Starting phenix.real_space_refine
on Thu Jun  5 23:48:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t2g_25612/06_2025/7t2g_25612.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.028 sd=   0.242
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      59      5.16       5
     C    4461      2.51       5
     N    1154      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6922
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1690
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 59
    Chain: "B"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2481
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 348
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2279
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 288, 2270
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 25
      Conformer: "B"
        Number of residues, atoms: 288, 2270
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 25
          bond proxies already assigned to first conformer: 2317
    Chain: "R"
      Number of atoms: 124
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 11, 94
          Unusual residues: {'CLR': 2, 'EIG': 1}
          Classifications: {'undetermined': 3, 'water': 8}
          Link IDs: {None: 10}
      Conformer: "B"
        Number of residues, atoms: 11, 94
          Unusual residues: {'CLR': 2, 'EIG': 1}
          Classifications: {'undetermined': 3, 'water': 8}
          Link IDs: {None: 10}
          bond proxies already assigned to first conformer: 62
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C01AEIG R 501 " occ=0.50
      ... (58 atoms not shown)
      pdb=" O05BEIG R 501 " occ=0.50
  Time building chain proxies: 5.69, per 1000 atoms: 0.82
  Number of scatterers: 6922
  At special positions: 0
  Unit cell: (91.84, 98.4, 114.8, 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      59     16.00
     O    1248      8.00
     N    1154      7.00
     C    4461      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 140 " - pdb=" SG  CYS R 217 " 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=0, symmetry=0
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      47.8% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.630A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.061A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.722A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.691A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 46
      removed outlier: 4.638A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 96
    Processing helix  chain 'R' and resid 101 through 120
      removed outlier: 3.630A  pdb=" N   THR R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 130
    Processing helix  chain 'R' and resid 135 through 171
      removed outlier: 4.173A  pdb=" N   LEU R 139 " --> pdb=" O   PHE R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 179
      removed outlier: 4.142A  pdb=" N   ASP R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 195
    Processing helix  chain 'R' and resid 195 through 206
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 224 through 241
      removed outlier: 3.598A  pdb=" N   TRP R 228 " --> pdb=" O   PRO R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 260
    Processing helix  chain 'R' and resid 268 through 306
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 311 through 337
      removed outlier: 3.852A  pdb=" N   VAL R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN R 328 " --> pdb=" O   LEU R 324 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   SER R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
    Processing helix  chain 'R' and resid 340 through 348
      removed outlier: 3.610A  pdb=" N   ARG R 345 " --> pdb=" O   GLU R 341 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS R 346 " --> pdb=" O   ASN R 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.189A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.524A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.826A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.987A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.524A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.696A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.526A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 5.826A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 208 through 211

    398 hydrogen bonds defined for protein.
    1158 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1094
        1.30 -     1.43: 1855
        1.43 -     1.56: 4029
        1.56 -     1.69: 6
        1.69 -     1.82: 83
  Bond restraints: 7067
  Sorted by residual:
  bond pdb=" C08BEIG R 501 "
       pdb=" N01BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.448  1.271  0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" C17BEIG R 501 "
       pdb=" C19BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.470  1.611 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C08BEIG R 501 "
       pdb=" C09BEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.529  1.404  0.125 2.00e-02 2.50e+03 3.89e+01
  bond pdb=" C   LEU B 252 "
       pdb=" O   LEU B 252 "
    ideal  model  delta    sigma   weight residual
