Starting phenix.real_space_refine
on Wed Mar  4 10:50:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ozs_13134/03_2026/7ozs_13134.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.013 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 102 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     119      5.49       5
     S      38      5.16       5
     C    7615      2.51       5
     N    2272      2.21       5
     O    2726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12770
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1147
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2166
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 6, 'TRANS': 268}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 44
    Chain: "D"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 641
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 13, 'TRANS': 74}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1901
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "3"
      Number of atoms: 2536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2536
          Classifications: {'RNA': 119}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 54}
          Link IDs: {'rna2p': 10, 'rna3p': 108}
    Chain: "E"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 115
          Classifications: {'peptide': 23}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 22}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'UNK:plan-1': 23}
          Unresolved non-hydrogen planarities: 23
    Chain: "F"
      Number of atoms: 4264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4264
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 544}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 79
  Time building chain proxies: 3.06, per 1000 atoms: 0.24
  Number of scatterers: 12770
  At special positions: 0
  Unit cell: (88.956, 119.667, 146.142, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P     119     15.00
     O    2726      8.00
     N    2272      7.00
     C    7615      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 529.9 milliseconds
  

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2536

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 7 sheets defined
      58.3% alpha, 8.8% beta
      33 base pairs and 78 stacking pairs defined.
    Time for finding SS restraints: 1.50
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 12
      removed outlier: 3.762A  pdb=" N   GLU B  12 " --> pdb=" O   PRO B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 43
      removed outlier: 3.737A  pdb=" N   LYS B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 88
      removed outlier: 4.171A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 97
      No H-bonds generated for 'chain 'B' and resid 95 through 97'
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 3.788A  pdb=" N   VAL B 139 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 168
      removed outlier: 3.813A  pdb=" N   PHE B 168 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 25
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 94 through 113
    Processing helix  chain 'A' and resid 160 through 173
      removed outlier: 3.697A  pdb=" N   GLY A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.605A  pdb=" N   TYR A 203 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 217
    Processing helix  chain 'A' and resid 219 through 225
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 235 through 253
    Processing helix  chain 'A' and resid 267 through 276
    Processing helix  chain 'A' and resid 283 through 298
    Processing helix  chain 'D' and resid 43 through 69
      removed outlier: 4.058A  pdb=" N   LEU D  47 " --> pdb=" O   ASP D  43 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   THR D  69 " --> pdb=" O   GLN D  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 20
    Processing helix  chain 'C' and resid 39 through 53
    Processing helix  chain 'C' and resid 72 through 83
    Processing helix  chain 'C' and resid 125 through 129
      removed outlier: 3.538A  pdb=" N   GLN C 128 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE C 129 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 125 through 129'
    Processing helix  chain 'C' and resid 148 through 150
      No H-bonds generated for 'chain 'C' and resid 148 through 150'
    Processing helix  chain 'C' and resid 155 through 169
      removed outlier: 4.014A  pdb=" N   ASP C 166 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 272
    Processing helix  chain 'E' and resid 9 through 17
      removed outlier: 4.049A  pdb=" N   UNK E  15 " --> pdb=" O   UNK E  12 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   UNK E  17 " --> pdb=" O   UNK E  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
    Processing helix  chain 'F' and resid 47 through 64
      removed outlier: 3.988A  pdb=" N   GLY F  56 " --> pdb=" O   THR F  52 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA F  57 " --> pdb=" O   THR F  53 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP F  64 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 74
    Processing helix  chain 'F' and resid 75 through 83
    Processing helix  chain 'F' and resid 89 through 107
      removed outlier: 3.598A  pdb=" N   ARG F  93 " --> pdb=" O   ASN F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 118
      removed outlier: 3.898A  pdb=" N   CYS F 112 " --> pdb=" O   GLU F 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 119 through 137
