    0.029 2.00e-02 2.50e+03
        pdb=" C6  18C R 401 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 178 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.03e+00
        pdb=" C   PHE R 178 "    0.042 2.00e-02 2.50e+03
        pdb=" O   PHE R 178 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN R 179 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  13 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" C   VAL A  13 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   VAL A  13 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU A  14 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1354 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 934
        2.75 -     3.28: 7642
        3.28 -     3.82: 12349
        3.82 -     4.36: 13356
        4.36 -     4.90: 23429
  Nonbonded interactions: 57710
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E  67 "
            pdb=" O   SER E  85 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER E 204 "
            pdb=" OG1 THR E 215 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" N   GLY E  33 "
            pdb=" O   SER E  99 "
     model   vdw
     2.279 3.120
  ... (remaining 57705 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.030
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
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      :  0.005   0.132   7922  Z= 0.295
  Angle     :  0.771  12.883  10818  Z= 0.440
  Chirality :  0.053   0.493   1309
  Planarity :  0.004   0.052   1357
  Dihedral  : 13.231  81.723   2492
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.90 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.27), residues: 1069
  helix:  1.30 (0.27), residues: 391
  sheet: -0.71 (0.35), residues: 214
  loop : -1.75 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  48 
 TYR   0.019   0.002   TYR E 103 
 PHE   0.017   0.002   PHE R 309 
 TRP   0.016   0.002   TRP B 339 
 HIS   0.004   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 7922)
  covalent geometry    : angle       0.77124 (10818)
  hydrogen bonds       : bond        0.18130 (  389)
  hydrogen bonds       : angle       6.95067 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.9021 (mpp) cc_final: 0.8812 (mpp)
REVERT: E  192 MET cc_start: 0.8071 (pmm) cc_final: 0.7859 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1148
  time to fit residues: 15.6748
Evaluate side-chains
  95 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.039712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.035020 restraints weight = 45063.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2593 rms_B_bonded: 2.83
r_work: 0.2506 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7922  Z= 0.195
  Angle     :  0.626   6.685  10818  Z= 0.337
  Chirality :  0.045   0.173   1309
  Planarity :  0.004   0.044   1357
  Dihedral  :  7.643  87.692   1188
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.18 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.27), residues: 1069
  helix:  1.68 (0.26), residues: 395
  sheet: -0.52 (0.34), residues: 220
  loop : -1.61 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  24 
 TYR   0.016   0.002   TYR E 103 
 PHE   0.018   0.002   PHE E 212 
 TRP   0.018   0.002   TRP E  47 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7922)
  covalent geometry    : angle       0.62648 (10818)
  hydrogen bonds       : bond        0.04975 (  389)
  hydrogen bonds       : angle       4.90024 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  192 MET cc_start: 0.8078 (pmm) cc_final: 0.7834 (pmm)
  outliers start: 7
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1136
  time to fit residues: 14.7319
Evaluate side-chains
  96 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 24 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** R  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.041182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.036491 restraints weight = 43947.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.2647 rms_B_bonded: 2.85
r_work: 0.2561 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7922  Z= 0.123
  Angle     :  0.531   6.084  10818  Z= 0.286
  Chirality :  0.042   0.157   1309
  Planarity :  0.004   0.043   1357
  Dihedral  :  6.852  85.715   1188
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 14.07 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.27), residues: 1069
  helix:  1.88 (0.27), residues: 402
  sheet: -0.30 (0.34), residues: 220
  loop : -1.38 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 238 
 TYR   0.015   0.001   TYR E 103 
 PHE   0.013   0.001   PHE R 273 
 TRP   0.017   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7922)
  covalent geometry    : angle       0.53089 (10818)
  hydrogen bonds       : bond        0.04058 (  389)
  hydrogen bonds       : angle       4.45200 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 TYR cc_start: 0.8474 (m-80) cc_final: 0.7988 (m-80)
REVERT: E  212 PHE cc_start: 0.8728 (m-10) cc_final: 0.8478 (m-10)
  outliers start: 5
  outliers final: 2
  residues processed: 102
  average time/residue: 0.1166
  time to fit residues: 15.4230
Evaluate side-chains
  99 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    0.0010
   chunk 0 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0870
   chunk 76 optimal weight:    0.3980
   chunk 31 optimal weight:    0.4980
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.9966

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
A 255 ASN
