Starting phenix.real_space_refine
on Wed Jul 30 09:41:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2025/7ly4_23587.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      51      5.16       5
     C    7647      2.51       5
     N    1989      2.21       5
     O    2245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11934
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2599
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 12, 'TRANS': 310}
    Chain: "D"
      Number of atoms: 2599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2599
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 12, 'TRANS': 310}
    Chain: "E"
      Number of atoms: 6674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 828, 6674
          Classifications: {'peptide': 828}
          Link IDs: {'PTRANS': 48, 'TRANS': 779}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'FMN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'FMN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.25, per 1000 atoms: 0.69
  Number of scatterers: 11934
  At special positions: 0
  Unit cell: (90.06, 103.74, 182.4, 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      51     16.00
     P       2     15.00
     O    2245      8.00
     N    1989      7.00
     C    7647      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: 3.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2778

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 17 sheets defined
      44.2% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
      removed outlier: 4.261A  pdb=" N   ILE A  32 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 43
      removed outlier: 4.049A  pdb=" N   TYR A  40 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 60 through 74
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 89 through 94
    Processing helix  chain 'A' and resid 100 through 105
      removed outlier: 3.522A  pdb=" N   ILE A 103 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 139 through 144
    Processing helix  chain 'A' and resid 158 through 168
      removed outlier: 3.691A  pdb=" N   SER A 168 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 187
      removed outlier: 3.911A  pdb=" N   LEU A 187 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 243
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 272 through 286
      removed outlier: 3.813A  pdb=" N   THR A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   THR A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 305
      removed outlier: 3.543A  pdb=" N   ILE A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 35
    Processing helix  chain 'D' and resid 35 through 46
      removed outlier: 3.694A  pdb=" N   PHE D  39 " --> pdb=" O   TRP D  35 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR D  40 " --> pdb=" O   PHE D  36 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR D  45 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLY D  46 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 57
    Processing helix  chain 'D' and resid 60 through 74
    Processing helix  chain 'D' and resid 83 through 88
    Processing helix  chain 'D' and resid 89 through 94
    Processing helix  chain 'D' and resid 100 through 105
    Processing helix  chain 'D' and resid 106 through 118
    Processing helix  chain 'D' and resid 139 through 144
    Processing helix  chain 'D' and resid 158 through 168
      removed outlier: 3.729A  pdb=" N   SER D 168 " --> pdb=" O   ASN D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 232
    Processing helix  chain 'D' and resid 233 through 235
      No H-bonds generated for 'chain 'D' and resid 233 through 235'
    Processing helix  chain 'D' and resid 236 through 243
    Processing helix  chain 'D' and resid 253 through 261
      Proline residue:  D 258  - end of helix
    Processing helix  chain 'D' and resid 262 through 286
      removed outlier: 4.248A  pdb=" N   GLY D 273 " --> pdb=" O   CYS D 269 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE D 274 " --> pdb=" O   ILE D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 305
    Processing helix  chain 'E' and resid 853 through 862
    Processing helix  chain 'E' and resid 885 through 900
    Processing helix  chain 'E' and resid 901 through 903
      No H-bonds generated for 'chain 'E' and resid 901 through 903'
    Processing helix  chain 'E' and resid 933 through 951
    Processing helix  chain 'E' and resid 982 through 984
      No H-bonds generated for 'chain 'E' and resid 982 through 984'
    Processing helix  chain 'E' and resid 985 through 1002
    Processing helix  chain 'E' and resid 1013 through 1025
    Processing helix  chain 'E' and resid 1027 through 1041
    Processing helix  chain 'E' and resid 1042 through 1044
      No H-bonds generated for 'chain 'E' and resid 1042 through 1044'
    Processing helix  chain 'E' and resid 1055 through 1059
    Processing helix  chain 'E' and resid 1072 through 1086
    Processing helix  chain 'E' and resid 1089 through 1107
    Processing helix  chain 'E' and resid 1126 through 1130
    Processing helix  chain 'E' and resid 1149 through 1165
    Processing helix  chain 'E' and resid 1171 through 1183
    Processing helix  chain 'E' and resid 1205 through 1211
    Processing helix  chain 'E' and resid 1245 through 1247
      No H-bonds generated for 'chain 'E' and resid 1245 through 1247'
    Processing helix  chain 'E' and resid 1248 through 1269
    Processing helix  chain 'E' and resid 1278 through 1289
      removed outlier: 4.081A  pdb=" N   ALA E1283 " --> pdb=" O   GLN E1279 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU E1284 " --> pdb=" O   LYS E1280 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1299 through 1311
