Starting phenix.real_space_refine
on Wed Feb  4 01:36:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kxs_62626/02_2026/9kxs_62626.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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      51      5.16       5
     C    5221      2.51       5
     N    1384      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8152
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2114
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 13, 'TRANS': 262}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1458
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 4, 'TRANS': 201}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 220
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 95
    Chain: "C"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2436
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 205
          Unresolved non-hydrogen dihedrals: 125
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASP:plan': 8, 'ASN:plan1': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 105
    Chain: "G"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 395
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "H"
      Number of atoms: 1674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1674
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 126
          Unresolved non-hydrogen angles: 150
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "D"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 58
          Classifications: {'peptide': 7}
          Link IDs: {'NMTRANS': 1, 'PTRANS': 1, 'TRANS': 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 1}
  Time building chain proxies: 2.10, per 1000 atoms: 0.26
  Number of scatterers: 8152
  At special positions: 0
  Unit cell: (89.4956, 129.406, 131.825, 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      51     16.00
     O    1496      8.00
     N    1384      7.00
     C    5221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 335.2 milliseconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL D   9 "
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      36.8% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 66
      removed outlier: 4.013A  pdb=" N   VAL A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A  39 " --> pdb=" O   PRO A  35 " (cutoff:3.500A)
      Proline residue:  A  53  - end of helix
    Processing helix  chain 'A' and resid 67 through 68
      No H-bonds generated for 'chain 'A' and resid 67 through 68'
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 72 through 88
      removed outlier: 3.904A  pdb=" N   ALA A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 98
      removed outlier: 3.767A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 110
      removed outlier: 3.617A  pdb=" N   ILE A 110 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 107 through 110'
    Processing helix  chain 'A' and resid 111 through 140
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.619A  pdb=" N   ALA A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      Proline residue:  A 170  - end of helix
      removed outlier: 3.635A  pdb=" N   ARG A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 231
      removed outlier: 5.594A  pdb=" N   LEU A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
    Processing helix  chain 'A' and resid 239 through 266
      removed outlier: 3.732A  pdb=" N   LYS A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      Proline residue:  A 258  - end of helix
      removed outlier: 3.790A  pdb=" N   VAL A 264 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE A 266 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 4.127A  pdb=" N   LYS A 277 " --> pdb=" O   SER A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 291
    Processing helix  chain 'A' and resid 291 through 304
      removed outlier: 4.151A  pdb=" N   CYS A 295 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      Proline residue:  A 298  - end of helix
    Processing helix  chain 'A' and resid 308 through 315
    Processing helix  chain 'B' and resid 8 through 30
      removed outlier: 3.959A  pdb=" N   ALA B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 53
    Processing helix  chain 'B' and resid 208 through 213
      removed outlier: 3.814A  pdb=" N   TRP B 212 " --> pdb=" O   GLU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 217
    Processing helix  chain 'B' and resid 246 through 256
      removed outlier: 3.708A  pdb=" N   ASN B 256 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 282
    Processing helix  chain 'B' and resid 297 through 310
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.642A  pdb=" N   VAL B 334 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 26