      removed outlier: 4.171A  pdb=" N   ALA F 123 " --> pdb=" O   ASP F 119 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR F 137 " --> pdb=" O   GLU F 133 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 146 through 169
    Processing helix  chain 'F' and resid 171 through 181
      removed outlier: 3.577A  pdb=" N   LYS F 181 " --> pdb=" O   ALA F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 181 through 195
      removed outlier: 4.056A  pdb=" N   LEU F 185 " --> pdb=" O   LYS F 181 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP F 195 " --> pdb=" O   LEU F 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 213
    Processing helix  chain 'F' and resid 216 through 225
    Processing helix  chain 'F' and resid 230 through 241
    Processing helix  chain 'F' and resid 245 through 260
      removed outlier: 3.957A  pdb=" N   ALA F 249 " --> pdb=" O   ARG F 245 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY F 251 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL F 252 " --> pdb=" O   MET F 248 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 277 through 288
      removed outlier: 3.873A  pdb=" N   LEU F 281 " --> pdb=" O   LEU F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 329
      removed outlier: 4.391A  pdb=" N   GLN F 320 " --> pdb=" O   GLY F 316 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   GLU F 321 " --> pdb=" O   THR F 317 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY F 329 " --> pdb=" O   LYS F 325 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 399
    Processing helix  chain 'F' and resid 411 through 420
    Processing helix  chain 'F' and resid 420 through 430
    Processing helix  chain 'F' and resid 435 through 458
    Processing helix  chain 'F' and resid 461 through 465
      removed outlier: 3.777A  pdb=" N   GLY F 464 " --> pdb=" O   PHE F 461 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 466 through 484
      Proline residue:  F 475  - end of helix
    Processing helix  chain 'F' and resid 484 through 491
      removed outlier: 3.647A  pdb=" N   ALA F 491 " --> pdb=" O   PRO F 487 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 496 through 514
      removed outlier: 3.874A  pdb=" N   VAL F 512 " --> pdb=" O   ALA F 508 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 522 through 535
      removed outlier: 3.682A  pdb=" N   LYS F 526 " --> pdb=" O   ASN F 522 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS F 535 " --> pdb=" O   TYR F 531 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 550 through 553
      removed outlier: 3.780A  pdb=" N   GLN F 553 " --> pdb=" O   ASP F 550 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 550 through 553'
    Processing helix  chain 'F' and resid 554 through 567
      removed outlier: 3.578A  pdb=" N   LYS F 558 " --> pdb=" O   GLY F 554 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ALA F 567 " --> pdb=" O   VAL F 563 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 572 through 589
      removed outlier: 3.511A  pdb=" N   ASN F 576 " --> pdb=" O   PRO F 572 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 594 through 609
    Processing helix  chain 'F' and resid 614 through 620
      removed outlier: 4.171A  pdb=" N   LYS F 618 " --> pdb=" O   LEU F 614 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 625 through 644
      removed outlier: 3.912A  pdb=" N   HIS F 629 " --> pdb=" O   GLY F 625 " (cutoff:3.500A)
      Proline residue:  F 635  - end of helix
    Processing helix  chain 'F' and resid 649 through 674
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48
      removed outlier: 6.936A  pdb=" N   CYS B 131 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   LEU B  18 " --> pdb=" O   TYR B 129 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TYR B 129 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LEU B  20 " --> pdb=" O   ASP B 127 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASP B 127 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 93
      removed outlier: 6.983A  pdb=" N   LEU B  92 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67
    Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 24
      removed outlier: 6.705A  pdb=" N   MET C 141 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL C 187 " --> pdb=" O   MET C 141 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL C 143 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   ALA C 189 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ALA C 145 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LEU C 225 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   MET C 253 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU C 227 " --> pdb=" O   PRO C 251 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL C 229 " --> pdb=" O   HIS C 249 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   GLU C 115 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   MET C 260 " --> pdb=" O   MET C 113 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   MET C 113 " --> pdb=" O   MET C 260 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   VAL C 110 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   PHE C 106 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU C  31 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   GLY C  90 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LEU C  33 " --> pdb=" O   GLY C  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 72

