Starting phenix.real_space_refine
on Thu Mar 13 03:57:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zje_60142/03_2025/8zje_60142_neut.cif"
  }
  resolution = 3.07
  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=   0.007 sd=   0.069
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      56      5.16       5
     C    5571      2.51       5
     N    1504      2.21       5
     O    1612      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8743
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1810
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2570
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 27
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 407
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2142
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 15, 'TRANS': 263}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "S"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1726
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "C"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 87
          Unusual residues: {'ACY': 1, 'XZA': 1}
          Classifications: {'peptide': 8, 'undetermined': 2}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 6, None: 3}
            Not linked:
              pdbres="ACY C   1 "
              pdbres="DTY C   2 "
            Not linked:
              pdbres="PHE C   6 "
              pdbres="XZA C   7 "
            Not linked:
              pdbres="XZA C   7 "
              pdbres="LEU C   8 "
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Planarities with less than four sites: {'ACY:plan-1': 1, 'NMM:plan-2': 1, 'HYP:plan-1': 1, 'XZA:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.25, per 1000 atoms: 0.60
  Number of scatterers: 8743
  At special positions: 0
  Unit cell: (94.9, 115.34, 129.21, 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      56     16.00
     O    1612      8.00
     N    1504      7.00
     C    5571      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTY C   2 "
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      39.6% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 27
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.695A  pdb=" N   GLN A 267 " --> pdb=" O   PRO A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
      removed outlier: 3.549A  pdb=" N   LEU A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   MET A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 293
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 10 through 31
      removed outlier: 4.355A  pdb=" N   GLN B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.838A  pdb=" N   ILE G  24 " --> pdb=" O   MET G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 44
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'G' and resid 54 through 58
      removed outlier: 4.243A  pdb=" N   ASN G  58 " --> pdb=" O   ALA G  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 43 through 68
      removed outlier: 4.592A  pdb=" N   LEU R  47 " --> pdb=" O   TRP R  43 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA R  51 " --> pdb=" O   LEU R  47 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU R  52 " --> pdb=" O   PHE R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 95
    Processing helix  chain 'R' and resid 97 through 103
      removed outlier: 4.143A  pdb=" N   LEU R 101 " --> pdb=" O   PRO R  97 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU R 102 " --> pdb=" O   PHE R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 146
      removed outlier: 3.626A  pdb=" N   ASN R 119 " --> pdb=" O   CYS R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 174
    Processing helix  chain 'R' and resid 175 through 180
      removed outlier: 4.060A  pdb=" N   ALA R 179 " --> pdb=" O   ALA R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 213
    Processing helix  chain 'R' and resid 213 through 234
    Processing helix  chain 'R' and resid 242 through 253
    Processing helix  chain 'R' and resid 253 through 289
      removed outlier: 3.871A  pdb=" N   ARG R 258 " --> pdb=" O   ALA R 254 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG R 263 " --> pdb=" O   ALA R 259 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 298 through 324
      removed outlier: 3.523A  pdb=" N   SER R 316 " --> pdb=" O   SER R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 327 through 336
    Processing helix  chain 'S' and resid 27 through 31
    Processing helix  chain 'S' and resid 52 through 55
      removed outlier: 4.015A  pdb=" N   GLY S  55 " --> pdb=" O   SER S  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 52 through 55'
    Processing helix  chain 'S' and resid 86 through 90
      removed outlier: 3.603A  pdb=" N   THR S  90 " --> pdb=" O   SER S  87 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197
      removed outlier: 6.405A  pdb=" N   LEU A  34 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL A 206 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 9.820A  pdb=" N   SER A 227 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   MET A 229 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   LEU A 231 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE A 228 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   PHE A 274 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   PHE A 230 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASN A 276 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   VAL A 232 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57
      removed outlier: 3.626A  pdb=" N   LEU B 341 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   PHE B 340 " --> pdb=" O   SER B 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.537A  pdb=" N   SER B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.806A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 6.327A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.678A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   SER B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 239
      removed outlier: 3.656A  pdb=" N   MET B 267 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 6.309A  pdb=" N   GLY B 293 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   VAL B 281 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU B 291 " --> pdb=" O   VAL B 281 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   PHE B 283 " --> pdb=" O   LEU B 289 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU B 289 " --> pdb=" O   PHE B 283 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 181 through 183
    Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 5
    Processing sheet with id=AB2, first strand: chain 'S' and resid 9 through 11
      removed outlier: 6.018A  pdb=" N   ARG S  37 " --> pdb=" O   TRP S  46 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   TRP S  46 " --> pdb=" O   ARG S  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.771A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    450 hydrogen bonds defined for protein.