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'G' and resid 8 through 25
      removed outlier: 3.640A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.559A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.643A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.727A  pdb=" N   ASP H 223 " --> pdb=" O   GLU H 220 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 220 through 224'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191
      removed outlier: 3.568A  pdb=" N   VAL B  34 " --> pdb=" O   HIS B 196 " (cutoff:3.500A)
      removed outlier: 10.250A  pdb=" N   ALA B 221 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ILE B 223 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   CYS B 225 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   ILE B 222 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   PHE B 268 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   PHE B 224 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASN B 270 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   VAL B 226 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 51
      removed outlier: 3.702A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ALA C 328 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LEU C 318 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   GLY C 330 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61
      removed outlier: 3.992A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105
      removed outlier: 3.650A  pdb=" N   GLY C 115 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL C 112 " --> pdb=" O   TYR C 124 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.599A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 198 through 202
      removed outlier: 3.972A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.496A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   PHE C 241 " --> pdb=" O   PHE C 253 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278
      removed outlier: 6.966A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.975A  pdb=" N   LEU H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.715A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS H  35 " --> pdb=" O   VAL H  97 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TYR H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.917A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR H 175 " --> pdb=" O   MET H 230 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 154 through 160
      removed outlier: 3.843A  pdb=" N   PHE H 212 " --> pdb=" O   CYS H 159 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2632
        1.35 -     1.46: 2091
        1.46 -     1.58: 3532
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8325
  Sorted by residual:
  bond pdb=" CA  MLE D   8 "
       pdb=" C   MLE D   8 "
    ideal  model  delta    sigma   weight residual
    1.525  1.569 -0.044 2.10e-02 2.27e+03 4.41e+00
  bond pdb=" C   MLE D   8 "
       pdb=" O   MLE D   8 "
    ideal  model  delta    sigma   weight residual
    1.231  1.261 -0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" CG  LEU A  49 "
       pdb=" CD2 LEU A  49 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.19e-01
  bond pdb=" N   ASN B 194 "
       pdb=" CA  ASN B 194 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 7.27e-01
  bond pdb=" CA  CYS H  22 "
       pdb=" CB  CYS H  22 "
    ideal  model  delta    sigma   weight residual
    1.531  1.557 -0.026 3.28e-02 9.30e+02 6.47e-01
  ... (remaining 8320 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11244
        1.92 -     3.85: 102
        3.85 -     5.77: 15
        5.77 -     7.69: 2
        7.69 -     9.62: 1
  Bond angle restraints: 11364
  Sorted by residual:
  angle pdb=" N   MLE D   8 "
        pdb=" CA  MLE D   8 "
        pdb=" CB  MLE D   8 "
      ideal   model   delta    sigma   weight residual
     110.50  116.55   -6.05 1.70e+00 3.46e-01 1.27e+01
  angle pdb=" N   GLY H 114 "
        pdb=" CA  GLY H 114 "
        pdb=" C   GLY H 114 "
      ideal   model   delta    sigma   weight residual
     111.72  115.91   -4.19 1.31e+00 5.83e-01 1.02e+01
  angle pdb=" CA  LEU A  49 "
        pdb=" CB  LEU A  49 "
        pdb=" CG  LEU A  49 "
      ideal   model   delta    sigma   weight residual
     116.30  125.92   -9.62 3.50e+00 8.16e-02 7.55e+00
  angle pdb=" C   PHE A  48 "
        pdb=" N   LEU A  49 "
        pdb=" CA  LEU A  49 "
      ideal   model   delta    sigma   weight residual
     121.58  116.50    5.08 1.95e+00 2.63e-01 6.79e+00
  angle pdb=" N   ILE A 169 "
        pdb=" CA  ILE A 169 "
        pdb=" C   ILE A 169 "
      ideal   model   delta    sigma   weight residual
     108.88  114.22   -5.34 2.16e+00 2.14e-01 6.10e+00
  ... (remaining 11359 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 4385