    557 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      83 hydrogen bonds
      158 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      78 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2952
        1.33 -     1.45: 3202
        1.45 -     1.57: 6794
        1.57 -     1.69: 238
        1.69 -     1.81: 61
  Bond restraints: 13247
  Sorted by residual:
  bond pdb=" CA  GLY D  78 "
       pdb=" C   GLY D  78 "
    ideal  model  delta    sigma   weight residual
    1.520  1.504  0.016 7.30e-03 1.88e+04 4.84e+00
  bond pdb=" CA  ALA F 571 "
       pdb=" CB  ALA F 571 "
    ideal  model  delta    sigma   weight residual
    1.537  1.508  0.030 1.47e-02 4.63e+03 4.04e+00
  bond pdb=" CB  GLN B 166 "
       pdb=" CG  GLN B 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.576 -0.056 3.00e-02 1.11e+03 3.52e+00
  bond pdb=" CB  LYS B  86 "
       pdb=" CG  LYS B  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.568 -0.048 3.00e-02 1.11e+03 2.61e+00
  bond pdb=" CA  ASP F 550 "
       pdb=" C   ASP F 550 "
    ideal  model  delta    sigma   weight residual
    1.525  1.558 -0.033 2.10e-02 2.27e+03 2.53e+00
  ... (remaining 13242 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 18247
        2.77 -     5.54: 223
        5.54 -     8.30: 37
        8.30 -    11.07: 9
       11.07 -    13.84: 2
  Bond angle restraints: 18518
  Sorted by residual:
  angle pdb=" N   ALA F 571 "
        pdb=" CA  ALA F 571 "
        pdb=" C   ALA F 571 "
      ideal   model   delta    sigma   weight residual
     108.22   99.47    8.75 9.00e-01 1.23e+00 9.45e+01
  angle pdb=" C   PRO F 140 "
        pdb=" N   PRO F 141 "
        pdb=" CA  PRO F 141 "
      ideal   model   delta    sigma   weight residual
     127.00  140.84  -13.84 2.40e+00 1.74e-01 3.33e+01
  angle pdb=" C   ASP F 569 "
        pdb=" N   PRO F 570 "
        pdb=" CA  PRO F 570 "
      ideal   model   delta    sigma   weight residual
     119.83  113.63    6.20 1.08e+00 8.57e-01 3.29e+01
  angle pdb=" C   PRO F 140 "
        pdb=" N   PRO F 141 "
        pdb=" CD  PRO F 141 "
      ideal   model   delta    sigma   weight residual
     120.60  109.00   11.60 2.20e+00 2.07e-01 2.78e+01
  angle pdb=" CB  LYS B  86 "
        pdb=" CG  LYS B  86 "
        pdb=" CD  LYS B  86 "
      ideal   model   delta    sigma   weight residual
     111.30  121.52  -10.22 2.30e+00 1.89e-01 1.98e+01
  ... (remaining 18513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.80: 7764
       31.80 -    63.61: 370
       63.61 -    95.41: 90
       95.41 -   127.21: 2
      127.21 -   159.02: 1
  Dihedral angle restraints: 8227
    sinusoidal: 4336
      harmonic: 3891
  Sorted by residual:
  dihedral pdb=" CA  ASN A  70 "
           pdb=" C   ASN A  70 "
           pdb=" N   GLY A  71 "
           pdb=" CA  GLY A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.62   27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  THR A  56 "
           pdb=" C   THR A  56 "
           pdb=" N   ASN A  57 "
           pdb=" CA  ASN A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.23   21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" C4'   G 3  52 "
           pdb=" C3'   G 3  52 "
           pdb=" O3'   G 3  52 "
           pdb=" P     U 3  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   60.98  159.02     1      3.50e+01 8.16e-04 1.52e+01
  ... (remaining 8224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1943
       0.065 -    0.129: 246
       0.129 -    0.194: 30
       0.194 -    0.259: 6
       0.259 -    0.324: 5
  Chirality restraints: 2230
  Sorted by residual:
  chirality pdb=" C3'   G 3  52 "
            pdb=" C4'   G 3  52 "
            pdb=" O3'   G 3  52 "
            pdb=" C2'   G 3  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.15   -0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  LEU F 566 "
            pdb=" N   LEU F 566 "
            pdb=" C   LEU F 566 "
            pdb=" CB  LEU F 566 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CB  ILE B  15 "
            pdb=" CA  ILE B  15 "
            pdb=" CG1 ILE B  15 "
            pdb=" CG2 ILE B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 2227 not shown)

  Planarity restraints: 1937
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 563 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.93e+00
        pdb=" C   VAL F 563 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL F 563 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLY F 564 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 569 "    0.048 5.00e-02 4.00e+02   7.29e-02 8.50e+00
        pdb=" N   PRO F 570 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO F 570 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO F 570 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 134 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO C 135 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 135 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 135 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1934 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3340
        2.81 -     3.33: 11346
        3.33 -     3.85: 22371
        3.85 -     4.38: 25127
        4.38 -     4.90: 40074
  Nonbonded interactions: 102258
  Sorted by model distance:
  nonbonded pdb=" O   LEU F 132 "
            pdb=" OG1 THR F 136 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR A  62 "