    1266 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: 2.37

  Time building geometry restraints manager: 2.96 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1409
        1.31 -     1.43: 2489
        1.43 -     1.56: 4943
        1.56 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 8924
  Sorted by residual:
  bond pdb=" CA  ARG A  29 "
       pdb=" C   ARG A  29 "
    ideal  model  delta    sigma   weight residual
    1.523  1.453  0.070 1.28e-02 6.10e+03 2.96e+01
  bond pdb=" CA  VAL A 201 "
       pdb=" CB  VAL A 201 "
    ideal  model  delta    sigma   weight residual
    1.548  1.479  0.068 1.46e-02 4.69e+03 2.19e+01
  bond pdb=" N   VAL A 201 "
       pdb=" CA  VAL A 201 "
    ideal  model  delta    sigma   weight residual
    1.458  1.413  0.045 1.17e-02 7.31e+03 1.47e+01
  bond pdb=" CA  GLU A  33 "
       pdb=" C   GLU A  33 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 1.17e-02 7.31e+03 1.44e+01
  bond pdb=" CA  GLU A  28 "
       pdb=" C   GLU A  28 "
    ideal  model  delta    sigma   weight residual
    1.522  1.474  0.047 1.25e-02 6.40e+03 1.43e+01
  ... (remaining 8919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11896
        2.38 -     4.76: 186
        4.76 -     7.13: 21
        7.13 -     9.51: 4
        9.51 -    11.89: 3
  Bond angle restraints: 12110
  Sorted by residual:
  angle pdb=" N   ARG A  29 "
        pdb=" CA  ARG A  29 "
        pdb=" C   ARG A  29 "
      ideal   model   delta    sigma   weight residual
     112.94  102.00   10.94 1.41e+00 5.03e-01 6.02e+01
  angle pdb=" N   GLU A  28 "
        pdb=" CA  GLU A  28 "
        pdb=" C   GLU A  28 "
      ideal   model   delta    sigma   weight residual
     114.09  102.20   11.89 1.55e+00 4.16e-01 5.89e+01
  angle pdb=" N   ARG A  31 "
        pdb=" CA  ARG A  31 "
        pdb=" C   ARG A  31 "
      ideal   model   delta    sigma   weight residual
     113.41  104.83    8.58 1.22e+00 6.72e-01 4.94e+01
  angle pdb=" N   HYP C   3 "
        pdb=" CA  HYP C   3 "
        pdb=" CB  HYP C   3 "
      ideal   model   delta    sigma   weight residual
     103.00  109.27   -6.27 1.10e+00 8.26e-01 3.25e+01
  angle pdb=" N   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" C   PHE A 222 "
      ideal   model   delta    sigma   weight residual
     111.55  105.34    6.21 1.37e+00 5.33e-01 2.06e+01
  ... (remaining 12105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4738
       17.96 -    35.92: 410
       35.92 -    53.87: 96
       53.87 -    71.83: 11
       71.83 -    89.79: 11
  Dihedral angle restraints: 5266
    sinusoidal: 1973
      harmonic: 3293
  Sorted by residual:
  dihedral pdb=" CA  THR B 254 "
           pdb=" C   THR B 254 "
           pdb=" N   CYS B 255 "
           pdb=" CA  CYS B 255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LYS B  83 "
           pdb=" C   LYS B  83 "
           pdb=" N   LEU B  84 "
           pdb=" CA  LEU B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.44   18.56     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  THR B 170 "
           pdb=" C   THR B 170 "
           pdb=" N   CYS B 171 "
           pdb=" CA  CYS B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 5263 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1331
       0.103 -    0.207: 50
       0.207 -    0.310: 2
       0.310 -    0.414: 2
       0.414 -    0.517: 1
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  HYP C   3 "
            pdb=" N   HYP C   3 "
            pdb=" C   HYP C   3 "
            pdb=" CB  HYP C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.20    0.52 2.00e-01 2.50e+01 6.69e+00
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.40 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" CA  THR A 226 "
            pdb=" N   THR A 226 "
            pdb=" C   THR A 226 "
            pdb=" CB  THR A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 1383 not shown)

  Planarity restraints: 1530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  NMM C   9 "   -0.066 2.00e-02 2.50e+03   1.51e-01 3.41e+02
        pdb=" NE  NMM C   9 "    0.223 2.00e-02 2.50e+03
        pdb=" CZ  NMM C   9 "   -0.025 2.00e-02 2.50e+03
        pdb=" NH1 NMM C   9 "   -0.088 2.00e-02 2.50e+03
        pdb=" NH2 NMM C   9 "   -0.212 2.00e-02 2.50e+03
        pdb=" CAA NMM C   9 "    0.169 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 197 "    0.027 2.00e-02 2.50e+03   5.60e-02 3.14e+01