       16.06 -    32.11: 353
       32.11 -    48.17: 84
       48.17 -    64.23: 11
       64.23 -    80.28: 6
  Dihedral angle restraints: 4839
    sinusoidal: 1612
      harmonic: 3227
  Sorted by residual:
  dihedral pdb=" N   MLE D   8 "
           pdb=" C   MLE D   8 "
           pdb=" CA  MLE D   8 "
           pdb=" CB  MLE D   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.97  -12.17     0      2.50e+00 1.60e-01 2.37e+01
  dihedral pdb=" CA  TYR H 101 "
           pdb=" C   TYR H 101 "
           pdb=" N   TYR H 102 "
           pdb=" CA  TYR H 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.85   20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" C   MLE D   8 "
           pdb=" N   MLE D   8 "
           pdb=" CA  MLE D   8 "
           pdb=" CB  MLE D   8 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.56    9.96     0      2.50e+00 1.60e-01 1.59e+01
  ... (remaining 4836 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1252
       0.080 -    0.160: 93
       0.160 -    0.239: 0
       0.239 -    0.319: 0
       0.319 -    0.399: 1
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" CA  MLE D   8 "
            pdb=" N   MLE D   8 "
            pdb=" C   MLE D   8 "
            pdb=" CB  MLE D   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" CA  ILE H 189 "
            pdb=" N   ILE H 189 "
            pdb=" C   ILE H 189 "
            pdb=" CB  ILE H 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  ILE C 338 "
            pdb=" N   ILE C 338 "
            pdb=" C   ILE C 338 "
            pdb=" CB  ILE C 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1343 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "   -0.027 5.00e-02 4.00e+02   4.10e-02 2.68e+00
        pdb=" N   PRO G  60 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 270 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.27e+00
        pdb=" N   PRO A 271 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 169 "   -0.021 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO A 170 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 558
        2.74 -     3.28: 7801
        3.28 -     3.82: 12669
        3.82 -     4.36: 13522
        4.36 -     4.90: 25110
  Nonbonded interactions: 59660
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OD1 ASN C 295 "
            pdb=" NH1 ARG C 304 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   ARG H  67 "
            pdb=" OG1 THR H  84 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG1 THR H  91 "
            pdb=" O   LEU H 117 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASP C 254 "
            pdb=" N   ARG C 256 "
     model   vdw
     2.359 3.120
  ... (remaining 59655 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.190
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   8328  Z= 0.166
  Angle     :  0.516   9.617  11368  Z= 0.273
  Chirality :  0.042   0.399   1346
  Planarity :  0.003   0.041   1438
  Dihedral  : 12.839  80.282   2749
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.27), residues: 1092
  helix:  2.35 (0.27), residues: 370
  sheet: -0.52 (0.32), residues: 308
  loop : -1.20 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  27 
 TYR   0.011   0.001   TYR H 190 
 PHE   0.017   0.001   PHE A 139 
 TRP   0.019   0.001   TRP C 332 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8325)
  covalent geometry    : angle       0.51346 (11364)
  SS BOND              : bond        0.00464 (    2)
  SS BOND              : angle       2.75165 (    4)
  hydrogen bonds       : bond        0.18692 (  383)
  hydrogen bonds       : angle       6.38144 ( 1098)
  Misc. bond           : bond        0.10256 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.324 
Fit side-chains
REVERT: B   19 ILE cc_start: 0.7659 (mm) cc_final: 0.7366 (mt)
REVERT: B   22 ASN cc_start: 0.7880 (t0) cc_final: 0.7540 (t0)
REVERT: B  193 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8201 (mtpp)
REVERT: B  270 ASN cc_start: 0.8354 (t0) cc_final: 0.8051 (t0)
REVERT: B  271 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7575 (mmtm)
REVERT: B  275 PHE cc_start: 0.7371 (t80) cc_final: 0.7158 (t80)
REVERT: B  303 TYR cc_start: 0.7759 (t80) cc_final: 0.7557 (t80)
REVERT: C   33 ILE cc_start: 0.8029 (mm) cc_final: 0.7719 (tp)
REVERT: C  223 THR cc_start: 0.8062 (p) cc_final: 0.7802 (p)
REVERT: C  264 TYR cc_start: 0.7853 (m-80) cc_final: 0.7634 (m-10)
REVERT: G   27 ARG cc_start: 0.6932 (mtt90) cc_final: 0.6523 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1017
  time to fit residues: 29.2472
Evaluate side-chains
  190 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 297 ASN
B 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.124161 restraints weight = 13779.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.50