            pdb=" O   ALA A  78 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O2'   G 3  76 "
            pdb=" O6    G 3 100 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD2 ASP C  48 "
            pdb=" OH  TYR C 123 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   GLU F 416 "
            pdb=" OG1 THR F 420 "
     model   vdw
     2.325 3.040
  ... (remaining 102253 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.930
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
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      :  0.004   0.056  13247  Z= 0.199
  Angle     :  0.795  13.842  18518  Z= 0.426
  Chirality :  0.046   0.324   2230
  Planarity :  0.006   0.073   1937
  Dihedral  : 17.904 159.017   5691
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.87 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.21), residues: 1282
  helix: -0.69 (0.17), residues: 688
  sheet: -0.10 (0.47), residues: 131
  loop : -1.41 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 173 
 TYR   0.018   0.001   TYR A 201 
 PHE   0.015   0.002   PHE A 163 
 TRP   0.015   0.002   TRP F 154 
 HIS   0.004   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (13247)
  covalent geometry    : angle       0.79451 (18518)
  hydrogen bonds       : bond        0.17479 (  640)
  hydrogen bonds       : angle       6.62450 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: D   48 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7921 (tp30)
REVERT: D   79 VAL cc_start: 0.8810 (t) cc_final: 0.8425 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 85
  average time/residue: 0.0872
  time to fit residues: 12.0267
Evaluate side-chains
  58 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  63 GLN
C  93 ASN
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 470 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.058548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.041536 restraints weight = 56794.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043208 restraints weight = 26229.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.044256 restraints weight = 17158.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.044864 restraints weight = 13413.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045277 restraints weight = 11634.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053  13247  Z= 0.380
  Angle     :  0.710   7.191  18518  Z= 0.367
  Chirality :  0.042   0.242   2230
  Planarity :  0.005   0.052   1937
  Dihedral  : 18.380 173.210   3319
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.60 %
    Favored  : 91.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.23), residues: 1282
  helix:  1.18 (0.19), residues: 704
  sheet: -0.15 (0.45), residues: 136
  loop : -1.15 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 173 
 TYR   0.022   0.002   TYR A 201 
 PHE   0.021   0.002   PHE C 149 
 TRP   0.013   0.002   TRP A  95 
 HIS   0.008   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00801 (13247)
  covalent geometry    : angle       0.70992 (18518)
  hydrogen bonds       : bond        0.04856 (  640)
  hydrogen bonds       : angle       4.47583 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8652 (tmm) cc_final: 0.8325 (tmm)
REVERT: D   48 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8347 (tp30)
REVERT: D   93 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6772 (tm-30)
REVERT: D   94 LYS cc_start: 0.8711 (mttp) cc_final: 0.8479 (mptt)
  outliers start: 11
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0864
  time to fit residues: 9.3659
Evaluate side-chains
  62 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue   93 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 128 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 87 optimal weight:   50.0000
   chunk 90 optimal weight:    7.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.060027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.043212 restraints weight = 56449.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.044943 restraints weight = 25461.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.046019 restraints weight = 16387.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.046631 restraints weight = 12709.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047079 restraints weight = 10991.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13247  Z= 0.141
  Angle     :  0.535   7.438  18518  Z= 0.275
  Chirality :  0.037   0.206   2230
  Planarity :  0.004   0.052   1937
  Dihedral  : 18.439 173.335   3316
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  8.94 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.24), residues: 1282
  helix:  1.76 (0.20), residues: 705
  sheet:  0.06 (0.46), residues: 135
  loop : -1.00 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  68 
 TYR   0.016   0.001   TYR A 201 
 PHE   0.009   0.001   PHE A 163 
 TRP   0.009   0.001   TRP F 473 
 HIS   0.004   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (13247)
  covalent geometry    : angle       0.53498 (18518)
  hydrogen bonds       : bond        0.03816 (  640)
  hydrogen bonds       : angle       3.92321 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.618 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8606 (tmm) cc_final: 0.8341 (tmm)
REVERT: D   48 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8185 (tp30)