        pdb=" C   ASP A 197 "   -0.097 2.00e-02 2.50e+03
        pdb=" O   ASP A 197 "    0.037 2.00e-02 2.50e+03
        pdb=" N   LEU A 198 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 319 "    0.060 5.00e-02 4.00e+02   8.99e-02 1.29e+01
        pdb=" N   PRO R 320 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO R 320 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO R 320 "    0.050 5.00e-02 4.00e+02
  ... (remaining 1527 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 912
        2.74 -     3.28: 8882
        3.28 -     3.82: 14382
        3.82 -     4.36: 17199
        4.36 -     4.90: 30801
  Nonbonded interactions: 72176
  Sorted by model distance:
  nonbonded pdb=" O   THR B  91 "
            pdb=" OG1 THR B  92 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG1 THR B 279 "
            pdb=" O   VAL B 320 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER B 286 "
            pdb=" OD2 ASP G  47 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ALA R 128 "
            pdb=" OG1 THR R 132 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR B  70 "
            pdb=" O   PRO B 112 "
     model   vdw
     2.257 3.040
  ... (remaining 72171 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.780
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
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   0.070   8924  Z= 0.328
  Angle     :  0.714  11.891  12110  Z= 0.417
  Chirality :  0.047   0.517   1386
  Planarity :  0.006   0.151   1530
  Dihedral  : 14.594  89.791   3138
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 14.46 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 1104
  helix:  2.42 (0.26), residues: 393
  sheet: -0.05 (0.32), residues: 288
  loop : -0.06 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  10 
 HIS   0.004   0.001   HIS R 309 
 PHE   0.022   0.001   PHE A 222 
 TYR   0.022   0.001   TYR S 190 
 ARG   0.006   0.000   ARG S 218 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 151
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7892 (pt0)
REVERT: A  310 PHE cc_start: 0.8285 (t80) cc_final: 0.8058 (t80)
REVERT: A  325 ILE cc_start: 0.8491 (tp) cc_final: 0.8271 (tt)
REVERT: A  358 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7731 (m-80)
REVERT: B   64 TYR cc_start: 0.9036 (m-80) cc_final: 0.8749 (m-80)
REVERT: B  231 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7634 (mp0)
REVERT: B  267 MET cc_start: 0.8377 (ttm) cc_final: 0.7934 (ttm)
REVERT: B  306 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8016 (mmtt)
REVERT: S    5 GLU cc_start: 0.8598 (mp0) cc_final: 0.7707 (mp0)
REVERT: S   67 PHE cc_start: 0.8173 (m-10) cc_final: 0.7833 (m-10)
REVERT: S   81 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7138 (tp40)
REVERT: S  223 ASP cc_start: 0.7616 (m-30) cc_final: 0.7307 (m-30)
REVERT: C   10 TRP cc_start: 0.7882 (OUTLIER) cc_final: 0.7582 (p90)
  outliers start: 3
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2668
  time to fit residues: 54.1625
Evaluate side-chains
  140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0670
   chunk 33 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    2.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS
B  18 GLN
B  22 GLN
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 122 GLN
R 208 ASN
R 295 HIS
S 183 GLN
S 186 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.166727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.112738 restraints weight = 10421.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 3.06
r_work: 0.3205 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8924  Z= 0.302
  Angle     :  0.590   8.110  12110  Z= 0.316
  Chirality :  0.044   0.180   1386
  Planarity :  0.004   0.058   1530
  Dihedral  :  5.617  59.350   1239
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.02 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1104
  helix:  2.31 (0.26), residues: 397
  sheet: -0.10 (0.32), residues: 276
  loop : -0.07 (0.33), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 174 
 HIS   0.005   0.001   HIS R 181 
 PHE   0.020   0.002   PHE A  49 
 TYR   0.028   0.002   TYR S 190 
 ARG   0.003   0.001   ARG S 218 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  259 THR cc_start: 0.8064 (m) cc_final: 0.7801 (p)
REVERT: A  289 HIS cc_start: 0.7753 (m-70) cc_final: 0.7543 (m-70)
REVERT: A  305 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6765 (tp-100)