    1.235  1.169  0.066 1.22e-02 6.72e+03 2.97e+01
  bond pdb=" C17AEIG R 501 "
       pdb=" C20AEIG R 501 "
    ideal  model  delta    sigma   weight residual
    1.348  1.445 -0.097 2.00e-02 2.50e+03 2.35e+01
  ... (remaining 7062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 9565
        4.04 -     8.08: 60
        8.08 -    12.12: 6
       12.12 -    16.16: 0
       16.16 -    20.20: 1
  Bond angle restraints: 9632
  Sorted by residual:
  angle pdb=" C09BEIG R 501 "
        pdb=" C08BEIG R 501 "
        pdb=" C12BEIG R 501 "
      ideal   model   delta    sigma   weight residual
     114.95   94.75   20.20 3.00e+00 1.11e-01 4.53e+01
  angle pdb=" N   GLY B  64 "
        pdb=" CA  GLY B  64 "
        pdb=" C   GLY B  64 "
      ideal   model   delta    sigma   weight residual
     112.82  105.38    7.44 1.38e+00 5.25e-01 2.90e+01
  angle pdb=" N   ASN R 328 "
        pdb=" CA  ASN R 328 "
        pdb=" C   ASN R 328 "
      ideal   model   delta    sigma   weight residual
     112.54  106.25    6.29 1.22e+00 6.72e-01 2.66e+01
  angle pdb=" N   SER R 329 "
        pdb=" CA  SER R 329 "
        pdb=" C   SER R 329 "
      ideal   model   delta    sigma   weight residual
     112.23  105.84    6.39 1.26e+00 6.30e-01 2.57e+01
  angle pdb=" N   LYS C  32 "
        pdb=" CA  LYS C  32 "
        pdb=" C   LYS C  32 "
      ideal   model   delta    sigma   weight residual
     112.90  106.27    6.63 1.31e+00 5.83e-01 2.56e+01
  ... (remaining 9627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 4044
       17.02 -    34.03: 238
       34.03 -    51.05: 35
       51.05 -    68.07: 18
       68.07 -    85.09: 4
  Dihedral angle restraints: 4339
    sinusoidal: 1710
      harmonic: 2629
  Sorted by residual:
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.17   18.83     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASN B 293 "
           pdb=" C   ASN B 293 "
           pdb=" N   CYS B 294 "
           pdb=" CA  CYS B 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4336 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1069
       0.096 -    0.192: 68
       0.192 -    0.288: 1
       0.288 -    0.383: 1
       0.383 -    0.479: 1
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" C08BEIG R 501 "
            pdb=" C09BEIG R 501 "
            pdb=" C10BEIG R 501 "
            pdb=" C12BEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.77   -2.29   -0.48 2.00e-01 2.50e+01 5.74e+00
  chirality pdb=" C14BEIG R 501 "
            pdb=" C13BEIG R 501 "
            pdb=" C15BEIG R 501 "
            pdb=" C17BEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.26   -2.58    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C10AEIG R 501 "
            pdb=" C08AEIG R 501 "
            pdb=" C13AEIG R 501 "
            pdb=" N02AEIG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1137 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C14BEIG R 501 "   -0.022 2.00e-02 2.50e+03   4.86e-02 2.95e+01
        pdb=" C17BEIG R 501 "    0.016 2.00e-02 2.50e+03
        pdb=" C19BEIG R 501 "    0.029 2.00e-02 2.50e+03
        pdb=" C20BEIG R 501 "   -0.082 2.00e-02 2.50e+03
        pdb=" O03BEIG R 501 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 251 "    0.413 9.50e-02 1.11e+02   1.85e-01 2.10e+01
        pdb=" NE  ARG B 251 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 251 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 251 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 251 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 252 "   -0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   LEU B 252 "    0.071 2.00e-02 2.50e+03
        pdb=" O   LEU B 252 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   PHE B 253 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1007
        2.75 -     3.29: 7286
        3.29 -     3.83: 12842
        3.83 -     4.36: 16022
        4.36 -     4.90: 25912
  Nonbonded interactions: 63069
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN B 110 "
            pdb=" NZ  LYS B 127 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OD2 ASP R 147 "
            pdb=" OH  TYR R 326 "
     model   vdw
     2.314 3.040
  ... (remaining 63064 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=0.43 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.680
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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      :  0.007   0.177   7068  Z= 0.421
  Angle     :  0.880  20.195   9634  Z= 0.534
  Chirality :  0.049   0.479   1140
  Planarity :  0.008   0.185   1190
  Dihedral  : 12.032  85.085   2630
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.30 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.28), residues: 890
  helix:  1.29 (0.27), residues: 376
  sheet:  0.19 (0.37), residues: 175
  loop : -0.38 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 192 
 HIS   0.010   0.001   HIS B 225 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.019   0.002   TYR R 326 
 ARG   0.005   0.001   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20224 (  398)
  hydrogen bonds       : angle       8.00504 ( 1158)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       0.54843 (    2)
