Starting phenix.real_space_refine
on Tue May 13 23:44:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jkd_36368/05_2025/8jkd_36368.cif"
  }
  resolution = 2.6
  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=   0.099
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     104      5.16       5
     C    6883      2.51       5
     N    1858      2.21       5
     O    2115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10960
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3688
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 19, 'TRANS': 452}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3629
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 19, 'TRANS': 444}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3643
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 19, 'TRANS': 447}
          Chain breaks: 3
  Time building chain proxies: 7.83, per 1000 atoms: 0.71
  Number of scatterers: 10960
  At special positions: 0
  Unit cell: (90.25, 90.25, 141.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     104     16.00
     O    2115      8.00
     N    1858      7.00
     C    6883      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=35, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1165 " - pdb=" SG  CYS A1198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1169 " - pdb=" SG  CYS A1205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1173 " - pdb=" SG  CYS A1207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1175 " - pdb=" SG  CYS A1180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1193 " - pdb=" SG  CYS A1360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1208 " - pdb=" SG  CYS A1368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1236 " - pdb=" SG  CYS A1246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1305 " - pdb=" SG  CYS A1310 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1452 " - pdb=" SG  CYS A1464 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1455 " - pdb=" SG  CYS A1458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1519 " - pdb=" SG  CYS A1539 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1528 " - pdb=" SG  CYS A1531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1165 " - pdb=" SG  CYS B1198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1169 " - pdb=" SG  CYS B1205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1173 " - pdb=" SG  CYS B1207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1175 " - pdb=" SG  CYS B1180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1193 " - pdb=" SG  CYS B1360 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1208 " - pdb=" SG  CYS B1368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1236 " - pdb=" SG  CYS B1246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1305 " - pdb=" SG  CYS B1310 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1452 " - pdb=" SG  CYS B1464 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1455 " - pdb=" SG  CYS B1458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1519 " - pdb=" SG  CYS B1539 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B1528 " - pdb=" SG  CYS B1531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1169 " - pdb=" SG  CYS C1205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1173 " - pdb=" SG  CYS C1207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1175 " - pdb=" SG  CYS C1180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1193 " - pdb=" SG  CYS C1360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1208 " - pdb=" SG  CYS C1368 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1236 " - pdb=" SG  CYS C1246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1305 " - pdb=" SG  CYS C1310 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1452 " - pdb=" SG  CYS C1464 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1455 " - pdb=" SG  CYS C1458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1519 " - pdb=" SG  CYS C1539 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1528 " - pdb=" SG  CYS C1531 " distance=2.04

  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2626

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 23 sheets defined
      5.4% alpha, 31.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1095 through 1099
      removed outlier: 3.702A  pdb=" N   ASN A1098 " --> pdb=" O   HIS A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1388
    Processing helix  chain 'A' and resid 1390 through 1394
      removed outlier: 3.929A  pdb=" N   ASN A1394 " --> pdb=" O   ASP A1390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1390 through 1394'
    Processing helix  chain 'A' and resid 1524 through 1528
    Processing helix  chain 'B' and resid 1095 through 1099
      removed outlier: 3.727A  pdb=" N   ASN B1098 " --> pdb=" O   HIS B1095 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1377 through 1388
    Processing helix  chain 'B' and resid 1390 through 1394
      removed outlier: 3.943A  pdb=" N   ASN B1394 " --> pdb=" O   ASP B1390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1390 through 1394'
    Processing helix  chain 'B' and resid 1524 through 1528
    Processing helix  chain 'C' and resid 1095 through 1099
      removed outlier: 3.791A  pdb=" N   ASN C1098 " --> pdb=" O   HIS C1095 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1377 through 1388
    Processing helix  chain 'C' and resid 1524 through 1528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1080 through 1081