REVERT: A  358 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7607 (m-80)
REVERT: B  231 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7383 (mp0)
REVERT: R  190 TYR cc_start: 0.6188 (m-80) cc_final: 0.5612 (m-80)
REVERT: R  325 PHE cc_start: 0.6981 (m-10) cc_final: 0.6621 (m-10)
REVERT: R  336 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.5206 (ttt180)
REVERT: S   42 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7376 (mptt)
REVERT: S   81 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7088 (tp40)
REVERT: S   92 MET cc_start: 0.8034 (ttm) cc_final: 0.7589 (tpp)
REVERT: C   10 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.7926 (p90)
  outliers start: 18
  outliers final: 5
  residues processed: 161
  average time/residue: 0.2242
  time to fit residues: 48.6421
Evaluate side-chains
  150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 122 GLN
S 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.170877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.116982 restraints weight = 10499.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.10
r_work: 0.3252 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8924  Z= 0.157
  Angle     :  0.500   6.254  12110  Z= 0.267
  Chirality :  0.040   0.155   1386
  Planarity :  0.004   0.050   1530
  Dihedral  :  5.094  56.622   1239
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.90 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.26), residues: 1104
  helix:  2.38 (0.25), residues: 397
  sheet: -0.07 (0.31), residues: 281
  loop :  0.00 (0.33), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 174 
 HIS   0.003   0.001   HIS R 309 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.014   0.001   TYR S 190 
 ARG   0.003   0.000   ARG B 202 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7142 (tt0) cc_final: 0.6562 (tm-30)
REVERT: A  259 THR cc_start: 0.8010 (m) cc_final: 0.7757 (p)
REVERT: A  289 HIS cc_start: 0.7714 (m-70) cc_final: 0.7489 (m-70)
REVERT: A  358 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7572 (m-80)
REVERT: B  194 SER cc_start: 0.8212 (m) cc_final: 0.7856 (p)
REVERT: B  231 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7415 (mp0)
REVERT: B  234 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7919 (mp)
REVERT: B  263 ASP cc_start: 0.7483 (t0) cc_final: 0.7207 (t0)
REVERT: R   53 MET cc_start: 0.6967 (tpt) cc_final: 0.6696 (tpt)
REVERT: R  325 PHE cc_start: 0.6974 (m-10) cc_final: 0.6476 (m-10)
REVERT: R  336 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.5082 (ttt180)
REVERT: S   19 LEU cc_start: 0.7778 (mt) cc_final: 0.7547 (mt)
REVERT: S   42 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7369 (mptt)
REVERT: S   81 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7035 (tp-100)
REVERT: S   92 MET cc_start: 0.7982 (ttm) cc_final: 0.7548 (tpp)
REVERT: S  230 MET cc_start: 0.9056 (ttp) cc_final: 0.8797 (ttp)
REVERT: C   10 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.7870 (p90)
  outliers start: 23
  outliers final: 7
  residues processed: 171
  average time/residue: 0.2314
  time to fit residues: 52.9675
Evaluate side-chains
  160 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0970
   chunk 104 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0050
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0970
   overall best weight:    1.4394

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.167023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113155 restraints weight = 10559.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 3.06
r_work: 0.3242 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8924  Z= 0.212
  Angle     :  0.515   6.212  12110  Z= 0.273
  Chirality :  0.041   0.149   1386
  Planarity :  0.004   0.058   1530
  Dihedral  :  5.068  56.433   1239
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.32 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.26), residues: 1104
  helix:  2.41 (0.25), residues: 397
  sheet: -0.14 (0.31), residues: 279
  loop :  0.00 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 309 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.019   0.001   TYR S 190 
 ARG   0.005   0.000   ARG B 202 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.7381 (tt0) cc_final: 0.6782 (tm-30)
REVERT: A  259 THR cc_start: 0.8237 (m) cc_final: 0.7998 (p)
REVERT: A  358 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7514 (m-80)
REVERT: B   24 ARG cc_start: 0.8284 (tmm-80) cc_final: 0.7997 (tmm-80)