  covalent geometry    : bond        0.00719 ( 7067)
  covalent geometry    : angle       0.87975 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 165
  time to evaluate  : 0.699 
Fit side-chains
REVERT: B   75 GLN cc_start: 0.7678 (mm110) cc_final: 0.7038 (mm110)
REVERT: B   83 ASP cc_start: 0.8110 (t0) cc_final: 0.7830 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 168
  average time/residue: 1.2298
  time to fit residues: 217.9180
Evaluate side-chains
  154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain R residue  160 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   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 195 HIS
A 269 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 259 GLN
B 293 ASN
B 340 ASN
R 109 ASN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.125579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.110326 restraints weight = 16403.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.29
r_work: 0.3320 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7068  Z= 0.167
  Angle     :  0.584   5.533   9634  Z= 0.316
  Chirality :  0.043   0.155   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  6.474  58.432   1208
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.87 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 890
  helix:  1.85 (0.26), residues: 390
  sheet:  0.21 (0.38), residues: 167
  loop : -0.72 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.015   0.002   PHE R 237 
 TYR   0.009   0.001   TYR R 148 
 ARG   0.004   0.001   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05123 (  398)
  hydrogen bonds       : angle       5.56685 ( 1158)
  SS BOND              : bond        0.00304 (    1)
  SS BOND              : angle       0.57377 (    2)
  covalent geometry    : bond        0.00363 ( 7067)
  covalent geometry    : angle       0.58374 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A  285 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7140 (mt)
REVERT: A  308 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7070 (mm-30)
REVERT: B   32 GLN cc_start: 0.7672 (mt0) cc_final: 0.7459 (mt0)
REVERT: B   75 GLN cc_start: 0.7657 (mm110) cc_final: 0.7090 (mm110)
REVERT: B   83 ASP cc_start: 0.8221 (t0) cc_final: 0.7974 (t0)
REVERT: R  230 ASN cc_start: 0.7800 (m-40) cc_final: 0.7499 (m-40)
REVERT: R  280 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (mtt-85)
  outliers start: 17
  outliers final: 6
  residues processed: 174
  average time/residue: 1.2025
  time to fit residues: 220.3817
Evaluate side-chains
  159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain R residue  160 THR
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  280 ARG
Chi-restraints excluded: chain R residue  316 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0030
   chunk 82 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 195 HIS
A 269 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 104 ASN
R 109 ASN
R 150 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.126649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.110800 restraints weight = 31116.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.63
r_work: 0.3211 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3208
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7068  Z= 0.145
  Angle     :  0.534   5.598   9634  Z= 0.289
  Chirality :  0.041   0.159   1140
  Planarity :  0.004   0.037   1190
  Dihedral  :  5.961  59.598   1208
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.88 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.28), residues: 890
  helix:  1.92 (0.26), residues: 392
  sheet:  0.04 (0.37), residues: 167
  loop : -0.78 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.011   0.001   TYR R 149 
 ARG   0.005   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04586 (  398)
  hydrogen bonds       : angle       5.27908 ( 1158)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.27004 (    2)
  covalent geometry    : bond        0.00317 ( 7067)
  covalent geometry    : angle       0.53454 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7274 (pt)
REVERT: A   53 MET cc_start: 0.4864 (mtt) cc_final: 0.4147 (tpp)
REVERT: A  207 GLU cc_start: 0.7212 (tp30) cc_final: 0.6774 (mm-30)
REVERT: A  285 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7105 (mt)
REVERT: A  308 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7016 (mm-30)
REVERT: B   75 GLN cc_start: 0.7711 (mm110) cc_final: 0.6816 (mm-40)
REVERT: B   83 ASP cc_start: 0.8147 (t0) cc_final: 0.7903 (t0)
  outliers start: 14
  outliers final: 3
  residues processed: 167
  average time/residue: 1.1793
  time to fit residues: 207.7988
Evaluate side-chains
  156 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  160 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 63 optimal weight:    0.3980
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 51 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 109 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.127333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111361 restraints weight = 28275.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.35