REVERT: D   65 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8833 (tp-100)
REVERT: D   93 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6769 (tm-30)
REVERT: D   94 LYS cc_start: 0.8621 (mttp) cc_final: 0.8338 (mptt)
REVERT: F  273 CYS cc_start: 0.7746 (p) cc_final: 0.7496 (m)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0859
  time to fit residues: 10.5077
Evaluate side-chains
  67 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  246 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 105 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0770
   chunk 99 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 123 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 89 optimal weight:   40.0000
   overall best weight:    3.8146

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 466 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.058950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.041926 restraints weight = 56568.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.043623 restraints weight = 25851.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.044667 restraints weight = 16806.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045329 restraints weight = 13143.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.045660 restraints weight = 11331.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13247  Z= 0.250
  Angle     :  0.588   7.208  18518  Z= 0.302
  Chirality :  0.038   0.215   2230
  Planarity :  0.004   0.049   1937
  Dihedral  : 18.360 174.007   3316
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.77 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.24), residues: 1282
  helix:  2.02 (0.20), residues: 702
  sheet: -0.19 (0.44), residues: 140
  loop : -0.82 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 182 
 TYR   0.017   0.001   TYR A 201 
 PHE   0.017   0.001   PHE A 163 
 TRP   0.008   0.002   TRP A  95 
 HIS   0.006   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 (13247)
  covalent geometry    : angle       0.58817 (18518)
  hydrogen bonds       : bond        0.04004 (  640)
  hydrogen bonds       : angle       3.94627 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8622 (tmm) cc_final: 0.8249 (tmm)
REVERT: D   48 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8334 (tp30)
REVERT: F  248 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8901 (mpp)
REVERT: F  273 CYS cc_start: 0.7887 (p) cc_final: 0.7569 (m)
  outliers start: 18
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0895
  time to fit residues: 10.5286
Evaluate side-chains
  69 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 141 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  70 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 182 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.060223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.043330 restraints weight = 56526.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.045066 restraints weight = 25705.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.046152 restraints weight = 16648.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.046841 restraints weight = 12899.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047175 restraints weight = 11066.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13247  Z= 0.130
  Angle     :  0.512   7.512  18518  Z= 0.263
  Chirality :  0.036   0.196   2230
  Planarity :  0.004   0.051   1937
  Dihedral  : 18.408 171.875   3316
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.92 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.24), residues: 1282
  helix:  2.26 (0.20), residues: 707
  sheet:  0.09 (0.45), residues: 133
  loop : -0.72 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.021   0.001   TYR C 108 
 PHE   0.009   0.001   PHE C 129 
 TRP   0.006   0.001   TRP F 473 
 HIS   0.004   0.001   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (13247)
  covalent geometry    : angle       0.51211 (18518)
  hydrogen bonds       : bond        0.03426 (  640)
  hydrogen bonds       : angle       3.63315 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8580 (tmm) cc_final: 0.8198 (tmm)
REVERT: D   65 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8864 (tp-100)
REVERT: D   93 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6941 (tm-30)
REVERT: D   94 LYS cc_start: 0.8596 (mttp) cc_final: 0.8340 (mttp)
REVERT: F  248 MET cc_start: 0.9122 (mtp) cc_final: 0.8849 (mpp)
REVERT: F  273 CYS cc_start: 0.7857 (p) cc_final: 0.7571 (m)
  outliers start: 20
  outliers final: 14
  residues processed: 78
  average time/residue: 0.0884
  time to fit residues: 11.1633
Evaluate side-chains
  72 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 132 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 122 optimal weight:    0.1980
   chunk 116 optimal weight:   50.0000
   chunk 39 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 109 optimal weight:   30.0000
   chunk 112 optimal weight:    0.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.059972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.043017 restraints weight = 56241.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.044731 restraints weight = 25737.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.045846 restraints weight = 16715.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.046378 restraints weight = 12958.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.046849 restraints weight = 11361.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13247  Z= 0.159