      removed outlier: 3.526A  pdb=" N   PHE E1304 " --> pdb=" O   LEU E1300 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1326 through 1342
    Processing helix  chain 'E' and resid 1358 through 1371
      removed outlier: 4.155A  pdb=" N   ILE E1362 " --> pdb=" O   GLN E1358 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE E1363 " --> pdb=" O   VAL E1359 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1383 through 1394
    Processing helix  chain 'E' and resid 1409 through 1413
    Processing helix  chain 'E' and resid 1447 through 1461
    Processing helix  chain 'E' and resid 1478 through 1489
      removed outlier: 3.985A  pdb=" N   TYR E1482 " --> pdb=" O   ASP E1478 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP E1483 " --> pdb=" O   LEU E1479 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1502 through 1514
    Processing helix  chain 'E' and resid 1521 through 1529
      removed outlier: 4.018A  pdb=" N   MET E1525 " --> pdb=" O   VAL E1521 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1530 through 1532
      No H-bonds generated for 'chain 'E' and resid 1530 through 1532'
    Processing helix  chain 'E' and resid 1554 through 1563
      removed outlier: 4.007A  pdb=" N   LYS E1558 " --> pdb=" O   PRO E1554 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1639 through 1646
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16
    Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131
      removed outlier: 6.794A  pdb=" N   PHE D 208 " --> pdb=" O   VAL D 221 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   VAL D 192 " --> pdb=" O   PHE D 211 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   TYR D 251 " --> pdb=" O   ILE D 313 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   ILE D 313 " --> pdb=" O   TYR D 251 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 173
    Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 293
      removed outlier: 4.121A  pdb=" N   ALA A 316 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   ILE A 313 " --> pdb=" O   TYR A 251 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   TYR A 251 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   VAL A 192 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   PHE A 208 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 47 through 48
    Processing sheet with id=AA7, first strand: chain 'D' and resid 14 through 16
    Processing sheet with id=AA8, first strand: chain 'D' and resid 172 through 173
    Processing sheet with id=AA9, first strand: chain 'E' and resid 849 through 850
    Processing sheet with id=AB1, first strand: chain 'E' and resid 925 through 928
      removed outlier: 6.000A  pdb=" N   GLU E 925 " --> pdb=" O   ALA E 965 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   GLN E 967 " --> pdb=" O   GLU E 925 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   GLU E 927 " --> pdb=" O   GLN E 967 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   GLN E 969 " --> pdb=" O   GLU E 927 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   THR E 972 " --> pdb=" O   LEU E 968 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   GLU E 881 " --> pdb=" O   LEU E1213 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LEU E1213 " --> pdb=" O   GLU E 881 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 1064 through 1071
      removed outlier: 12.392A  pdb=" N   ILE E1193 " --> pdb=" O   ARG E1110 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ALA E1112 " --> pdb=" O   ILE E1193 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   PHE E1195 " --> pdb=" O   ALA E1112 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ASN E1114 " --> pdb=" O   PHE E1195 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   SER E1197 " --> pdb=" O   ASN E1114 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   THR E1116 " --> pdb=" O   SER E1197 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 1323 through 1325
      removed outlier: 6.625A  pdb=" N   LEU E1324 " --> pdb=" O   ALA E1316 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 1374 through 1378
      removed outlier: 6.520A  pdb=" N   VAL E1351 " --> pdb=" O   VAL E1376 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ILE E1378 " --> pdb=" O   VAL E1351 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   VAL E1353 " --> pdb=" O   ILE E1378 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   ARG E1350 " --> pdb=" O   ILE E1398 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   LEU E1400 " --> pdb=" O   ARG E1350 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   GLY E1352 " --> pdb=" O   LEU E1400 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 1427 through 1433
      removed outlier: 7.215A  pdb=" N   ILE E1445 " --> pdb=" O   ALA E1428 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL E1430 " --> pdb=" O   VAL E1443 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   VAL E1443 " --> pdb=" O   VAL E1430 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   TYR E1432 " --> pdb=" O   LYS E1441 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   LYS E1441 " --> pdb=" O   TYR E1432 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY E1442 " --> pdb=" O   LEU E1637 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 1517 through 1520
      removed outlier: 6.443A  pdb=" N   TRP E1518 " --> pdb=" O   LEU E1545 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   SER E1547 " --> pdb=" O   TRP E1518 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   THR E1520 " --> pdb=" O   SER E1547 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 1605 through 1610