r_work: 0.3246 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7068  Z= 0.139
  Angle     :  0.526   5.544   9634  Z= 0.281
  Chirality :  0.041   0.159   1140
  Planarity :  0.004   0.036   1190
  Dihedral  :  5.600  54.669   1208
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.31 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 890
  helix:  1.84 (0.25), residues: 402
  sheet: -0.06 (0.37), residues: 167
  loop : -0.93 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.011   0.001   TYR R 326 
 ARG   0.006   0.000   ARG R 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  398)
  hydrogen bonds       : angle       5.13344 ( 1158)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.10428 (    2)
  covalent geometry    : bond        0.00303 ( 7067)
  covalent geometry    : angle       0.52610 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7491 (tp30)
REVERT: A   19 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7234 (pt)
REVERT: A   52 GLN cc_start: 0.7292 (mm-40) cc_final: 0.7021 (mm110)
REVERT: A   53 MET cc_start: 0.4889 (mtt) cc_final: 0.4167 (tpp)
REVERT: A  285 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7079 (mt)
REVERT: B   44 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7573 (mp10)
REVERT: B   75 GLN cc_start: 0.7674 (mm110) cc_final: 0.6780 (mm-40)
REVERT: R  276 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7579 (ttp80)
  outliers start: 15
  outliers final: 6
  residues processed: 160
  average time/residue: 1.1773
  time to fit residues: 198.2758
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  264 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
B 220 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.124467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.108545 restraints weight = 24091.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.95
r_work: 0.3219 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7068  Z= 0.203
  Angle     :  0.604   6.236   9634  Z= 0.320
  Chirality :  0.043   0.166   1140
  Planarity :  0.004   0.034   1190
  Dihedral  :  5.918  57.915   1207
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.88 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.27), residues: 890
  helix:  1.65 (0.25), residues: 398
  sheet: -0.18 (0.36), residues: 172
  loop : -0.96 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B  54 
 PHE   0.016   0.002   PHE R 241 
 TYR   0.016   0.002   TYR R 149 
 ARG   0.006   0.001   ARG R 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04866 (  398)
  hydrogen bonds       : angle       5.31609 ( 1158)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.20768 (    2)
  covalent geometry    : bond        0.00448 ( 7067)
  covalent geometry    : angle       0.60451 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7275 (pt)
REVERT: A   52 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7022 (mm110)
REVERT: A  207 GLU cc_start: 0.7398 (tp30) cc_final: 0.6937 (mm-30)
REVERT: A  285 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7105 (mt)
REVERT: A  308 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7096 (mm-30)
REVERT: B   44 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7794 (mt0)
REVERT: B   75 GLN cc_start: 0.7865 (mm110) cc_final: 0.6986 (mm-40)
REVERT: B   83 ASP cc_start: 0.8271 (t0) cc_final: 0.7924 (t0)
REVERT: R  243 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7979 (mpm)
  outliers start: 18
  outliers final: 8
  residues processed: 158
  average time/residue: 1.1957
  time to fit residues: 198.8684
Evaluate side-chains
  163 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  316 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 55 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B 259 GLN
B 293 ASN
B 340 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.127700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111758 restraints weight = 25732.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.16
r_work: 0.3275 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7068  Z= 0.134
  Angle     :  0.527   6.392   9634  Z= 0.282
  Chirality :  0.041   0.157   1140
  Planarity :  0.004   0.036   1190
  Dihedral  :  5.424  54.423   1207
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.88 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 890
  helix:  1.78 (0.25), residues: 402
  sheet: -0.09 (0.37), residues: 170
  loop : -0.96 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.009   0.001   TYR R 128 
 ARG   0.005   0.000   ARG R 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04206 (  398)
  hydrogen bonds       : angle       5.08012 ( 1158)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.18978 (    2)
  covalent geometry    : bond        0.00290 ( 7067)
  covalent geometry    : angle       0.52702 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A   19 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7218 (pt)
REVERT: A   52 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6941 (mm110)
REVERT: A   53 MET cc_start: 0.4890 (mtt) cc_final: 0.3915 (mpp)
REVERT: A  207 GLU cc_start: 0.7342 (tp30) cc_final: 0.6906 (mm-30)