r_work: 0.3484 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8328  Z= 0.218
  Angle     :  0.645   9.100  11368  Z= 0.339
  Chirality :  0.045   0.145   1346
  Planarity :  0.005   0.065   1438
  Dihedral  :  4.793  50.272   1185
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.27 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.26), residues: 1092
  helix:  1.86 (0.27), residues: 367
  sheet: -0.22 (0.33), residues: 283
  loop : -1.53 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  72 
 TYR   0.022   0.002   TYR H 101 
 PHE   0.017   0.002   PHE C 278 
 TRP   0.019   0.003   TRP C 332 
 HIS   0.006   0.002   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8325)
  covalent geometry    : angle       0.64314 (11364)
  SS BOND              : bond        0.01209 (    2)
  SS BOND              : angle       2.98642 (    4)
  hydrogen bonds       : bond        0.06098 (  383)
  hydrogen bonds       : angle       4.92170 ( 1098)
  Misc. bond           : bond        0.00052 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 206
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  102 TRP cc_start: 0.6726 (t-100) cc_final: 0.6513 (t-100)
REVERT: A  110 ILE cc_start: 0.7392 (pt) cc_final: 0.7064 (mm)
REVERT: A  210 VAL cc_start: 0.8504 (p) cc_final: 0.8285 (p)
REVERT: B   46 LYS cc_start: 0.7582 (ptpt) cc_final: 0.7230 (ptpp)
REVERT: B  193 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8226 (mtpp)
REVERT: B  212 TRP cc_start: 0.7142 (p-90) cc_final: 0.6845 (p-90)
REVERT: B  270 ASN cc_start: 0.8563 (t0) cc_final: 0.8321 (t0)
REVERT: B  271 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7726 (mmtm)
REVERT: B  297 TYR cc_start: 0.7121 (t80) cc_final: 0.6511 (t80)
REVERT: C  128 THR cc_start: 0.7998 (m) cc_final: 0.7738 (t)
REVERT: C  147 SER cc_start: 0.8490 (m) cc_final: 0.7815 (t)
REVERT: C  186 ASP cc_start: 0.7613 (m-30) cc_final: 0.7400 (m-30)
REVERT: C  320 VAL cc_start: 0.8041 (m) cc_final: 0.7781 (t)
REVERT: G   21 MET cc_start: 0.6762 (tmm) cc_final: 0.6501 (tmm)
REVERT: G   27 ARG cc_start: 0.7292 (mtt90) cc_final: 0.6983 (mmt-90)
REVERT: H   83 MET cc_start: 0.7563 (mmp) cc_final: 0.6975 (mmm)
  outliers start: 15
  outliers final: 12
  residues processed: 212
  average time/residue: 0.0919
  time to fit residues: 26.1478
Evaluate side-chains
  205 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  312 ASN
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0770
   chunk 41 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.126039 restraints weight = 13736.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.54
r_work: 0.3511 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8328  Z= 0.132
  Angle     :  0.558  10.518  11368  Z= 0.291
  Chirality :  0.041   0.144   1346
  Planarity :  0.004   0.051   1438
  Dihedral  :  4.457  49.975   1185
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.21 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.26), residues: 1092
  helix:  1.93 (0.27), residues: 373
  sheet: -0.14 (0.32), residues: 294
  loop : -1.56 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.012   0.001   TYR B 303 
 PHE   0.022   0.001   PHE C 235 
 TRP   0.012   0.001   TRP C 332 
 HIS   0.003   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8325)
  covalent geometry    : angle       0.55707 (11364)
  SS BOND              : bond        0.00666 (    2)
  SS BOND              : angle       1.58004 (    4)
  hydrogen bonds       : bond        0.04856 (  383)
  hydrogen bonds       : angle       4.60951 ( 1098)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  102 TRP cc_start: 0.6743 (t-100) cc_final: 0.6521 (t-100)
REVERT: A  110 ILE cc_start: 0.7429 (pt) cc_final: 0.7084 (mm)
REVERT: A  206 LEU cc_start: 0.8142 (tp) cc_final: 0.7907 (tp)
REVERT: A  210 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (p)
REVERT: B   46 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7240 (ptpp)
REVERT: B  212 TRP cc_start: 0.7205 (p-90) cc_final: 0.6929 (p-90)
REVERT: B  270 ASN cc_start: 0.8626 (t0) cc_final: 0.8352 (t0)
REVERT: B  271 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7445 (mmtt)
REVERT: B  297 TYR cc_start: 0.7021 (t80) cc_final: 0.6267 (t80)
REVERT: C   33 ILE cc_start: 0.7838 (mm) cc_final: 0.7537 (tp)
REVERT: C  128 THR cc_start: 0.7923 (m) cc_final: 0.7689 (t)
REVERT: C  147 SER cc_start: 0.8470 (m) cc_final: 0.7762 (t)
REVERT: C  186 ASP cc_start: 0.7519 (m-30) cc_final: 0.7282 (m-30)
REVERT: G   21 MET cc_start: 0.6805 (tmm) cc_final: 0.6520 (tmm)
REVERT: G   27 ARG cc_start: 0.7289 (mtt90) cc_final: 0.6977 (mmt-90)
REVERT: G   38 MET cc_start: 0.7960 (ptm) cc_final: 0.7577 (ptm)