REVERT: B  231 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7508 (mp0)
REVERT: B  234 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8129 (mp)
REVERT: B  263 ASP cc_start: 0.7589 (t0) cc_final: 0.7276 (t70)
REVERT: R  336 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.5038 (ttt180)
REVERT: S    2 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7851 (mm-40)
REVERT: S   42 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7449 (mptt)
REVERT: S   81 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7087 (tp-100)
REVERT: S   92 MET cc_start: 0.8146 (ttm) cc_final: 0.7620 (tpp)
REVERT: C   10 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.8167 (p90)
  outliers start: 22
  outliers final: 15
  residues processed: 163
  average time/residue: 0.2383
  time to fit residues: 52.7659
Evaluate side-chains
  159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 96 optimal weight:    7.9990
   chunk 41 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0170
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 82 optimal weight:    0.1980
   overall best weight:    0.5420

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.170001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116751 restraints weight = 10489.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.13
r_work: 0.3267 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8924  Z= 0.137
  Angle     :  0.493   8.767  12110  Z= 0.255
  Chirality :  0.040   0.148   1386
  Planarity :  0.004   0.052   1530
  Dihedral  :  4.847  55.855   1239
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.20 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.32 (0.26), residues: 1104
  helix:  2.55 (0.25), residues: 395
  sheet: -0.04 (0.31), residues: 278
  loop :  0.00 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 174 
 HIS   0.003   0.001   HIS R 309 
 PHE   0.015   0.001   PHE R  79 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.002   0.000   ARG R  74 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7223 (tt0) cc_final: 0.6615 (tm-30)
REVERT: A   29 ARG cc_start: 0.8246 (mtm110) cc_final: 0.8008 (mtm110)
REVERT: A  259 THR cc_start: 0.8045 (m) cc_final: 0.7782 (p)
REVERT: A  286 MET cc_start: 0.8176 (mmm) cc_final: 0.7631 (mtt)
REVERT: A  358 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7431 (m-80)
REVERT: B   24 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7901 (tmm-80)
REVERT: B  202 ARG cc_start: 0.7619 (tpp80) cc_final: 0.7392 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6719 (mm-40)
REVERT: B  231 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7483 (mp0)
REVERT: B  234 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7882 (mp)
REVERT: B  308 ASP cc_start: 0.7148 (m-30) cc_final: 0.6460 (p0)
REVERT: R  336 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.5073 (ttt180)
REVERT: S    2 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7808 (mm-40)
REVERT: S   19 LEU cc_start: 0.7454 (mt) cc_final: 0.7192 (mt)
REVERT: S   42 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7402 (mptt)
REVERT: S   81 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7064 (tp-100)
REVERT: S   92 MET cc_start: 0.7961 (ttm) cc_final: 0.7445 (tpp)
  outliers start: 22
  outliers final: 10
  residues processed: 163
  average time/residue: 0.2254
  time to fit residues: 49.8082
Evaluate side-chains
  156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue  139 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 65 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS
B 244 ASN
S 183 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.168377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.114963 restraints weight = 10475.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.13
r_work: 0.3249 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8924  Z= 0.191
  Angle     :  0.512   7.480  12110  Z= 0.268
  Chirality :  0.041   0.172   1386
  Planarity :  0.004   0.056   1530
  Dihedral  :  4.812  56.896   1237
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.20 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1104
  helix:  2.56 (0.25), residues: 395
  sheet: -0.17 (0.30), residues: 286
  loop : -0.00 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.002   0.001   HIS R 309 
 PHE   0.031   0.002   PHE S  67 
 TYR   0.017   0.001   TYR S 190 
 ARG   0.002   0.000   ARG B 202 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7173 (tt0) cc_final: 0.6567 (tm-30)