REVERT: A  285 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7057 (mt)
REVERT: A  308 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6873 (mm-30)
REVERT: B   75 GLN cc_start: 0.7626 (mm110) cc_final: 0.7234 (mm110)
REVERT: R  243 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7409 (mpm)
REVERT: R  276 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7490 (ttp80)
  outliers start: 14
  outliers final: 5
  residues processed: 160
  average time/residue: 1.1763
  time to fit residues: 198.1347
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0980
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B 220 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.127253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.111721 restraints weight = 21089.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.68
r_work: 0.3313 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7068  Z= 0.146
  Angle     :  0.541   6.645   9634  Z= 0.289
  Chirality :  0.041   0.158   1140
  Planarity :  0.003   0.036   1190
  Dihedral  :  5.443  54.765   1207
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.31 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 890
  helix:  1.74 (0.25), residues: 401
  sheet: -0.19 (0.37), residues: 174
  loop : -0.94 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.002   PHE R 237 
 TYR   0.015   0.001   TYR R 149 
 ARG   0.004   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  398)
  hydrogen bonds       : angle       5.08949 ( 1158)
  SS BOND              : bond        0.00181 (    1)
  SS BOND              : angle       0.02109 (    2)
  covalent geometry    : bond        0.00319 ( 7067)
  covalent geometry    : angle       0.54156 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.072 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7657 (tp30)
REVERT: A   19 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7244 (pt)
REVERT: A   52 GLN cc_start: 0.7256 (mm-40) cc_final: 0.7000 (mm110)
REVERT: A   53 MET cc_start: 0.4905 (mtt) cc_final: 0.3954 (mpp)
REVERT: A  207 GLU cc_start: 0.7448 (tp30) cc_final: 0.6937 (mm-30)
REVERT: A  285 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7042 (mt)
REVERT: A  308 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6948 (mm-30)
REVERT: B   44 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7623 (mt0)
REVERT: B   75 GLN cc_start: 0.7748 (mm110) cc_final: 0.6820 (mm-40)
REVERT: B   83 ASP cc_start: 0.8211 (t0) cc_final: 0.7913 (t0)
REVERT: B  220 GLN cc_start: 0.8369 (mt0) cc_final: 0.8149 (mt0)
REVERT: R  243 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7635 (mpm)
REVERT: R  276 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7554 (ttp80)
  outliers start: 18
  outliers final: 8
  residues processed: 155
  average time/residue: 1.5678
  time to fit residues: 257.3106
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  125 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  282 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0570
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0050
   chunk 35 optimal weight:    0.0980
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.3712

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.130135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.114543 restraints weight = 22754.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.77
r_work: 0.3357 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7068  Z= 0.116
  Angle     :  0.505   6.923   9634  Z= 0.270
  Chirality :  0.041   0.159   1140
  Planarity :  0.003   0.038   1190
  Dihedral  :  5.202  55.563   1207
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 20.31 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 890
  helix:  1.82 (0.25), residues: 401
  sheet: -0.04 (0.37), residues: 170
  loop : -0.93 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.010   0.001   TYR R 128 
 ARG   0.007   0.001   ARG R 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  398)
  hydrogen bonds       : angle       4.93651 ( 1158)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.16691 (    2)
  covalent geometry    : bond        0.00248 ( 7067)
  covalent geometry    : angle       0.50503 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7554 (tp30)
REVERT: A   52 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6996 (mm110)
REVERT: A   53 MET cc_start: 0.4714 (mtt) cc_final: 0.3830 (mpp)
REVERT: A  285 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7031 (mt)
REVERT: A  308 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6911 (mm-30)
REVERT: B   75 GLN cc_start: 0.7741 (mm110) cc_final: 0.7364 (mm110)
REVERT: B   83 ASP cc_start: 0.8175 (t0) cc_final: 0.7847 (t0)
REVERT: B  220 GLN cc_start: 0.8302 (mt0) cc_final: 0.8060 (mt0)
  outliers start: 10
  outliers final: 3
  residues processed: 162
  average time/residue: 1.4338
  time to fit residues: 245.0275
Evaluate side-chains
  154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  125 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    0.3980
   chunk 43 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0570
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  17 GLN