      removed outlier: 6.667A  pdb=" N   GLY E1623 " --> pdb=" O   ASP E1661 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASP E1661 " --> pdb=" O   GLY E1623 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LEU E1625 " --> pdb=" O   THR E1659 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   GLY E1629 " --> pdb=" O   PRO E1655 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 1605 through 1610
      removed outlier: 6.667A  pdb=" N   GLY E1623 " --> pdb=" O   ASP E1661 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASP E1661 " --> pdb=" O   GLY E1623 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LEU E1625 " --> pdb=" O   THR E1659 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   GLY E1629 " --> pdb=" O   PRO E1655 " (cutoff:3.500A)

    556 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.62

  Time building geometry restraints manager: 3.59 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2775
        1.32 -     1.46: 3728
        1.46 -     1.59: 5616
        1.59 -     1.72: 16
        1.72 -     1.85: 87
  Bond restraints: 12222
  Sorted by residual:
  bond pdb=" CB  HIS E1301 "
       pdb=" CG  HIS E1301 "
    ideal  model  delta    sigma   weight residual
    1.497  1.406  0.091 1.40e-02 5.10e+03 4.20e+01
  bond pdb=" CG  ARG E1120 "
       pdb=" CD  ARG E1120 "
    ideal  model  delta    sigma   weight residual
    1.520  1.327  0.193 3.00e-02 1.11e+03 4.13e+01
  bond pdb=" CB  HIS A 216 "
       pdb=" CG  HIS A 216 "
    ideal  model  delta    sigma   weight residual
    1.497  1.409  0.088 1.40e-02 5.10e+03 3.92e+01
  bond pdb=" C10 FMN D 401 "
       pdb=" C4A FMN D 401 "
    ideal  model  delta    sigma   weight residual
    1.443  1.549 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" CG  GLN E1158 "
       pdb=" CD  GLN E1158 "
    ideal  model  delta    sigma   weight residual
    1.516  1.390  0.126 2.50e-02 1.60e+03 2.54e+01
  ... (remaining 12217 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 15561
        3.33 -     6.66: 950
        6.66 -     9.99: 80
        9.99 -    13.32: 5
       13.32 -    16.65: 2
  Bond angle restraints: 16598
  Sorted by residual:
  angle pdb=" N   LEU E1602 "
        pdb=" CA  LEU E1602 "
        pdb=" C   LEU E1602 "
      ideal   model   delta    sigma   weight residual
     111.03  125.16  -14.13 1.11e+00 8.12e-01 1.62e+02
  angle pdb=" N   ILE A 274 "
        pdb=" CA  ILE A 274 "
        pdb=" C   ILE A 274 "
      ideal   model   delta    sigma   weight residual
     110.21   97.64   12.57 1.13e+00 7.83e-01 1.24e+02
  angle pdb=" N   SER E 873 "
        pdb=" CA  SER E 873 "
        pdb=" C   SER E 873 "
      ideal   model   delta    sigma   weight residual
     109.83   97.67   12.16 1.27e+00 6.20e-01 9.16e+01
  angle pdb=" C   ARG E1666 "
        pdb=" N   PRO E1667 "
        pdb=" CA  PRO E1667 "
      ideal   model   delta    sigma   weight residual
     119.82  128.29   -8.47 9.80e-01 1.04e+00 7.46e+01
  angle pdb=" C   ASP E1499 "
        pdb=" N   PRO E1500 "
        pdb=" CA  PRO E1500 "
      ideal   model   delta    sigma   weight residual
     119.56  128.13   -8.57 1.02e+00 9.61e-01 7.06e+01
  ... (remaining 16593 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 7013
       17.79 -    35.57: 194
       35.57 -    53.35: 54
       53.35 -    71.14: 27
       71.14 -    88.92: 6
  Dihedral angle restraints: 7294
    sinusoidal: 2971
      harmonic: 4323
  Sorted by residual:
  dihedral pdb=" C   PHE A  36 "
           pdb=" N   PHE A  36 "
           pdb=" CA  PHE A  36 "
           pdb=" CB  PHE A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.94   14.34     0      2.50e+00 1.60e-01 3.29e+01
  dihedral pdb=" C   ARG E1120 "
           pdb=" N   ARG E1120 "
           pdb=" CA  ARG E1120 "
           pdb=" CB  ARG E1120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.05    9.45     0      2.50e+00 1.60e-01 1.43e+01
  dihedral pdb=" CA  PHE A  36 "
           pdb=" C   PHE A  36 "
           pdb=" N   PRO A  37 "
           pdb=" CA  PRO A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 7291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1305
       0.103 -    0.206: 431
       0.206 -    0.309: 72
       0.309 -    0.412: 0
       0.412 -    0.515: 2
  Chirality restraints: 1810
  Sorted by residual:
  chirality pdb=" CA  PHE A  36 "
            pdb=" N   PHE A  36 "
            pdb=" C   PHE A  36 "
            pdb=" CB  PHE A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.62e+00
  chirality pdb=" CA  ARG E1120 "
            pdb=" N   ARG E1120 "
            pdb=" C   ARG E1120 "
            pdb=" CB  ARG E1120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.23e+00
  chirality pdb=" CA  LEU E1041 "
            pdb=" N   LEU E1041 "
            pdb=" C   LEU E1041 "
            pdb=" CB  LEU E1041 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 1807 not shown)

  Planarity restraints: 2147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN A 401 "    0.637 2.00e-02 2.50e+03   2.37e-01 2.54e+03
        pdb=" C10 FMN A 401 "    0.033 2.00e-02 2.50e+03
        pdb=" C2  FMN A 401 "   -0.219 2.00e-02 2.50e+03
        pdb=" C4  FMN A 401 "    0.190 2.00e-02 2.50e+03
        pdb=" C4A FMN A 401 "    0.145 2.00e-02 2.50e+03
        pdb=" C5A FMN A 401 "    0.100 2.00e-02 2.50e+03
        pdb=" C6  FMN A 401 "    0.041 2.00e-02 2.50e+03
        pdb=" C7  FMN A 401 "   -0.069 2.00e-02 2.50e+03
        pdb=" C7M FMN A 401 "   -0.120 2.00e-02 2.50e+03
        pdb=" C8  FMN A 401 "   -0.139 2.00e-02 2.50e+03
        pdb=" C8M FMN A 401 "   -0.274 2.00e-02 2.50e+03
        pdb=" C9  FMN A 401 "   -0.076 2.00e-02 2.50e+03
        pdb=" C9A FMN A 401 "    0.051 2.00e-02 2.50e+03
        pdb=" N1  FMN A 401 "   -0.150 2.00e-02 2.50e+03