      removed outlier: 6.235A  pdb=" N   THR A1080 " --> pdb=" O   GLY A1117 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   SER A1119 " --> pdb=" O   THR A1080 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR A1116 " --> pdb=" O   VAL A1137 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   LYS A1131 " --> pdb=" O   LEU A1122 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   VAL A1135 " --> pdb=" O   GLU A1238 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   GLU A1238 " --> pdb=" O   VAL A1135 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   VAL A1137 " --> pdb=" O   CYS A1236 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   CYS A1236 " --> pdb=" O   VAL A1137 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASP A1139 " --> pdb=" O   ILE A1234 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS A1230 " --> pdb=" O   MET A1143 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1245 through 1248
    current: chain 'A' and resid 1409 through 1417
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1086 through 1093
      removed outlier: 3.582A  pdb=" N   THR A1253 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1147 through 1153
      removed outlier: 5.485A  pdb=" N   PHE A1148 " --> pdb=" O   LYS A1225 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LYS A1225 " --> pdb=" O   PHE A1148 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR A1150 " --> pdb=" O   LYS A1223 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET A1220 " --> pdb=" O   HIS A1282 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS A1297 " --> pdb=" O   LEU A1281 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1157 through 1163
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1318 through 1320
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1327 through 1328
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1355 through 1359
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1446 through 1454
      removed outlier: 5.259A  pdb=" N   PHE A1447 " --> pdb=" O   HIS A1469 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   HIS A1469 " --> pdb=" O   PHE A1447 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1480 through 1482
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1080 through 1082
      removed outlier: 6.262A  pdb=" N   THR B1080 " --> pdb=" O   GLY B1117 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   SER B1119 " --> pdb=" O   THR B1080 " (cutoff:3.500A)
      removed outlier: 9.425A  pdb=" N   SER B1082 " --> pdb=" O   SER B1119 " (cutoff:3.500A)
      removed outlier: 13.398A  pdb=" N   ASP B1121 " --> pdb=" O   SER B1082 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   THR B1116 " --> pdb=" O   VAL B1137 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LYS B1131 " --> pdb=" O   LEU B1122 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   VAL B1135 " --> pdb=" O   GLU B1238 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   GLU B1238 " --> pdb=" O   VAL B1135 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   VAL B1137 " --> pdb=" O   CYS B1236 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   CYS B1236 " --> pdb=" O   VAL B1137 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ASP B1139 " --> pdb=" O   ILE B1234 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS B1230 " --> pdb=" O   MET B1143 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   SER B1145 " --> pdb=" O   TYR B1228 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   TYR B1228 " --> pdb=" O   SER B1145 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL B1147 " --> pdb=" O   VAL B1226 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   VAL B1226 " --> pdb=" O   VAL B1147 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLU B1149 " --> pdb=" O   TRP B1224 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   TRP B1224 " --> pdb=" O   GLU B1149 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   LEU B1151 " --> pdb=" O   VAL B1222 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B1222 " --> pdb=" O   LEU B1151 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLY B1153 " --> pdb=" O   MET B1220 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   MET B1220 " --> pdb=" O   GLY B1153 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1245 through 1248
    current: chain 'B' and resid 1297 through 1300
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1297 through 1300
    current: chain 'B' and resid 1409 through 1417
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1409 through 1417
    current: chain 'B' and resid 1494 through 1496
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1086 through 1093
      removed outlier: 3.613A  pdb=" N   THR B1253 " --> pdb=" O   LEU B1264 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1157 through 1163
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1318 through 1320
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1355 through 1359
    Processing sheet with id=AB6, first strand: chain 'B' and resid 1446 through 1454
      removed outlier: 5.042A  pdb=" N   PHE B1447 " --> pdb=" O   HIS B1469 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   HIS B1469 " --> pdb=" O   PHE B1447 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1480 through 1482
    Processing sheet with id=AB8, first strand: chain 'C' and resid 1080 through 1082
      removed outlier: 6.257A  pdb=" N   THR C1080 " --> pdb=" O   GLY C1117 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   SER C1119 " --> pdb=" O   THR C1080 " (cutoff:3.500A)