B 259 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114165 restraints weight = 20451.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.67
r_work: 0.3345 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7068  Z= 0.130
  Angle     :  0.531   6.867   9634  Z= 0.282
  Chirality :  0.041   0.161   1140
  Planarity :  0.003   0.038   1190
  Dihedral  :  5.281  56.149   1205
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 21.89 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 890
  helix:  1.77 (0.25), residues: 401
  sheet: -0.08 (0.37), residues: 177
  loop : -0.89 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 171 
 PHE   0.011   0.001   PHE R 237 
 TYR   0.014   0.001   TYR R 149 
 ARG   0.004   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  398)
  hydrogen bonds       : angle       4.95274 ( 1158)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       0.01286 (    2)
  covalent geometry    : bond        0.00285 ( 7067)
  covalent geometry    : angle       0.53121 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7568 (tp30)
REVERT: A   52 GLN cc_start: 0.7227 (mm-40) cc_final: 0.7003 (mm110)
REVERT: A   53 MET cc_start: 0.4618 (mtt) cc_final: 0.3827 (mpp)
REVERT: A  285 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7010 (mt)
REVERT: A  308 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6938 (mm-30)
REVERT: B   33 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.6528 (mt)
REVERT: B   75 GLN cc_start: 0.7738 (mm110) cc_final: 0.6805 (mm-40)
REVERT: B   83 ASP cc_start: 0.8212 (t0) cc_final: 0.7876 (t0)
REVERT: B  220 GLN cc_start: 0.8324 (mt0) cc_final: 0.8037 (mt0)
  outliers start: 8
  outliers final: 2
  residues processed: 156
  average time/residue: 1.4484
  time to fit residues: 238.2069
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain R residue  125 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  17 GLN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 109 ASN
R 188 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.129765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.113969 restraints weight = 24831.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.06
r_work: 0.3308 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7068  Z= 0.129
  Angle     :  0.536   7.644   9634  Z= 0.285
  Chirality :  0.041   0.167   1140
  Planarity :  0.004   0.039   1190
  Dihedral  :  5.280  56.237   1205
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.60 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 890
  helix:  1.70 (0.25), residues: 402
  sheet:  0.01 (0.37), residues: 175
  loop : -0.88 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 171 
 PHE   0.011   0.001   PHE R 237 
 TYR   0.009   0.001   TYR R 128 
 ARG   0.007   0.001   ARG R 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  398)
  hydrogen bonds       : angle       4.96223 ( 1158)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       0.00684 (    2)
  covalent geometry    : bond        0.00281 ( 7067)
  covalent geometry    : angle       0.53616 ( 9632)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7399 (tp30)
REVERT: A   52 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6915 (mm110)
REVERT: A   53 MET cc_start: 0.4600 (mtt) cc_final: 0.3778 (mpp)
REVERT: A  285 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.6989 (mt)
REVERT: A  308 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6914 (mm-30)
REVERT: B   75 GLN cc_start: 0.7598 (mm110) cc_final: 0.7199 (mm110)
REVERT: B   83 ASP cc_start: 0.8065 (t0) cc_final: 0.7860 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 158
  average time/residue: 1.7399
  time to fit residues: 291.6860
Evaluate side-chains
  158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 153
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain R residue  125 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 87 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0670
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B  17 GLN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 188 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.112914 restraints weight = 21145.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.81
r_work: 0.3336 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7068  Z= 0.142
  Angle     :  0.551   7.117   9634  Z= 0.295
  Chirality :  0.042   0.171   1140
  Planarity :  0.004   0.038   1190
  Dihedral  :  5.399  56.404   1205
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.75 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.27), residues: 890
  helix:  1.63 (0.25), residues: 402
  sheet: -0.04 (0.38), residues: 172
  loop : -0.94 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.011   0.001   PHE R 237 
 TYR   0.015   0.001   TYR R 149 
 ARG   0.004   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  398)
  hydrogen bonds       : angle       5.01873 ( 1158)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       0.06993 (    2)
  covalent geometry    : bond        0.00311 ( 7067)
  covalent geometry    : angle       0.55068 ( 9632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7883.87 seconds
wall clock time: 141 minutes 3.49 seconds (8463.49 seconds total)