REVERT: H   83 MET cc_start: 0.7549 (mmp) cc_final: 0.6833 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 210
  average time/residue: 0.0797
  time to fit residues: 22.6771
Evaluate side-chains
  212 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  338 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  195 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0070
   chunk 52 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 107 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.143522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.126518 restraints weight = 14060.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.46
r_work: 0.3522 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8328  Z= 0.130
  Angle     :  0.536   8.191  11368  Z= 0.281
  Chirality :  0.041   0.138   1346
  Planarity :  0.004   0.047   1438
  Dihedral  :  4.394  49.658   1185
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.11 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.26), residues: 1092
  helix:  1.95 (0.26), residues: 373
  sheet: -0.17 (0.32), residues: 292
  loop : -1.51 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.010   0.001   TYR C 105 
 PHE   0.010   0.001   PHE A 139 
 TRP   0.010   0.001   TRP C 332 
 HIS   0.006   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8325)
  covalent geometry    : angle       0.53595 (11364)
  SS BOND              : bond        0.00644 (    2)
  SS BOND              : angle       1.39480 (    4)
  hydrogen bonds       : bond        0.04642 (  383)
  hydrogen bonds       : angle       4.48896 ( 1098)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7486 (pt) cc_final: 0.7148 (mm)
REVERT: A  206 LEU cc_start: 0.8070 (tp) cc_final: 0.7845 (tp)
REVERT: A  210 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (p)
REVERT: B   46 LYS cc_start: 0.7572 (ptpt) cc_final: 0.7225 (ptpp)
REVERT: B  212 TRP cc_start: 0.7223 (p-90) cc_final: 0.6918 (p-90)
REVERT: B  270 ASN cc_start: 0.8550 (t0) cc_final: 0.8288 (t0)
REVERT: B  271 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7290 (mmtt)
REVERT: B  297 TYR cc_start: 0.6946 (t80) cc_final: 0.6283 (t80)
REVERT: C   33 ILE cc_start: 0.7810 (mm) cc_final: 0.7523 (tp)
REVERT: C  128 THR cc_start: 0.7919 (m) cc_final: 0.7663 (t)
REVERT: C  147 SER cc_start: 0.8350 (m) cc_final: 0.7766 (t)
REVERT: C  318 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7455 (tp)
REVERT: G   21 MET cc_start: 0.6752 (tmm) cc_final: 0.6512 (tmm)
REVERT: G   27 ARG cc_start: 0.7316 (mtt90) cc_final: 0.7018 (mmt-90)
REVERT: G   38 MET cc_start: 0.8013 (ptm) cc_final: 0.7690 (ptm)
REVERT: H   83 MET cc_start: 0.7522 (mmp) cc_final: 0.6788 (mmm)
REVERT: H  140 MET cc_start: 0.8097 (mtp) cc_final: 0.7818 (mtp)
REVERT: H  213 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7785 (p)
  outliers start: 25
  outliers final: 17
  residues processed: 202
  average time/residue: 0.0865
  time to fit residues: 23.5348
Evaluate side-chains
  206 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  338 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  213 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0270
   chunk 60 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0870
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.145509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.128173 restraints weight = 13915.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.57
r_work: 0.3541 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8328  Z= 0.102
  Angle     :  0.503   8.138  11368  Z= 0.261
  Chirality :  0.040   0.135   1346
  Planarity :  0.004   0.046   1438
  Dihedral  :  4.114  47.961   1185
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.25 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1092
  helix:  2.26 (0.27), residues: 367
  sheet: -0.10 (0.32), residues: 293
  loop : -1.32 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.009   0.001   TYR B 303 
 PHE   0.008   0.001   PHE A 139 
 TRP   0.010   0.001   TRP C 332 
 HIS   0.002   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 8325)
  covalent geometry    : angle       0.50309 (11364)
  SS BOND              : bond        0.00458 (    2)
  SS BOND              : angle       1.09415 (    4)
  hydrogen bonds       : bond        0.03922 (  383)
  hydrogen bonds       : angle       4.31256 ( 1098)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7457 (pt) cc_final: 0.7067 (mm)
REVERT: B   46 LYS cc_start: 0.7555 (ptpt) cc_final: 0.7288 (ptpp)
REVERT: B  270 ASN cc_start: 0.8606 (t0) cc_final: 0.8335 (t0)
REVERT: B  271 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7512 (mmtt)
REVERT: B  297 TYR cc_start: 0.6890 (t80) cc_final: 0.6179 (t80)
REVERT: C   33 ILE cc_start: 0.7823 (mm) cc_final: 0.7535 (tp)
REVERT: C  147 SER cc_start: 0.8361 (m) cc_final: 0.7889 (p)