        pdb=" N10 FMN A 401 "    0.136 2.00e-02 2.50e+03
        pdb=" N3  FMN A 401 "    0.073 2.00e-02 2.50e+03
        pdb=" N5  FMN A 401 "    0.180 2.00e-02 2.50e+03
        pdb=" O2  FMN A 401 "   -0.540 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN D 401 "   -0.734 2.00e-02 2.50e+03   2.29e-01 2.36e+03
        pdb=" C10 FMN D 401 "    0.027 2.00e-02 2.50e+03
        pdb=" C2  FMN D 401 "    0.199 2.00e-02 2.50e+03
        pdb=" C4  FMN D 401 "   -0.145 2.00e-02 2.50e+03
        pdb=" C4A FMN D 401 "   -0.118 2.00e-02 2.50e+03
        pdb=" C5A FMN D 401 "   -0.102 2.00e-02 2.50e+03
        pdb=" C6  FMN D 401 "   -0.084 2.00e-02 2.50e+03
        pdb=" C7  FMN D 401 "    0.033 2.00e-02 2.50e+03
        pdb=" C7M FMN D 401 "    0.023 2.00e-02 2.50e+03
        pdb=" C8  FMN D 401 "    0.158 2.00e-02 2.50e+03
        pdb=" C8M FMN D 401 "    0.282 2.00e-02 2.50e+03
        pdb=" C9  FMN D 401 "    0.148 2.00e-02 2.50e+03
        pdb=" C9A FMN D 401 "    0.006 2.00e-02 2.50e+03
        pdb=" N1  FMN D 401 "    0.186 2.00e-02 2.50e+03
        pdb=" N10 FMN D 401 "   -0.039 2.00e-02 2.50e+03
        pdb=" N3  FMN D 401 "    0.026 2.00e-02 2.50e+03
        pdb=" N5  FMN D 401 "   -0.194 2.00e-02 2.50e+03
        pdb=" O2  FMN D 401 "    0.328 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 265 "   -0.076 2.00e-02 2.50e+03   4.12e-02 3.40e+01
        pdb=" CG  TYR D 265 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 265 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 265 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 265 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 265 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 265 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR D 265 "   -0.065 2.00e-02 2.50e+03
  ... (remaining 2144 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3449
        2.81 -     3.34: 11340
        3.34 -     3.86: 20008
        3.86 -     4.38: 24770
        4.38 -     4.90: 38841
  Nonbonded interactions: 98408
  Sorted by model distance:
  nonbonded pdb=" N   ILE A 274 "
            pdb=" O   ILE A 274 "
     model   vdw
     2.293 2.496
  nonbonded pdb=" N   ASP E1478 "
            pdb=" OD1 ASP E1478 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" NZ  LYS E1147 "
            pdb=" OD1 ASP E1613 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" OD2 ASP E1074 "
            pdb=" NZ  LYS E1078 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" N   LYS E1147 "
            pdb=" N   GLN E1148 "
     model   vdw
     2.402 2.560
  ... (remaining 98403 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}

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:             5.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.830
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
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      :  0.019   0.193  12222  Z= 1.020
  Angle     :  1.741  16.647  16598  Z= 1.185
  Chirality :  0.097   0.515   1810
  Planarity :  0.012   0.237   2147
  Dihedral  : 10.550  88.924   4516
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  1.84 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.20), residues: 1466
  helix:  0.01 (0.20), residues: 517
  sheet:  0.91 (0.31), residues: 279
  loop :  0.81 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.009   TRP E1323 
 HIS   0.010   0.002   HIS D 122 
 PHE   0.034   0.007   PHE D 162 
 TYR   0.076   0.010   TYR D 265 
 ARG   0.007   0.001   ARG D 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17843 (  547)
  hydrogen bonds       : angle       7.68096 ( 1530)
  covalent geometry    : bond        0.01903 (12222)
  covalent geometry    : angle       1.74142 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   16 MET cc_start: 0.8226 (mtt) cc_final: 0.7939 (mtt)
REVERT: D  103 ILE cc_start: 0.8368 (pt) cc_final: 0.7982 (mt)
REVERT: D  257 MET cc_start: 0.8811 (mmm) cc_final: 0.8443 (mmm)
REVERT: E  984 MET cc_start: 0.5465 (ptm) cc_final: 0.4355 (ppp)
REVERT: E 1018 MET cc_start: 0.7223 (mmm) cc_final: 0.6881 (tpp)
REVERT: E 1079 LEU cc_start: 0.8598 (mt) cc_final: 0.8188 (pp)
REVERT: E 1175 PHE cc_start: 0.9220 (t80) cc_final: 0.8938 (t80)
REVERT: E 1207 TRP cc_start: 0.6880 (m100) cc_final: 0.6320 (m100)
REVERT: E 1241 ASN cc_start: 0.8061 (m-40) cc_final: 0.7489 (m-40)
REVERT: E 1366 MET cc_start: 0.8683 (mmm) cc_final: 0.8459 (mmm)
REVERT: E 1525 MET cc_start: 0.8731 (tpp) cc_final: 0.8380 (tpp)
REVERT: E 1665 MET cc_start: 0.8302 (ttt) cc_final: 0.7846 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.2825
  time to fit residues: 81.3266
Evaluate side-chains
  94 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 132 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 117 GLN
** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1382 HIS
E1560 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.091293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.077860 restraints weight = 48905.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.079625 restraints weight = 26859.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.080783 restraints weight = 17948.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12222  Z= 0.177
  Angle     :  0.692   9.295  16598  Z= 0.372
  Chirality :  0.047   0.182   1810
  Planarity :  0.005   0.058   2147
  Dihedral  :  5.278  32.149   1641
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.25 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  4.97 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.21), residues: 1466
  helix:  1.03 (0.22), residues: 520
  sheet:  0.52 (0.31), residues: 283
  loop :  0.59 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E1518 