      removed outlier: 9.667A  pdb=" N   SER C1082 " --> pdb=" O   SER C1119 " (cutoff:3.500A)
      removed outlier: 13.513A  pdb=" N   ASP C1121 " --> pdb=" O   SER C1082 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   THR C1116 " --> pdb=" O   VAL C1137 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   VAL C1135 " --> pdb=" O   GLU C1238 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   GLU C1238 " --> pdb=" O   VAL C1135 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   VAL C1137 " --> pdb=" O   CYS C1236 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   CYS C1236 " --> pdb=" O   VAL C1137 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASP C1139 " --> pdb=" O   ILE C1234 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS C1230 " --> pdb=" O   MET C1143 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   SER C1145 " --> pdb=" O   TYR C1228 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   TYR C1228 " --> pdb=" O   SER C1145 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   VAL C1147 " --> pdb=" O   VAL C1226 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   VAL C1226 " --> pdb=" O   VAL C1147 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   GLU C1149 " --> pdb=" O   TRP C1224 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   TRP C1224 " --> pdb=" O   GLU C1149 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU C1151 " --> pdb=" O   VAL C1222 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL C1222 " --> pdb=" O   LEU C1151 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY C1153 " --> pdb=" O   MET C1220 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   MET C1220 " --> pdb=" O   GLY C1153 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 1245 through 1248
    current: chain 'C' and resid 1297 through 1300
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 1297 through 1300
    current: chain 'C' and resid 1409 through 1417
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 1409 through 1417
    current: chain 'C' and resid 1462 through 1469
    Processing sheet with id=AB9, first strand: chain 'C' and resid 1086 through 1093
    Processing sheet with id=AC1, first strand: chain 'C' and resid 1157 through 1163
    Processing sheet with id=AC2, first strand: chain 'C' and resid 1289 through 1291
      removed outlier: 3.661A  pdb=" N   LYS C1331 " --> pdb=" O   LYS C1328 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 1318 through 1320
    Processing sheet with id=AC4, first strand: chain 'C' and resid 1355 through 1359
      removed outlier: 3.694A  pdb=" N   TYR C1359 " --> pdb=" O   SER C1367 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER C1367 " --> pdb=" O   TYR C1359 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 1480 through 1482

    258 hydrogen bonds defined for protein.
    684 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: 4.23

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3562
        1.34 -     1.47: 2635
        1.47 -     1.59: 4872
        1.59 -     1.71: 0
        1.71 -     1.83: 134
  Bond restraints: 11203
  Sorted by residual:
  bond pdb=" CB  CYS B1539 "
       pdb=" SG  CYS B1539 "
    ideal  model  delta    sigma   weight residual
    1.808  1.766  0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  ASP B1317 "
       pdb=" CG  ASP B1317 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.20e+00
  bond pdb=" CB  CYS A1519 "
       pdb=" SG  CYS A1519 "
    ideal  model  delta    sigma   weight residual
    1.808  1.773  0.035 3.30e-02 9.18e+02 1.10e+00
  bond pdb=" CB  CYS A1539 "
       pdb=" SG  CYS A1539 "
    ideal  model  delta    sigma   weight residual
    1.808  1.774  0.034 3.30e-02 9.18e+02 1.07e+00
  bond pdb=" CB  CYS B1519 "
       pdb=" SG  CYS B1519 "
    ideal  model  delta    sigma   weight residual
    1.808  1.775  0.033 3.30e-02 9.18e+02 1.03e+00
  ... (remaining 11198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 14814
        1.80 -     3.61: 326
        3.61 -     5.41: 37
        5.41 -     7.22: 6
        7.22 -     9.02: 2
  Bond angle restraints: 15185
  Sorted by residual:
  angle pdb=" CA  CYS B1519 "
        pdb=" CB  CYS B1519 "
        pdb=" SG  CYS B1519 "
      ideal   model   delta    sigma   weight residual
     114.40  120.76   -6.36 2.30e+00 1.89e-01 7.65e+00
  angle pdb=" C   LEU A1518 "
        pdb=" N   CYS A1519 "
        pdb=" CA  CYS A1519 "
      ideal   model   delta    sigma   weight residual
     121.40  117.20    4.20 1.52e+00 4.33e-01 7.63e+00
  angle pdb=" CA  LEU A1215 "
        pdb=" CB  LEU A1215 "
        pdb=" CG  LEU A1215 "
      ideal   model   delta    sigma   weight residual
     116.30  125.32   -9.02 3.50e+00 8.16e-02 6.65e+00
  angle pdb=" C   GLY C1406 "
        pdb=" N   ASP C1407 "
        pdb=" CA  ASP C1407 "
      ideal   model   delta    sigma   weight residual
     121.54  126.12   -4.58 1.91e+00 2.74e-01 5.74e+00
  angle pdb=" CA  CYS A1519 "
        pdb=" CB  CYS A1519 "
        pdb=" SG  CYS A1519 "
      ideal   model   delta    sigma   weight residual
     114.40  119.88   -5.48 2.30e+00 1.89e-01 5.68e+00
  ... (remaining 15180 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 6072
       17.82 -    35.64: 594
       35.64 -    53.46: 110
       53.46 -    71.28: 17
       71.28 -    89.10: 10
  Dihedral angle restraints: 6803
    sinusoidal: 2748
      harmonic: 4055
  Sorted by residual:
  dihedral pdb=" CB  CYS B1528 "