  Angle     :  0.530   9.648  18518  Z= 0.269
  Chirality :  0.037   0.207   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.351 168.736   3316
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.31 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.24), residues: 1282
  helix:  2.35 (0.20), residues: 709
  sheet:  0.08 (0.46), residues: 134
  loop : -0.56 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.012   0.001   TYR F 116 
 PHE   0.012   0.001   PHE A 163 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.004   0.001   HIS A 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (13247)
  covalent geometry    : angle       0.53041 (18518)
  hydrogen bonds       : bond        0.03467 (  640)
  hydrogen bonds       : angle       3.63904 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8572 (tmm) cc_final: 0.8163 (tmm)
REVERT: D   93 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7140 (tm-30)
REVERT: F  160 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9370 (mm)
REVERT: F  248 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8916 (mpp)
REVERT: F  273 CYS cc_start: 0.7906 (p) cc_final: 0.7575 (m)
REVERT: F  637 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8314 (ppp)
  outliers start: 24
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0827
  time to fit residues: 10.3704
Evaluate side-chains
  76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 135 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    0.1980
   chunk 88 optimal weight:   30.0000
   chunk 92 optimal weight:    6.9990
   chunk 124 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.060354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.043463 restraints weight = 56152.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.045196 restraints weight = 25590.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.046280 restraints weight = 16582.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.046818 restraints weight = 12877.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.047294 restraints weight = 11295.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13247  Z= 0.135
  Angle     :  0.514  10.814  18518  Z= 0.262
  Chirality :  0.036   0.211   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.374 166.216   3316
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.98 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.24), residues: 1282
  helix:  2.42 (0.20), residues: 705
  sheet:  0.10 (0.46), residues: 134
  loop : -0.44 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.011   0.001   TYR C 108 
 PHE   0.009   0.001   PHE A 163 
 TRP   0.006   0.001   TRP A 270 
 HIS   0.012   0.001   HIS F 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13247)
  covalent geometry    : angle       0.51403 (18518)
  hydrogen bonds       : bond        0.03337 (  640)
  hydrogen bonds       : angle       3.56018 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8577 (tmm) cc_final: 0.8171 (tmm)
REVERT: F  160 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9333 (mm)
REVERT: F  248 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8924 (mpp)
REVERT: F  273 CYS cc_start: 0.7888 (p) cc_final: 0.7568 (m)
REVERT: F  637 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (ppp)
  outliers start: 25
  outliers final: 18
  residues processed: 75
  average time/residue: 0.0840
  time to fit residues: 10.5131
Evaluate side-chains
  75 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 126 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 12 optimal weight:    0.4980
   chunk 92 optimal weight:   20.0000
   chunk 67 optimal weight:    0.9990
   chunk 112 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.060079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.043168 restraints weight = 55676.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.044890 restraints weight = 25541.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.045968 restraints weight = 16574.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.046533 restraints weight = 12903.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.046950 restraints weight = 11262.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13247  Z= 0.161
  Angle     :  0.542  13.170  18518  Z= 0.273
  Chirality :  0.037   0.382   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.359 163.537   3316
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.88 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.24), residues: 1282
  helix:  2.43 (0.20), residues: 706
  sheet:  0.38 (0.48), residues: 118
  loop : -0.43 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.011   0.001   TYR F 116 
 PHE   0.011   0.001   PHE A 163 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.012   0.001   HIS F 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (13247)
  covalent geometry    : angle       0.54218 (18518)
  hydrogen bonds       : bond        0.03405 (  640)
  hydrogen bonds       : angle       3.60424 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8566 (tmm) cc_final: 0.8142 (tmm)
REVERT: C  177 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7615 (p0)
REVERT: F  273 CYS cc_start: 0.7942 (p) cc_final: 0.7587 (m)
REVERT: F  637 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8299 (ppp)
  outliers start: 26
  outliers final: 19
  residues processed: 77
  average time/residue: 0.0855
  time to fit residues: 10.8712