 HIS   0.012   0.001   HIS E1382 
 PHE   0.022   0.002   PHE E1150 
 TYR   0.018   0.002   TYR E1036 
 ARG   0.006   0.001   ARG E 904 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05560 (  547)
  hydrogen bonds       : angle       5.62086 ( 1530)
  covalent geometry    : bond        0.00379 (12222)
  covalent geometry    : angle       0.69223 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.7970 (tp) cc_final: 0.7770 (tt)
REVERT: A  141 ILE cc_start: 0.8553 (tt) cc_final: 0.8285 (pt)
REVERT: D   42 PHE cc_start: 0.7389 (m-80) cc_final: 0.6929 (m-80)
REVERT: D  103 ILE cc_start: 0.8785 (pt) cc_final: 0.8423 (mm)
REVERT: E  932 MET cc_start: 0.4608 (mtm) cc_final: 0.3254 (mmt)
REVERT: E  984 MET cc_start: 0.5420 (ptm) cc_final: 0.4772 (ppp)
REVERT: E 1018 MET cc_start: 0.6850 (mmm) cc_final: 0.6300 (tpp)
REVERT: E 1118 PHE cc_start: 0.6156 (m-80) cc_final: 0.5744 (m-80)
REVERT: E 1175 PHE cc_start: 0.8728 (t80) cc_final: 0.8350 (t80)
REVERT: E 1185 MET cc_start: 0.7474 (tpp) cc_final: 0.7021 (ttm)
REVERT: E 1366 MET cc_start: 0.8702 (mmm) cc_final: 0.8452 (mmm)
  outliers start: 24
  outliers final: 14
  residues processed: 144
  average time/residue: 0.2171
  time to fit residues: 47.8676
Evaluate side-chains
  99 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain E residue  977 PHE
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1101 VAL
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1165 LEU
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1226 ASP
Chi-restraints excluded: chain E residue 1281 ASP
Chi-restraints excluded: chain E residue 1396 CYS
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1476 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 144 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 121 optimal weight:    0.2980
   chunk 106 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0170
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN
** E 875 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.090265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.076936 restraints weight = 49813.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.078659 restraints weight = 26827.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.079772 restraints weight = 17844.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12222  Z= 0.135
  Angle     :  0.607   8.429  16598  Z= 0.318
  Chirality :  0.044   0.153   1810
  Planarity :  0.004   0.058   2147
  Dihedral  :  4.705  30.418   1641
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.80 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.61 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.22), residues: 1466
  helix:  1.30 (0.23), residues: 510
  sheet:  0.53 (0.33), residues: 249
  loop :  0.40 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E1076 
 HIS   0.009   0.001   HIS E 998 
 PHE   0.019   0.002   PHE E1150 
 TYR   0.019   0.001   TYR E1098 
 ARG   0.006   0.000   ARG E 891 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  547)
  hydrogen bonds       : angle       5.12219 ( 1530)
  covalent geometry    : bond        0.00293 (12222)
  covalent geometry    : angle       0.60693 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.7300 (pttt) cc_final: 0.7094 (mmmm)
REVERT: D  103 ILE cc_start: 0.8839 (pt) cc_final: 0.8540 (mm)
REVERT: E  932 MET cc_start: 0.5217 (mtm) cc_final: 0.4055 (mmt)
REVERT: E  984 MET cc_start: 0.5638 (ptm) cc_final: 0.4626 (ptp)
REVERT: E 1079 LEU cc_start: 0.8509 (mt) cc_final: 0.8091 (pp)
REVERT: E 1185 MET cc_start: 0.7630 (tpp) cc_final: 0.7146 (ttm)
  outliers start: 12
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2459
  time to fit residues: 39.2040
Evaluate side-chains
  79 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 2.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1583 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 132 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  91 GLN
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1233 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.088049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.074663 restraints weight = 49085.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.076392 restraints weight = 26528.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.077516 restraints weight = 17719.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12222  Z= 0.153
  Angle     :  0.608   8.640  16598  Z= 0.315
  Chirality :  0.044   0.151   1810
  Planarity :  0.004   0.057   2147
  Dihedral  :  4.712  31.269   1641
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.07 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.39 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.22), residues: 1466
  helix:  1.14 (0.23), residues: 524
  sheet:  0.39 (0.31), residues: 272
  loop :  0.18 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E1518 
 HIS   0.004   0.001   HIS E 998 
 PHE   0.014   0.002   PHE D   6 
 TYR   0.016   0.001   TYR E1036 
 ARG   0.004   0.000   ARG E1168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  547)
  hydrogen bonds       : angle       5.03699 ( 1530)
  covalent geometry    : bond        0.00333 (12222)
  covalent geometry    : angle       0.60815 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.7422 (pttt) cc_final: 0.7218 (mmmm)
REVERT: D  103 ILE cc_start: 0.8876 (pt) cc_final: 0.8580 (mm)
REVERT: E  932 MET cc_start: 0.5032 (mtm) cc_final: 0.4289 (mmt)
REVERT: E  948 MET cc_start: 0.3366 (ttt) cc_final: 0.2466 (mmm)
REVERT: E  977 PHE cc_start: 0.6426 (p90) cc_final: 0.5778 (p90)
REVERT: E  984 MET cc_start: 0.5833 (ptm) cc_final: 0.5116 (ptt)
REVERT: E 1079 LEU cc_start: 0.8626 (mt) cc_final: 0.8216 (pp)