           pdb=" SG  CYS B1528 "
           pdb=" SG  CYS B1531 "
           pdb=" CB  CYS B1531 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.58  -86.58     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS C1455 "
           pdb=" SG  CYS C1455 "
           pdb=" SG  CYS C1458 "
           pdb=" CB  CYS C1458 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -161.36   75.36     1      1.00e+01 1.00e-02 7.17e+01
  dihedral pdb=" CB  CYS B1455 "
           pdb=" SG  CYS B1455 "
           pdb=" SG  CYS B1458 "
           pdb=" CB  CYS B1458 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.32   56.32     1      1.00e+01 1.00e-02 4.28e+01
  ... (remaining 6800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1042
       0.033 -    0.066: 436
       0.066 -    0.100: 142
       0.100 -    0.133: 88
       0.133 -    0.166: 12
  Chirality restraints: 1720
  Sorted by residual:
  chirality pdb=" CA  ILE B1468 "
            pdb=" N   ILE B1468 "
            pdb=" C   ILE B1468 "
            pdb=" CB  ILE B1468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.90e-01
  chirality pdb=" CA  ILE A1552 "
            pdb=" N   ILE A1552 "
            pdb=" C   ILE A1552 "
            pdb=" CB  ILE A1552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.71e-01
  chirality pdb=" CA  ILE C1468 "
            pdb=" N   ILE C1468 "
            pdb=" C   ILE C1468 "
            pdb=" CB  ILE C1468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  ... (remaining 1717 not shown)

  Planarity restraints: 1921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C1365 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.18e+00
        pdb=" N   PRO C1366 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C1366 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C1366 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1194 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO A1195 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A1195 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1195 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C1215 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   LEU C1215 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LEU C1215 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PHE C1216 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1918 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 866
        2.75 -     3.28: 9922
        3.28 -     3.82: 18268
        3.82 -     4.36: 22785
        4.36 -     4.90: 39406
  Nonbonded interactions: 91247
  Sorted by model distance:
  nonbonded pdb=" OG  SER C1302 "
            pdb=" OE1 GLU C1388 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER A1302 "
            pdb=" OE1 GLU A1388 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE1 GLN C1319 "
            pdb=" OH  TYR C1321 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ARG A1189 "
            pdb=" N   GLY A1202 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OG1 THR A1164 "
            pdb=" O   GLY A1167 "
     model   vdw
     2.252 3.040
  ... (remaining 91242 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' and (resid 1078 through 1196 or resid 1202 through 1327 or resid 1344 \ 
 through 1559))
  selection = (chain 'B' and (resid 1078 through 1125 or resid 1129 through 1196 or resid 1202 \ 
 through 1559))
  selection = (chain 'C' and (resid 1078 through 1125 or resid 1129 through 1327 or resid 1344 \ 
 through 1559))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.860
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.110
  Find NCS groups from input model:        0.600
  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:13.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11238  Z= 0.136
  Angle     :  0.639   9.025  15255  Z= 0.343
  Chirality :  0.046   0.166   1720
  Planarity :  0.005   0.062   1921
  Dihedral  : 14.089  89.103   4072
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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: -0.71 (0.23), residues: 1383
  helix:  0.82 (1.09), residues: 33
  sheet:  0.49 (0.22), residues: 638
  loop : -1.49 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1197 
 HIS   0.004   0.001   HIS C1469 
 PHE   0.028   0.002   PHE B1447 
 TYR   0.013   0.001   TYR A1359 
 ARG   0.004   0.000   ARG B1401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10344 (  258)
  hydrogen bonds       : angle       6.27023 (  684)
  SS BOND              : bond        0.00306 (   35)
  SS BOND              : angle       1.57476 (   70)
  covalent geometry    : bond        0.00307 (11203)
  covalent geometry    : angle       0.63158 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
REVERT: A 1191 TRP cc_start: 0.6859 (p-90) cc_final: 0.5591 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 1.3131
  time to fit residues: 235.6108
Evaluate side-chains
  122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1333 ASN
A1377 ASN
A1378 HIS
A1546 GLN
B1156 GLN
B1375 GLN
C1245 GLN
C1296 GLN
C1394 ASN
C1546 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.154629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124799 restraints weight = 11356.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.65
r_work: 0.3275 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  11238  Z= 0.192
  Angle     :  0.688  12.959  15255  Z= 0.360
  Chirality :  0.048   0.263   1720
  Planarity :  0.005   0.054   1921
  Dihedral  :  5.916  22.971   1477
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.76 %