REVERT: A   29 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7993 (mtm110)
REVERT: A  231 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7890 (tp)
REVERT: A  239 GLN cc_start: 0.7821 (mm110) cc_final: 0.7533 (mm110)
REVERT: A  250 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6642 (ttm)
REVERT: A  259 THR cc_start: 0.8002 (m) cc_final: 0.7738 (p)
REVERT: A  358 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7239 (m-80)
REVERT: B   24 ARG cc_start: 0.8165 (tmm-80) cc_final: 0.7852 (tmm-80)
REVERT: B  202 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7347 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6834 (mm-40)
REVERT: B  231 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7463 (mp0)
REVERT: B  234 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7850 (mp)
REVERT: B  263 ASP cc_start: 0.7477 (t0) cc_final: 0.7102 (t0)
REVERT: B  267 MET cc_start: 0.8317 (tpp) cc_final: 0.7813 (mtp)
REVERT: B  308 ASP cc_start: 0.7099 (m-30) cc_final: 0.6421 (p0)
REVERT: R  336 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.5145 (ttt180)
REVERT: S   42 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7330 (mptt)
REVERT: S   81 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7037 (tp-100)
REVERT: C   10 TRP cc_start: 0.8529 (OUTLIER) cc_final: 0.8190 (p90)
  outliers start: 23
  outliers final: 15
  residues processed: 164
  average time/residue: 0.2367
  time to fit residues: 51.9652
Evaluate side-chains
  161 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue   90 THR
Chi-restraints excluded: chain S residue  108 ASP
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.169367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.116156 restraints weight = 10546.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 3.14
r_work: 0.3284 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8924  Z= 0.175
  Angle     :  0.518   9.345  12110  Z= 0.266
  Chirality :  0.041   0.162   1386
  Planarity :  0.004   0.053   1530
  Dihedral  :  4.727  56.586   1237
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.85 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1104
  helix:  2.60 (0.26), residues: 396
  sheet: -0.14 (0.30), residues: 285
  loop : -0.05 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  87 
 HIS   0.002   0.001   HIS S  34 
 PHE   0.021   0.001   PHE S  67 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.002   0.000   ARG B 202 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7268 (tt0) cc_final: 0.6665 (tm-30)
REVERT: A   29 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8035 (mtm110)
REVERT: A  231 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7924 (tp)
REVERT: A  250 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6808 (ttm)
REVERT: A  259 THR cc_start: 0.8097 (m) cc_final: 0.7820 (p)
REVERT: A  286 MET cc_start: 0.8104 (mmm) cc_final: 0.7560 (mtt)
REVERT: B   24 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7998 (ttp-170)
REVERT: B  202 ARG cc_start: 0.7594 (tpp80) cc_final: 0.7338 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6921 (mm-40)
REVERT: B  231 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7475 (mp0)
REVERT: B  234 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: B  263 ASP cc_start: 0.7517 (t0) cc_final: 0.7153 (t0)
REVERT: B  267 MET cc_start: 0.8274 (tpp) cc_final: 0.7696 (mtp)
REVERT: B  274 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6064 (pp)
REVERT: B  308 ASP cc_start: 0.7109 (m-30) cc_final: 0.6495 (p0)
REVERT: R  336 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.5162 (ttt180)
REVERT: S   37 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7316 (ptt90)
REVERT: S   81 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7040 (tp-100)
REVERT: C   10 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8266 (p90)
  outliers start: 22
  outliers final: 14
  residues processed: 159
  average time/residue: 0.2389
  time to fit residues: 50.7918
Evaluate side-chains
  157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue   90 THR
Chi-restraints excluded: chain S residue  108 ASP
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain C residue   10 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 109 optimal weight:   10.0000
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS
R 280 GLN
S 142 GLN