REVERT: E 1150 PHE cc_start: 0.7378 (t80) cc_final: 0.7163 (t80)
REVERT: E 1185 MET cc_start: 0.7838 (tpp) cc_final: 0.7485 (ttm)
REVERT: E 1191 MET cc_start: 0.8733 (mmm) cc_final: 0.8508 (mmm)
REVERT: E 1252 MET cc_start: 0.7026 (tpp) cc_final: 0.6826 (tpt)
REVERT: E 1408 MET cc_start: 0.8457 (mmm) cc_final: 0.8227 (tpt)
REVERT: E 1593 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.6468 (p90)
REVERT: E 1607 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8407 (m-80)
  outliers start: 22
  outliers final: 15
  residues processed: 97
  average time/residue: 0.2353
  time to fit residues: 36.3292
Evaluate side-chains
  86 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1226 ASP
Chi-restraints excluded: chain E residue 1396 CYS
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Chi-restraints excluded: chain E residue 1607 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0970
   chunk 133 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1063 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.086387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.072984 restraints weight = 49492.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.074655 restraints weight = 26724.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.075762 restraints weight = 17877.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12222  Z= 0.164
  Angle     :  0.607  10.610  16598  Z= 0.316
  Chirality :  0.045   0.149   1810
  Planarity :  0.004   0.059   2147
  Dihedral  :  4.707  31.707   1641
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.34 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.62 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.21), residues: 1466
  helix:  1.10 (0.23), residues: 522
  sheet:  0.20 (0.31), residues: 280
  loop : -0.01 (0.23), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E1518 
 HIS   0.004   0.001   HIS E 900 
 PHE   0.014   0.001   PHE E 850 
 TYR   0.016   0.001   TYR E 999 
 ARG   0.004   0.000   ARG E1168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  547)
  hydrogen bonds       : angle       4.98888 ( 1530)
  covalent geometry    : bond        0.00363 (12222)
  covalent geometry    : angle       0.60673 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.8037 (t) cc_final: 0.7728 (m)
REVERT: D  103 ILE cc_start: 0.8855 (pt) cc_final: 0.8551 (mm)
REVERT: E  984 MET cc_start: 0.6165 (ptm) cc_final: 0.4776 (ptp)
REVERT: E 1004 ASP cc_start: 0.9153 (p0) cc_final: 0.8889 (p0)
REVERT: E 1018 MET cc_start: 0.6280 (tpp) cc_final: 0.5998 (tpp)
REVERT: E 1150 PHE cc_start: 0.7531 (t80) cc_final: 0.7291 (t80)
REVERT: E 1252 MET cc_start: 0.7101 (tpp) cc_final: 0.6759 (tpt)
REVERT: E 1366 MET cc_start: 0.8763 (mmm) cc_final: 0.8283 (mmm)
REVERT: E 1593 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.6791 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1969
  time to fit residues: 29.8042
Evaluate side-chains
  83 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1396 CYS
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Chi-restraints excluded: chain E residue 1643 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 143 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.087416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.074425 restraints weight = 50780.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.076108 restraints weight = 27574.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.077203 restraints weight = 18380.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12222  Z= 0.142
  Angle     :  0.590  10.102  16598  Z= 0.303
  Chirality :  0.044   0.151   1810
  Planarity :  0.004   0.059   2147
  Dihedral  :  4.680  30.888   1641
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.41 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.32 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1466
  helix:  1.04 (0.23), residues: 524
  sheet:  0.16 (0.31), residues: 280
  loop : -0.04 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E1518 
 HIS   0.004   0.001   HIS E 900 
 PHE   0.011   0.001   PHE E1304 
 TYR   0.018   0.001   TYR E 999 
 ARG   0.003   0.000   ARG E1168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  547)
  hydrogen bonds       : angle       4.90471 ( 1530)
  covalent geometry    : bond        0.00310 (12222)
  covalent geometry    : angle       0.58980 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.7945 (t) cc_final: 0.7631 (m)
REVERT: D  103 ILE cc_start: 0.9007 (pt) cc_final: 0.8714 (mm)
REVERT: E  984 MET cc_start: 0.6065 (ptm) cc_final: 0.4989 (ptp)
REVERT: E 1004 ASP cc_start: 0.9136 (p0) cc_final: 0.8849 (p0)
REVERT: E 1018 MET cc_start: 0.6272 (tpp) cc_final: 0.5953 (tpp)
REVERT: E 1185 MET cc_start: 0.8014 (tpp) cc_final: 0.7534 (ttm)
REVERT: E 1252 MET cc_start: 0.7056 (tpp) cc_final: 0.6849 (tpt)
REVERT: E 1488 LEU cc_start: 0.9318 (mm) cc_final: 0.9072 (mp)
REVERT: E 1593 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.6866 (p90)
  outliers start: 17
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1927
  time to fit residues: 28.3700
Evaluate side-chains
  88 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  313 ILE
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Chi-restraints excluded: chain E residue 1643 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 125 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0020
   chunk 145 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 127 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.087828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.074780 restraints weight = 50795.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.076478 restraints weight = 27436.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.077600 restraints weight = 18294.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.5246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12222  Z= 0.121