Evaluate side-chains
  76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 89 optimal weight:   40.0000
   chunk 76 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 135 optimal weight:    0.7980
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 470 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.059484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.042486 restraints weight = 56106.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.044185 restraints weight = 25806.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.045256 restraints weight = 16779.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.045864 restraints weight = 13073.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.046305 restraints weight = 11312.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13247  Z= 0.219
  Angle     :  0.582  11.460  18518  Z= 0.293
  Chirality :  0.038   0.317   2230
  Planarity :  0.004   0.051   1937
  Dihedral  : 18.355 158.217   3316
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.17 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.24), residues: 1282
  helix:  2.36 (0.20), residues: 712
  sheet:  0.33 (0.48), residues: 118
  loop : -0.50 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 245 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.014   0.001   PHE A 163 
 TRP   0.008   0.001   TRP A  95 
 HIS   0.005   0.001   HIS F 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (13247)
  covalent geometry    : angle       0.58166 (18518)
  hydrogen bonds       : bond        0.03655 (  640)
  hydrogen bonds       : angle       3.74851 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8599 (tmm) cc_final: 0.8168 (tmm)
REVERT: C  177 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7637 (p0)
REVERT: F  273 CYS cc_start: 0.8107 (p) cc_final: 0.7649 (m)
  outliers start: 23
  outliers final: 19
  residues processed: 75
  average time/residue: 0.0796
  time to fit residues: 9.9503
Evaluate side-chains
  73 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 138 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.058727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.041613 restraints weight = 56753.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.043293 restraints weight = 26130.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044372 restraints weight = 17046.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.045019 restraints weight = 13295.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.045254 restraints weight = 11473.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  13247  Z= 0.278
  Angle     :  0.638  12.107  18518  Z= 0.321
  Chirality :  0.040   0.304   2230
  Planarity :  0.004   0.051   1937
  Dihedral  : 18.370 142.526   3316
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.27 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.24), residues: 1282
  helix:  2.19 (0.20), residues: 708
  sheet:  0.21 (0.48), residues: 118
  loop : -0.57 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  54 
 TYR   0.011   0.001   TYR A 201 
 PHE   0.017   0.001   PHE A 163 
 TRP   0.022   0.002   TRP F  97 
 HIS   0.010   0.001   HIS F 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (13247)
  covalent geometry    : angle       0.63751 (18518)
  hydrogen bonds       : bond        0.04056 (  640)
  hydrogen bonds       : angle       3.95928 ( 1760)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8626 (tmm) cc_final: 0.8184 (tmm)
REVERT: C   30 CYS cc_start: 0.8776 (t) cc_final: 0.8498 (t)
REVERT: C  177 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.7657 (p0)
REVERT: F  273 CYS cc_start: 0.8166 (p) cc_final: 0.7652 (m)
  outliers start: 22
  outliers final: 19
  residues processed: 73
  average time/residue: 0.0852
  time to fit residues: 10.4134
Evaluate side-chains
  73 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 29 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 111 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 131 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.060621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.043814 restraints weight = 56200.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045544 restraints weight = 25581.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.046639 restraints weight = 16525.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.047310 restraints weight = 12807.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.047627 restraints weight = 11002.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  13247  Z= 0.109
  Angle     :  0.561  13.273  18518  Z= 0.281
  Chirality :  0.037   0.346   2230
  Planarity :  0.004   0.051   1937
  Dihedral  : 18.436 133.615   3316
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.04 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.24), residues: 1282
  helix:  2.37 (0.20), residues: 709
  sheet:  0.16 (0.46), residues: 123
  loop : -0.46 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.011   0.001   TYR F 116 
 PHE   0.014   0.001   PHE C 102 
 TRP   0.009   0.001   TRP F 473 
 HIS   0.007   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (13247)
  covalent geometry    : angle       0.56080 (18518)
  hydrogen bonds       : bond        0.03332 (  640)
  hydrogen bonds       : angle       3.61583 ( 1760)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1972.18 seconds
wall clock time: 34 minutes 47.65 seconds (2087.65 seconds total)