    Favored  : 89.09 %
  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: -0.71 (0.22), residues: 1383
  helix:  0.60 (1.12), residues: 33
  sheet:  0.59 (0.22), residues: 611
  loop : -1.51 (0.21), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1197 
 HIS   0.005   0.001   HIS C1312 
 PHE   0.014   0.002   PHE C1381 
 TYR   0.017   0.002   TYR B1359 
 ARG   0.003   0.000   ARG A1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  258)
  hydrogen bonds       : angle       5.51416 (  684)
  SS BOND              : bond        0.00368 (   35)
  SS BOND              : angle       1.56431 (   70)
  covalent geometry    : bond        0.00466 (11203)
  covalent geometry    : angle       0.68151 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.393 
Fit side-chains
REVERT: A 1177 SER cc_start: 0.8395 (t) cc_final: 0.8167 (p)
REVERT: A 1387 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8961 (mt)
REVERT: A 1412 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7635 (p0)
REVERT: B 1306 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8399 (mtpm)
REVERT: B 1401 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8204 (ttm170)
  outliers start: 27
  outliers final: 6
  residues processed: 150
  average time/residue: 1.3777
  time to fit residues: 221.6800
Evaluate side-chains
  128 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1401 ARG
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 117 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1378 HIS
A1546 GLN
B1156 GLN
C1296 GLN
C1377 ASN
C1394 ASN
C1554 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.154029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124269 restraints weight = 11569.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.65
r_work: 0.3271 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  11238  Z= 0.185
  Angle     :  0.668  11.985  15255  Z= 0.349
  Chirality :  0.047   0.264   1720
  Planarity :  0.005   0.050   1921
  Dihedral  :  5.875  24.171   1477
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.66 %
    Favored  : 84.71 %
  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: -0.75 (0.22), residues: 1383
  helix:  0.50 (1.12), residues: 33
  sheet:  0.58 (0.22), residues: 624
  loop : -1.60 (0.20), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1197 
 HIS   0.006   0.001   HIS A1378 
 PHE   0.014   0.002   PHE C1381 
 TYR   0.013   0.002   TYR B1150 
 ARG   0.003   0.000   ARG C1525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  258)
  hydrogen bonds       : angle       5.41966 (  684)
  SS BOND              : bond        0.00434 (   35)
  SS BOND              : angle       1.42494 (   70)
  covalent geometry    : bond        0.00448 (11203)
  covalent geometry    : angle       0.66213 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A 1138 MET cc_start: 0.8501 (mtp) cc_final: 0.8282 (ttm)
REVERT: A 1333 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7392 (t0)
REVERT: A 1387 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8902 (mt)
REVERT: A 1412 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7756 (p0)
REVERT: A 1486 ASP cc_start: 0.7612 (m-30) cc_final: 0.7048 (t0)
REVERT: B 1306 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (mtpm)
REVERT: C 1138 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (ttp)
REVERT: C 1387 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8841 (mp)
  outliers start: 33
  outliers final: 13
  residues processed: 146
  average time/residue: 1.3897
  time to fit residues: 217.4819
Evaluate side-chains
  134 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1333 ASN
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1131 LYS
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1387 ILE
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1516 THR
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 133 optimal weight:    0.0980
   chunk 80 optimal weight:    3.9990
   chunk 127 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 120 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 115 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A1194 ASN
A1378 HIS
A1546 GLN
B1156 GLN
B1182 HIS
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125846 restraints weight = 11454.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.65
r_work: 0.3289 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  11238  Z= 0.145
  Angle     :  0.619  10.705  15255  Z= 0.323
  Chirality :  0.045   0.265   1720
  Planarity :  0.005   0.049   1921
  Dihedral  :  5.595  29.233   1477
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.41 %
    Favored  : 83.20 %
  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: -0.66 (0.23), residues: 1383
  helix:  0.54 (1.12), residues: 33
  sheet:  0.65 (0.22), residues: 618
  loop : -1.52 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.012   0.002   PHE B1507 
 TYR   0.018   0.002   TYR A1358 
 ARG   0.002   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  258)
  hydrogen bonds       : angle       5.23336 (  684)
  SS BOND              : bond        0.00370 (   35)
  SS BOND              : angle       1.45227 (   70)
  covalent geometry    : bond        0.00350 (11203)
  covalent geometry    : angle       0.61276 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 1.329 
Fit side-chains
REVERT: A 1232 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8036 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7827 (m-40) cc_final: 0.7352 (t0)