  Angle     :  0.577  11.056  16598  Z= 0.292
  Chirality :  0.044   0.152   1810
  Planarity :  0.004   0.057   2147
  Dihedral  :  4.513  29.316   1641
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.68 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.48 %
    Favored  : 89.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.22), residues: 1466
  helix:  1.01 (0.23), residues: 535
  sheet:  0.17 (0.31), residues: 280
  loop : -0.05 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E1207 
 HIS   0.003   0.001   HIS E1169 
 PHE   0.030   0.001   PHE A  36 
 TYR   0.013   0.001   TYR E1036 
 ARG   0.004   0.000   ARG E 978 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  547)
  hydrogen bonds       : angle       4.75063 ( 1530)
  covalent geometry    : bond        0.00265 (12222)
  covalent geometry    : angle       0.57651 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.8153 (t) cc_final: 0.7836 (m)
REVERT: D   16 MET cc_start: 0.7327 (mtt) cc_final: 0.7093 (mtt)
REVERT: D  103 ILE cc_start: 0.8990 (pt) cc_final: 0.8675 (mm)
REVERT: E  932 MET cc_start: 0.3498 (ptt) cc_final: 0.0325 (mmt)
REVERT: E  984 MET cc_start: 0.5917 (ptm) cc_final: 0.5372 (ptp)
REVERT: E  997 MET cc_start: 0.7527 (ppp) cc_final: 0.7113 (ppp)
REVERT: E 1004 ASP cc_start: 0.9115 (p0) cc_final: 0.8795 (p0)
REVERT: E 1185 MET cc_start: 0.8082 (tpp) cc_final: 0.7573 (ttm)
REVERT: E 1191 MET cc_start: 0.8714 (mmm) cc_final: 0.8428 (mmm)
REVERT: E 1531 HIS cc_start: 0.7085 (m170) cc_final: 0.6789 (m170)
REVERT: E 1593 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.6946 (p90)
  outliers start: 17
  outliers final: 13
  residues processed: 88
  average time/residue: 0.2590
  time to fit residues: 37.2814
Evaluate side-chains
  83 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  313 ILE
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1473 SER
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0030
   chunk 88 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 ASN
D 315 HIS
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.087693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.074684 restraints weight = 50742.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.076384 restraints weight = 27348.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.077496 restraints weight = 18166.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12222  Z= 0.112
  Angle     :  0.564  11.689  16598  Z= 0.284
  Chirality :  0.043   0.196   1810
  Planarity :  0.004   0.056   2147
  Dihedral  :  4.400  28.986   1641
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.48 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.25 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1466
  helix:  1.12 (0.23), residues: 526
  sheet:  0.35 (0.32), residues: 266
  loop :  0.07 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E1207 
 HIS   0.004   0.001   HIS E 900 
 PHE   0.018   0.001   PHE A  36 
 TYR   0.012   0.001   TYR E1036 
 ARG   0.004   0.000   ARG E 947 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  547)
  hydrogen bonds       : angle       4.68000 ( 1530)
  covalent geometry    : bond        0.00244 (12222)
  covalent geometry    : angle       0.56432 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.8191 (t) cc_final: 0.7864 (m)
REVERT: D  103 ILE cc_start: 0.9027 (pt) cc_final: 0.8696 (mm)
REVERT: E  932 MET cc_start: 0.3349 (ptt) cc_final: 0.0229 (tpp)
REVERT: E  984 MET cc_start: 0.5883 (ptm) cc_final: 0.5321 (ptp)
REVERT: E  997 MET cc_start: 0.7495 (ppp) cc_final: 0.7049 (ppp)
REVERT: E 1185 MET cc_start: 0.8091 (tpp) cc_final: 0.7483 (ttm)
REVERT: E 1593 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.6958 (p90)
  outliers start: 18
  outliers final: 16
  residues processed: 86
  average time/residue: 0.2334
  time to fit residues: 32.6790
Evaluate side-chains
  86 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 2.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  313 ILE
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1111 LEU
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1473 SER
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0870
   chunk 118 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 122 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.087495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.074476 restraints weight = 50541.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.076152 restraints weight = 27440.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.077269 restraints weight = 18286.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.5614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12222  Z= 0.127
  Angle     :  0.597  12.182  16598  Z= 0.297
  Chirality :  0.044   0.207   1810
  Planarity :  0.004   0.058   2147
  Dihedral  :  4.387  28.244   1641
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.96 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.10 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1466
  helix:  1.02 (0.23), residues: 538
  sheet:  0.32 (0.32), residues: 266
  loop : -0.02 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1076 
 HIS   0.003   0.001   HIS E 900 
 PHE   0.015   0.001   PHE A  36 
 TYR   0.013   0.001   TYR E1036 
 ARG   0.003   0.000   ARG E1168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  547)
  hydrogen bonds       : angle       4.64000 ( 1530)
  covalent geometry    : bond        0.00282 (12222)
  covalent geometry    : angle       0.59683 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 2.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.8016 (t) cc_final: 0.7727 (m)