S 183 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.166992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.112571 restraints weight = 10630.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.10
r_work: 0.3198 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8924  Z= 0.306
  Angle     :  0.575   7.731  12110  Z= 0.299
  Chirality :  0.043   0.178   1386
  Planarity :  0.004   0.056   1530
  Dihedral  :  5.039  57.699   1237
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.85 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1104
  helix:  2.42 (0.26), residues: 398
  sheet: -0.18 (0.31), residues: 276
  loop : -0.15 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  46 
 HIS   0.003   0.001   HIS S  34 
 PHE   0.026   0.002   PHE S  67 
 TYR   0.025   0.002   TYR S 190 
 ARG   0.002   0.000   ARG B 202 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7239 (tt0) cc_final: 0.6643 (tm-30)
REVERT: A  239 GLN cc_start: 0.7979 (mm110) cc_final: 0.7707 (mm110)
REVERT: A  250 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6707 (ttm)
REVERT: A  358 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7221 (m-80)
REVERT: B   24 ARG cc_start: 0.8193 (tmm-80) cc_final: 0.7872 (tmm-80)
REVERT: B  202 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7299 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6631 (mm-40)
REVERT: B  231 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7414 (mp0)
REVERT: B  234 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8054 (mp)
REVERT: B  267 MET cc_start: 0.8281 (tpp) cc_final: 0.7728 (mtp)
REVERT: B  308 ASP cc_start: 0.7157 (m-30) cc_final: 0.6358 (p0)
REVERT: R  190 TYR cc_start: 0.6587 (m-80) cc_final: 0.6028 (m-80)
REVERT: R  336 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.5125 (ttt180)
REVERT: S   81 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7027 (tp-100)
  outliers start: 25
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2448
  time to fit residues: 52.5034
Evaluate side-chains
  158 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue   90 THR
Chi-restraints excluded: chain S residue  108 ASP
Chi-restraints excluded: chain S residue  139 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.167063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.113784 restraints weight = 10583.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.12
r_work: 0.3254 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8924  Z= 0.200
  Angle     :  0.534  10.847  12110  Z= 0.275
  Chirality :  0.041   0.200   1386
  Planarity :  0.004   0.052   1530
  Dihedral  :  4.838  56.988   1237
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.18 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.09 (0.26), residues: 1104
  helix:  2.42 (0.26), residues: 402
  sheet: -0.16 (0.31), residues: 276
  loop : -0.25 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  87 
 HIS   0.002   0.001   HIS S  34 
 PHE   0.020   0.001   PHE S  67 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.008   0.000   ARG A  29 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7216 (tt0) cc_final: 0.6655 (tm-30)
REVERT: A  239 GLN cc_start: 0.7960 (mm110) cc_final: 0.7696 (mm110)
REVERT: A  250 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6701 (ttm)
REVERT: A  259 THR cc_start: 0.8127 (m) cc_final: 0.7875 (p)
REVERT: A  286 MET cc_start: 0.8160 (mmm) cc_final: 0.7559 (mtt)
REVERT: A  357 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8155 (tt0)
REVERT: B   24 ARG cc_start: 0.8201 (tmm-80) cc_final: 0.7880 (tmm-80)
REVERT: B  202 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7319 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6691 (mm-40)
REVERT: B  231 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7436 (mp0)
REVERT: B  234 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: B  267 MET cc_start: 0.8273 (tpp) cc_final: 0.7742 (mtp)
REVERT: B  308 ASP cc_start: 0.7137 (m-30) cc_final: 0.6300 (p0)
REVERT: G   57 GLU cc_start: 0.6338 (mm-30) cc_final: 0.5626 (mp0)
REVERT: R  190 TYR cc_start: 0.6558 (m-80) cc_final: 0.5991 (m-80)
REVERT: R  336 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.5024 (ttt180)
REVERT: S   81 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7007 (tp-100)
REVERT: S  153 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7579 (mm-30)
  outliers start: 23
  outliers final: 17
  residues processed: 154
  average time/residue: 0.2252
  time to fit residues: 46.6793
Evaluate side-chains
  157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  234 VAL