REVERT: G   21 MET cc_start: 0.6827 (tmm) cc_final: 0.6584 (tmm)
REVERT: G   27 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6981 (mmt-90)
REVERT: G   38 MET cc_start: 0.7937 (ptm) cc_final: 0.7552 (ptm)
REVERT: H   83 MET cc_start: 0.7502 (mmp) cc_final: 0.6878 (mmt)
REVERT: H  116 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.7966 (p)
REVERT: H  213 THR cc_start: 0.8123 (t) cc_final: 0.7740 (p)
REVERT: H  229 CYS cc_start: 0.6918 (p) cc_final: 0.6651 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 204
  average time/residue: 0.0787
  time to fit residues: 21.7813
Evaluate side-chains
  206 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 192
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 GLN
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  148 CYS
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  338 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0270
   chunk 30 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.126209 restraints weight = 13763.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.44
r_work: 0.3517 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8328  Z= 0.145
  Angle     :  0.561  10.211  11368  Z= 0.290
  Chirality :  0.042   0.179   1346
  Planarity :  0.004   0.043   1438
  Dihedral  :  4.347  49.464   1185
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.39 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.26), residues: 1092
  helix:  2.11 (0.27), residues: 367
  sheet: -0.17 (0.32), residues: 295
  loop : -1.34 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 304 
 TYR   0.016   0.002   TYR H 101 
 PHE   0.011   0.001   PHE C 199 
 TRP   0.023   0.002   TRP B 212 
 HIS   0.003   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8325)
  covalent geometry    : angle       0.56042 (11364)
  SS BOND              : bond        0.00745 (    2)
  SS BOND              : angle       1.45261 (    4)
  hydrogen bonds       : bond        0.04756 (  383)
  hydrogen bonds       : angle       4.42506 ( 1098)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7480 (pt) cc_final: 0.7157 (mm)
REVERT: B  270 ASN cc_start: 0.8567 (t0) cc_final: 0.8332 (t0)
REVERT: B  271 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7479 (mmtt)
REVERT: B  297 TYR cc_start: 0.6973 (t80) cc_final: 0.6353 (t80)
REVERT: C   33 ILE cc_start: 0.7765 (mm) cc_final: 0.7466 (tp)
REVERT: C   45 MET cc_start: 0.7695 (ptp) cc_final: 0.7425 (ptp)
REVERT: C  147 SER cc_start: 0.8449 (m) cc_final: 0.7794 (t)
REVERT: G   21 MET cc_start: 0.6807 (tmm) cc_final: 0.6597 (tmm)
REVERT: G   27 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6867 (mmt-90)
REVERT: G   38 MET cc_start: 0.7984 (ptm) cc_final: 0.7633 (ptm)
REVERT: H   83 MET cc_start: 0.7533 (mmp) cc_final: 0.6683 (mmm)
REVERT: H  116 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8025 (p)
REVERT: H  213 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7739 (p)
  outliers start: 24
  outliers final: 17
  residues processed: 204
  average time/residue: 0.0865
  time to fit residues: 23.8142
Evaluate side-chains
  211 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  338 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
B 205 GLN
C 239 ASN
G  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.124373 restraints weight = 13762.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 2.53
r_work: 0.3487 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8328  Z= 0.184
  Angle     :  0.603  11.689  11368  Z= 0.314
  Chirality :  0.043   0.164   1346
  Planarity :  0.004   0.044   1438
  Dihedral  :  4.744  50.851   1185
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.79 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.26), residues: 1092
  helix:  1.77 (0.27), residues: 372
  sheet: -0.25 (0.31), residues: 305
  loop : -1.47 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.016   0.002   TYR H 101 
 PHE   0.013   0.002   PHE C 199 
 TRP   0.020   0.002   TRP C 332 
 HIS   0.004   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8325)
  covalent geometry    : angle       0.60206 (11364)
  SS BOND              : bond        0.00948 (    2)
  SS BOND              : angle       1.83376 (    4)
  hydrogen bonds       : bond        0.05463 (  383)
  hydrogen bonds       : angle       4.57544 ( 1098)
  Misc. bond           : bond        0.00072 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  210 VAL cc_start: 0.8513 (p) cc_final: 0.8296 (p)
REVERT: B  270 ASN cc_start: 0.8582 (t0) cc_final: 0.8335 (t0)
REVERT: B  271 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7407 (mmtt)
REVERT: B  297 TYR cc_start: 0.7055 (t80) cc_final: 0.6393 (t80)
REVERT: C   45 MET cc_start: 0.7910 (ptp) cc_final: 0.7646 (ptp)
REVERT: C  147 SER cc_start: 0.8462 (m) cc_final: 0.7911 (p)