B 266 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.041922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.037205 restraints weight = 44387.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 2.88
r_work: 0.2590 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7922  Z= 0.106
  Angle     :  0.498   5.541  10818  Z= 0.268
  Chirality :  0.041   0.151   1309
  Planarity :  0.004   0.041   1357
  Dihedral  :  6.421  83.408   1188
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 15.57 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.27), residues: 1069
  helix:  2.00 (0.27), residues: 404
  sheet: -0.26 (0.34), residues: 222
  loop : -1.31 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 312 
 TYR   0.014   0.001   TYR E 235 
 PHE   0.014   0.001   PHE R 309 
 TRP   0.014   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7922)
  covalent geometry    : angle       0.49849 (10818)
  hydrogen bonds       : bond        0.03661 (  389)
  hydrogen bonds       : angle       4.22279 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 TYR cc_start: 0.8441 (m-80) cc_final: 0.8028 (m-80)
REVERT: E  212 PHE cc_start: 0.8761 (m-10) cc_final: 0.8518 (m-10)
  outliers start: 7
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1053
  time to fit residues: 14.1375
Evaluate side-chains
  97 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.042332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.037617 restraints weight = 43963.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 2.88
r_work: 0.2603 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7922  Z= 0.103
  Angle     :  0.494   6.415  10818  Z= 0.265
  Chirality :  0.041   0.148   1309
  Planarity :  0.004   0.040   1357
  Dihedral  :  6.216  79.524   1188
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.32 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.27), residues: 1069
  helix:  2.05 (0.27), residues: 404
  sheet: -0.25 (0.34), residues: 223
  loop : -1.30 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  48 
 TYR   0.015   0.001   TYR E 235 
 PHE   0.016   0.001   PHE R 309 
 TRP   0.024   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7922)
  covalent geometry    : angle       0.49423 (10818)
  hydrogen bonds       : bond        0.03546 (  389)
  hydrogen bonds       : angle       4.11639 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 TYR cc_start: 0.8482 (m-80) cc_final: 0.8129 (m-80)
REVERT: E  212 PHE cc_start: 0.8755 (m-10) cc_final: 0.8511 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 103
  average time/residue: 0.1034
  time to fit residues: 13.8611
Evaluate side-chains
  95 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 75 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.039767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.035069 restraints weight = 44626.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2597 rms_B_bonded: 2.83
r_work: 0.2509 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7922  Z= 0.206
  Angle     :  0.594   5.973  10818  Z= 0.321
  Chirality :  0.044   0.152   1309
  Planarity :  0.004   0.042   1357
  Dihedral  :  6.677  77.054   1188
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.66 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.27), residues: 1069
  helix:  1.81 (0.27), residues: 401
  sheet: -0.17 (0.34), residues: 216
  loop : -1.41 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.015   0.002   TYR E 235 
 PHE   0.016   0.002   PHE R 309 
 TRP   0.018   0.002   TRP E  47 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7922)
  covalent geometry    : angle       0.59432 (10818)
  hydrogen bonds       : bond        0.04875 (  389)
  hydrogen bonds       : angle       4.48199 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  212 PHE cc_start: 0.8745 (m-10) cc_final: 0.8395 (m-10)
  outliers start: 10
  outliers final: 5
  residues processed: 102
  average time/residue: 0.1067
  time to fit residues: 14.4924
Evaluate side-chains
  93 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  108 ASN
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 108 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.041307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.036599 restraints weight = 44454.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2653 rms_B_bonded: 2.86
r_work: 0.2566 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7922  Z= 0.124
  Angle     :  0.527   5.585  10818  Z= 0.283
  Chirality :  0.042   0.145   1309
  Planarity :  0.004   0.041   1357
  Dihedral  :  6.379  72.634   1188
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 18.71 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.27), residues: 1069
  helix:  1.85 (0.27), residues: 404
  sheet: -0.18 (0.35), residues: 217
  loop : -1.37 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.015   0.001   TYR B  85 
 PHE   0.014   0.001   PHE R 309 
 TRP   0.022   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7922)
  covalent geometry    : angle       0.52668 (10818)
  hydrogen bonds       : bond        0.03940 (  389)
  hydrogen bonds       : angle       4.26654 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  219 ARG cc_start: 0.9022 (ptp-110) cc_final: 0.8788 (ptp90)
REVERT: E  212 PHE cc_start: 0.8752 (m-10) cc_final: 0.8524 (m-10)
  outliers start: 8
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1024
  time to fit residues: 13.4356
Evaluate side-chains
  100 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 95 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    4.1186