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue   90 THR
Chi-restraints excluded: chain S residue  108 ASP
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  153 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0970
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 171 ASN
S 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.169790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116589 restraints weight = 10631.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.14
r_work: 0.3267 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8924  Z= 0.154
  Angle     :  0.515  10.831  12110  Z= 0.264
  Chirality :  0.040   0.180   1386
  Planarity :  0.004   0.054   1530
  Dihedral  :  4.645  57.371   1237
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.40 %
    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 (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:  1.23 (0.26), residues: 1104
  helix:  2.52 (0.26), residues: 401
  sheet: -0.12 (0.31), residues: 280
  loop : -0.12 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  87 
 HIS   0.002   0.000   HIS S  34 
 PHE   0.021   0.001   PHE S  67 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.006   0.000   ARG A  29 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   25 GLU cc_start: 0.7161 (tt0) cc_final: 0.6613 (tm-30)
REVERT: A  239 GLN cc_start: 0.7965 (mm110) cc_final: 0.7687 (mm110)
REVERT: A  250 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6599 (ttm)
REVERT: A  259 THR cc_start: 0.8015 (m) cc_final: 0.7768 (p)
REVERT: A  286 MET cc_start: 0.8191 (mmm) cc_final: 0.7579 (mtt)
REVERT: B   24 ARG cc_start: 0.8135 (tmm-80) cc_final: 0.7897 (ttp-170)
REVERT: B  202 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7252 (ttm-80)
REVERT: B  225 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6728 (mm-40)
REVERT: B  231 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7408 (mp0)
REVERT: B  234 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7813 (mp)
REVERT: B  267 MET cc_start: 0.8214 (tpp) cc_final: 0.7642 (mtp)
REVERT: B  274 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.5727 (tp)
REVERT: B  275 ILE cc_start: 0.8252 (pp) cc_final: 0.7832 (mm)
REVERT: R  190 TYR cc_start: 0.6480 (m-80) cc_final: 0.5956 (m-80)
REVERT: R  336 ARG cc_start: 0.5350 (OUTLIER) cc_final: 0.5013 (ttt180)
REVERT: S   81 GLN cc_start: 0.7897 (tp-100) cc_final: 0.6965 (tp-100)
REVERT: S  153 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7581 (mm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 164
  average time/residue: 0.2198
  time to fit residues: 49.2582
Evaluate side-chains
  159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  250 MET
Chi-restraints excluded: chain A residue  358 TYR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  225 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  137 SER
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  264 LEU
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain S residue   82 MET
Chi-restraints excluded: chain S residue   90 THR
Chi-restraints excluded: chain S residue  108 ASP
Chi-restraints excluded: chain S residue  139 VAL
Chi-restraints excluded: chain S residue  153 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    0.0060
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 51 optimal weight:    0.2980
   chunk 79 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
B  22 GLN
B 300 ASN
S 171 ASN
S 183 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.170873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118066 restraints weight = 10514.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 3.13
r_work: 0.3284 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8924  Z= 0.145
  Angle     :  0.527  17.409  12110  Z= 0.265
  Chirality :  0.040   0.215   1386
  Planarity :  0.004   0.054   1530
  Dihedral  :  4.578  58.018   1237
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.51 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1104
  helix:  2.54 (0.26), residues: 402
  sheet: -0.10 (0.31), residues: 280
  loop : -0.06 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  87 
 HIS   0.002   0.000   HIS S  34 
 PHE   0.018   0.001   PHE S  67 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.007   0.000   ARG A  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5107.52 seconds
wall clock time: 88 minutes 20.77 seconds (5300.77 seconds total)