REVERT: C  186 ASP cc_start: 0.7523 (m-30) cc_final: 0.7313 (m-30)
REVERT: G   21 MET cc_start: 0.6798 (tmm) cc_final: 0.6590 (tmm)
REVERT: G   27 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6841 (mmt-90)
REVERT: H   83 MET cc_start: 0.7563 (mmp) cc_final: 0.6567 (mmm)
REVERT: H  116 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8060 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 213
  average time/residue: 0.0794
  time to fit residues: 23.2638
Evaluate side-chains
  223 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  334 VAL
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  273 ILE
Chi-restraints excluded: chain C residue  338 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    0.0370
   chunk 103 optimal weight:    0.9980
   chunk 40 optimal weight:    0.1980
   chunk 78 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.2658

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

Flipped N/Q/H residues before XYZ refinement:
B 205 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.144959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127840 restraints weight = 13711.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.53
r_work: 0.3539 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8328  Z= 0.105
  Angle     :  0.528   8.804  11368  Z= 0.270
  Chirality :  0.041   0.135   1346
  Planarity :  0.004   0.044   1438
  Dihedral  :  4.231  48.487   1185
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.94 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1092
  helix:  2.08 (0.27), residues: 373
  sheet: -0.13 (0.32), residues: 299
  loop : -1.34 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.015   0.001   TYR H 101 
 PHE   0.010   0.001   PHE A 172 
 TRP   0.021   0.001   TRP B 212 
 HIS   0.003   0.001   HIS C 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8325)
  covalent geometry    : angle       0.52735 (11364)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       1.06246 (    4)
  hydrogen bonds       : bond        0.03975 (  383)
  hydrogen bonds       : angle       4.32705 ( 1098)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 206
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7383 (pt) cc_final: 0.7148 (mt)
REVERT: A  210 VAL cc_start: 0.8465 (p) cc_final: 0.8244 (p)
REVERT: B  270 ASN cc_start: 0.8560 (t0) cc_final: 0.8303 (t0)
REVERT: B  271 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7343 (mmtt)
REVERT: B  297 TYR cc_start: 0.6714 (t80) cc_final: 0.6093 (t80)
REVERT: C   18 ILE cc_start: 0.7897 (pt) cc_final: 0.7574 (mt)
REVERT: C   45 MET cc_start: 0.7858 (ptp) cc_final: 0.7606 (ptp)
REVERT: C  147 SER cc_start: 0.8398 (m) cc_final: 0.7936 (p)
REVERT: C  304 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6980 (mtp85)
REVERT: G   21 MET cc_start: 0.6851 (tmm) cc_final: 0.6648 (tmm)
REVERT: G   27 ARG cc_start: 0.7144 (mtt90) cc_final: 0.6777 (mpt180)
REVERT: H   83 MET cc_start: 0.7447 (mmp) cc_final: 0.6602 (mmm)
REVERT: H  101 TYR cc_start: 0.7340 (m-80) cc_final: 0.6917 (m-80)
REVERT: H  116 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.7959 (p)
REVERT: H  229 CYS cc_start: 0.6959 (p) cc_final: 0.6699 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 211
  average time/residue: 0.0911
  time to fit residues: 26.0419
Evaluate side-chains
  215 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 101 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0010
   chunk 71 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
C 239 ASN
** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.143931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.126741 restraints weight = 13791.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.53
r_work: 0.3523 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8328  Z= 0.123
  Angle     :  0.554   9.603  11368  Z= 0.283
  Chirality :  0.042   0.282   1346
  Planarity :  0.004   0.043   1438
  Dihedral  :  4.285  50.121   1185
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.07 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1092
  helix:  2.08 (0.27), residues: 372
  sheet: -0.11 (0.31), residues: 298
  loop : -1.34 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.013   0.001   TYR H 101 
 PHE   0.011   0.001   PHE A 172 
 TRP   0.015   0.001   TRP C 332 
 HIS   0.008   0.001   HIS H 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8325)
  covalent geometry    : angle       0.55403 (11364)
  SS BOND              : bond        0.00620 (    2)
  SS BOND              : angle       1.25568 (    4)
  hydrogen bonds       : bond        0.04314 (  383)
  hydrogen bonds       : angle       4.35640 ( 1098)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 203