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.039017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.034371 restraints weight = 45014.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 2.85
r_work: 0.2478 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   7922  Z= 0.271
  Angle     :  0.658   5.741  10818  Z= 0.356
  Chirality :  0.046   0.158   1309
  Planarity :  0.004   0.042   1357
  Dihedral  :  6.916  70.864   1188
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.71 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.26), residues: 1069
  helix:  1.50 (0.26), residues: 401
  sheet: -0.24 (0.35), residues: 214
  loop : -1.49 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 312 
 TYR   0.016   0.002   TYR E 103 
 PHE   0.018   0.002   PHE B 235 
 TRP   0.019   0.002   TRP E  47 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 7922)
  covalent geometry    : angle       0.65797 (10818)
  hydrogen bonds       : bond        0.05425 (  389)
  hydrogen bonds       : angle       4.67809 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: E  192 MET cc_start: 0.8806 (ppp) cc_final: 0.7523 (ppp)
  outliers start: 11
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1019
  time to fit residues: 13.5687
Evaluate side-chains
  95 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    0.0010
   chunk 46 optimal weight:    0.0270
   chunk 102 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.0048

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.041443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.036780 restraints weight = 44118.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.2658 rms_B_bonded: 2.85
r_work: 0.2571 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7922  Z= 0.116
  Angle     :  0.531   5.567  10818  Z= 0.285
  Chirality :  0.042   0.143   1309
  Planarity :  0.004   0.042   1357
  Dihedral  :  6.318  65.373   1188
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 19.16 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.27), residues: 1069
  helix:  1.85 (0.27), residues: 405
  sheet: -0.26 (0.35), residues: 217
  loop : -1.37 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  21 
 TYR   0.017   0.001   TYR E 103 
 PHE   0.014   0.001   PHE R 309 
 TRP   0.016   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7922)
  covalent geometry    : angle       0.53130 (10818)
  hydrogen bonds       : bond        0.03820 (  389)
  hydrogen bonds       : angle       4.30950 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8732 (mp10)
REVERT: B  219 ARG cc_start: 0.8958 (ptp-110) cc_final: 0.8733 (ptp90)
  outliers start: 9
  outliers final: 8
  residues processed: 101
  average time/residue: 0.1078
  time to fit residues: 14.3732
Evaluate side-chains
  102 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  168 THR
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    0.0570
   chunk 59 optimal weight:    0.0870
   chunk 99 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.042525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.037842 restraints weight = 43621.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.2695 rms_B_bonded: 2.86
r_work: 0.2609 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7922  Z= 0.103
  Angle     :  0.519   6.730  10818  Z= 0.276
  Chirality :  0.041   0.152   1309
  Planarity :  0.004   0.042   1357
  Dihedral  :  6.053  60.642   1188
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 19.76 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.27), residues: 1069
  helix:  1.91 (0.27), residues: 405
  sheet: -0.14 (0.35), residues: 213
  loop : -1.31 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 238 
 TYR   0.017   0.001   TYR E 103 
 PHE   0.021   0.001   PHE E 212 
 TRP   0.017   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7922)
  covalent geometry    : angle       0.51864 (10818)
  hydrogen bonds       : bond        0.03521 (  389)
  hydrogen bonds       : angle       4.21657 ( 1107)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1131
  time to fit residues: 14.6687
Evaluate side-chains
  101 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 ASN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain E residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 39 optimal weight:    0.0370
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.0066

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.041086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.036413 restraints weight = 43946.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2644 rms_B_bonded: 2.83
r_work: 0.2558 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7922  Z= 0.155
  Angle     :  0.558   7.356  10818  Z= 0.299
  Chirality :  0.043   0.152   1309
  Planarity :  0.004   0.044   1357
  Dihedral  :  6.182  58.925   1188
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.61 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.27), residues: 1069
  helix:  1.85 (0.27), residues: 403
  sheet: -0.17 (0.35), residues: 217
  loop : -1.34 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 238 
 TYR   0.015   0.001   TYR E 103 
 PHE   0.011   0.001   PHE R 309 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7922)
  covalent geometry    : angle       0.55771 (10818)
  hydrogen bonds       : bond        0.04205 (  389)
  hydrogen bonds       : angle       4.30598 ( 1107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1766.28 seconds
wall clock time: 31 minutes 5.73 seconds (1865.73 seconds total)