REVERT: D  103 ILE cc_start: 0.9040 (pt) cc_final: 0.8701 (mm)
REVERT: E  932 MET cc_start: 0.3311 (ptt) cc_final: 0.0393 (tpp)
REVERT: E  984 MET cc_start: 0.6036 (ptm) cc_final: 0.5484 (ptp)
REVERT: E  997 MET cc_start: 0.7584 (ppp) cc_final: 0.7230 (ppp)
REVERT: E 1018 MET cc_start: 0.5981 (tpp) cc_final: 0.5497 (tpp)
REVERT: E 1185 MET cc_start: 0.8084 (tpp) cc_final: 0.7591 (ttm)
REVERT: E 1593 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7038 (p90)
  outliers start: 19
  outliers final: 17
  residues processed: 86
  average time/residue: 0.2938
  time to fit residues: 41.1287
Evaluate side-chains
  86 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 4.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  313 ILE
Chi-restraints excluded: chain E residue 1011 SER
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1117 VAL
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1404 LEU
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1473 SER
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Chi-restraints excluded: chain E residue 1643 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0670
   chunk 44 optimal weight:    0.2980
   chunk 17 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 132 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 140 optimal weight:    0.0010
   overall best weight:    0.2924

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

Flipped N/Q/H residues before XYZ refinement:
** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** 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 = 0.3835 r_free = 0.3835 target = 0.088785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.075797 restraints weight = 50069.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.077473 restraints weight = 27185.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.078605 restraints weight = 18071.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.5747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12222  Z= 0.101
  Angle     :  0.566  12.780  16598  Z= 0.281
  Chirality :  0.043   0.212   1810
  Planarity :  0.004   0.053   2147
  Dihedral  :  4.228  25.801   1641
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.14 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.41 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.22), residues: 1466
  helix:  1.36 (0.23), residues: 516
  sheet:  0.39 (0.32), residues: 266
  loop :  0.09 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1207 
 HIS   0.002   0.001   HIS E 951 
 PHE   0.015   0.001   PHE E1150 
 TYR   0.010   0.001   TYR E1036 
 ARG   0.002   0.000   ARG E 888 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03412 (  547)
  hydrogen bonds       : angle       4.50019 ( 1530)
  covalent geometry    : bond        0.00216 (12222)
  covalent geometry    : angle       0.56573 (16598)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 VAL cc_start: 0.8161 (t) cc_final: 0.7858 (m)
REVERT: D  103 ILE cc_start: 0.9025 (pt) cc_final: 0.8671 (mm)
REVERT: E  932 MET cc_start: 0.2748 (ptt) cc_final: -0.0167 (mmt)
REVERT: E  984 MET cc_start: 0.5923 (ptm) cc_final: 0.5409 (ptp)
REVERT: E  997 MET cc_start: 0.7560 (ppp) cc_final: 0.7174 (ppp)
REVERT: E 1018 MET cc_start: 0.5938 (tpp) cc_final: 0.5350 (tpp)
REVERT: E 1185 MET cc_start: 0.8010 (tpp) cc_final: 0.7648 (ttm)
REVERT: E 1191 MET cc_start: 0.8575 (mmm) cc_final: 0.8339 (mmm)
REVERT: E 1593 TRP cc_start: 0.7946 (OUTLIER) cc_final: 0.7066 (p90)
  outliers start: 13
  outliers final: 11
  residues processed: 89
  average time/residue: 0.2320
  time to fit residues: 33.9949
Evaluate side-chains
  82 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TRP
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  313 ILE
Chi-restraints excluded: chain E residue 1094 LEU
Chi-restraints excluded: chain E residue 1194 VAL
Chi-restraints excluded: chain E residue 1418 LEU
Chi-restraints excluded: chain E residue 1476 CYS
Chi-restraints excluded: chain E residue 1583 TYR
Chi-restraints excluded: chain E residue 1593 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 129 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0030
   chunk 0 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 121 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 875 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.087665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.074298 restraints weight = 49754.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.075986 restraints weight = 26498.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.077108 restraints weight = 17567.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12222  Z= 0.107
  Angle     :  0.577  12.429  16598  Z= 0.284
  Chirality :  0.043   0.210   1810
  Planarity :  0.004   0.055   2147
  Dihedral  :  4.173  24.922   1641
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.21 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.19 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.22), residues: 1466
  helix:  1.36 (0.23), residues: 526
  sheet:  0.40 (0.31), residues: 268
  loop :  0.09 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E1076 
 HIS   0.004   0.001   HIS E 900 
 PHE   0.016   0.001   PHE E1014 
 TYR   0.011   0.001   TYR E1036 
 ARG   0.002   0.000   ARG D  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  547)
  hydrogen bonds       : angle       4.47769 ( 1530)
  covalent geometry    : bond        0.00234 (12222)
  covalent geometry    : angle       0.57678 (16598)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4796.03 seconds
wall clock time: 88 minutes 35.24 seconds (5315.24 seconds total)