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A  110 ILE cc_start: 0.7372 (pt) cc_final: 0.7136 (mt)
REVERT: B  270 ASN cc_start: 0.8562 (t0) cc_final: 0.8314 (t0)
REVERT: B  271 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7298 (mmtt)
REVERT: B  297 TYR cc_start: 0.6867 (t80) cc_final: 0.6235 (t80)
REVERT: C   18 ILE cc_start: 0.7883 (pt) cc_final: 0.7563 (mt)
REVERT: C  147 SER cc_start: 0.8381 (m) cc_final: 0.7911 (p)
REVERT: C  199 PHE cc_start: 0.8123 (p90) cc_final: 0.7912 (p90)
REVERT: C  292 PHE cc_start: 0.7057 (m-80) cc_final: 0.6846 (m-80)
REVERT: C  304 ARG cc_start: 0.7392 (tpp80) cc_final: 0.7073 (mtp85)
REVERT: G   27 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6799 (mpt180)
REVERT: H   83 MET cc_start: 0.7497 (mmp) cc_final: 0.6576 (mmm)
REVERT: H  101 TYR cc_start: 0.7366 (m-80) cc_final: 0.6942 (m-80)
REVERT: H  116 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7962 (p)
REVERT: H  229 CYS cc_start: 0.6962 (p) cc_final: 0.6705 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 211
  average time/residue: 0.0766
  time to fit residues: 21.9009
Evaluate side-chains
  219 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 181 HIS
C 239 ASN
G  18 GLN
** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.141859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.124906 restraints weight = 13705.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.49
r_work: 0.3498 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8328  Z= 0.173
  Angle     :  0.619  13.496  11368  Z= 0.315
  Chirality :  0.044   0.233   1346
  Planarity :  0.004   0.042   1438
  Dihedral  :  4.644  51.538   1185
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.45 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.26), residues: 1092
  helix:  1.89 (0.27), residues: 372
  sheet: -0.18 (0.31), residues: 302
  loop : -1.47 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.015   0.002   TYR H 190 
 PHE   0.011   0.002   PHE A 139 
 TRP   0.035   0.002   TRP C 332 
 HIS   0.007   0.001   HIS H 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8325)
  covalent geometry    : angle       0.61815 (11364)
  SS BOND              : bond        0.00894 (    2)
  SS BOND              : angle       1.72691 (    4)
  hydrogen bonds       : bond        0.05297 (  383)
  hydrogen bonds       : angle       4.52600 ( 1098)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  209 MET cc_start: 0.7697 (mmt) cc_final: 0.7489 (mmm)
REVERT: B  270 ASN cc_start: 0.8584 (t0) cc_final: 0.8356 (t0)
REVERT: B  271 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7352 (mmtt)
REVERT: B  297 TYR cc_start: 0.7005 (t80) cc_final: 0.6361 (t80)
REVERT: C   18 ILE cc_start: 0.7887 (pt) cc_final: 0.7586 (mt)
REVERT: C  147 SER cc_start: 0.8376 (m) cc_final: 0.7930 (p)
REVERT: C  304 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7224 (mtp85)
REVERT: G   27 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6803 (mpt180)
REVERT: H   83 MET cc_start: 0.7541 (mmp) cc_final: 0.6627 (mmm)
REVERT: H  101 TYR cc_start: 0.7418 (m-80) cc_final: 0.6891 (m-80)
REVERT: H  116 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8018 (p)
  outliers start: 19
  outliers final: 17
  residues processed: 210
  average time/residue: 0.0722
  time to fit residues: 20.9283
Evaluate side-chains
  215 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  231 TRP
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  195 LEU
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.142003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.124984 restraints weight = 13771.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.52
r_work: 0.3497 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8328  Z= 0.168
  Angle     :  0.614  13.089  11368  Z= 0.315
  Chirality :  0.043   0.228   1346
  Planarity :  0.004   0.044   1438
  Dihedral  :  4.706  51.553   1185
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 23.70 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.26), residues: 1092
  helix:  1.84 (0.26), residues: 372
  sheet: -0.18 (0.31), residues: 302
  loop : -1.49 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 304 
 TYR   0.013   0.002   TYR H 190 
 PHE   0.012   0.002   PHE A 139 
 TRP   0.039   0.003   TRP B 212 
 HIS   0.008   0.001   HIS H 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8325)
  covalent geometry    : angle       0.61337 (11364)
  SS BOND              : bond        0.00825 (    2)
  SS BOND              : angle       1.63929 (    4)
  hydrogen bonds       : bond        0.05167 (  383)
  hydrogen bonds       : angle       4.53139 ( 1098)
  Misc. bond           : bond        0.00065 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1735.23 seconds
wall clock time: 30 minutes 19.90 seconds (1819.90 seconds total)