REVERT: A 1387 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8886 (mt)
REVERT: A 1412 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7644 (p0)
REVERT: A 1486 ASP cc_start: 0.7642 (m-30) cc_final: 0.7161 (t0)
REVERT: A 1545 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7647 (tt0)
REVERT: B 1306 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8260 (mtpm)
REVERT: B 1375 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7791 (tm130)
REVERT: C 1138 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8398 (ttp)
  outliers start: 30
  outliers final: 13
  residues processed: 147
  average time/residue: 1.3908
  time to fit residues: 219.7381
Evaluate side-chains
  138 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1131 LYS
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1375 GLN
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1516 THR
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 66 optimal weight:    0.0970
   chunk 124 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A1378 HIS
A1546 GLN
B1156 GLN
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.149184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.117697 restraints weight = 10750.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.62
r_work: 0.3159 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  11238  Z= 0.180
  Angle     :  0.660  11.865  15255  Z= 0.344
  Chirality :  0.047   0.290   1720
  Planarity :  0.005   0.049   1921
  Dihedral  :  5.771  27.427   1477
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.13 %
    Favored  : 82.09 %
  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: 1383
  helix:  0.57 (1.13), residues: 33
  sheet:  0.58 (0.22), residues: 619
  loop : -1.47 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1197 
 HIS   0.006   0.001   HIS A1378 
 PHE   0.014   0.002   PHE C1381 
 TYR   0.020   0.002   TYR A1358 
 ARG   0.002   0.000   ARG C1525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  258)
  hydrogen bonds       : angle       5.26366 (  684)
  SS BOND              : bond        0.00414 (   35)
  SS BOND              : angle       1.56980 (   70)
  covalent geometry    : bond        0.00437 (11203)
  covalent geometry    : angle       0.65274 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
REVERT: A 1232 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8022 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7873 (m-40) cc_final: 0.7341 (t0)
REVERT: A 1387 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8861 (mt)
REVERT: A 1412 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7686 (p0)
REVERT: A 1486 ASP cc_start: 0.7664 (m-30) cc_final: 0.7164 (t0)
REVERT: A 1545 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7678 (mt-10)
REVERT: B 1306 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8310 (mtpm)
REVERT: B 1375 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7795 (tm130)
REVERT: C 1138 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8508 (ttp)
  outliers start: 35
  outliers final: 15
  residues processed: 153
  average time/residue: 1.4180
  time to fit residues: 232.9049
Evaluate side-chains
  140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1156 GLN
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1375 GLN
Chi-restraints excluded: chain B residue 1408 THR
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 137 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A1378 HIS
A1546 GLN
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.150466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.118977 restraints weight = 10834.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.64
r_work: 0.3171 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082  11238  Z= 0.151
  Angle     :  0.657  18.858  15255  Z= 0.340
  Chirality :  0.046   0.288   1720
  Planarity :  0.004   0.048   1921
  Dihedral  :  5.582  26.608   1477
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.24 %
    Favored  : 81.13 %
  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: -0.63 (0.23), residues: 1383
  helix:  0.60 (1.12), residues: 33
  sheet:  0.61 (0.22), residues: 624
  loop : -1.45 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.015   0.002   PHE A1216 
 TYR   0.022   0.002   TYR A1358 
 ARG   0.002   0.000   ARG B1155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  258)
  hydrogen bonds       : angle       5.24603 (  684)
  SS BOND              : bond        0.00473 (   35)
  SS BOND              : angle       1.97957 (   70)
  covalent geometry    : bond        0.00371 (11203)
  covalent geometry    : angle       0.64454 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
REVERT: A 1140 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8649 (tp)
REVERT: A 1232 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8045 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7831 (m-40) cc_final: 0.7311 (t0)
REVERT: A 1412 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7668 (p0)
REVERT: A 1486 ASP cc_start: 0.7655 (m-30) cc_final: 0.7197 (t0)
REVERT: A 1545 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7682 (mt-10)
REVERT: B 1113 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7880 (mt-10)
REVERT: B 1156 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7666 (mp10)
REVERT: B 1306 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (mtpm)
REVERT: C 1138 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8489 (ttp)
REVERT: C 1465 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7719 (mptt)
REVERT: C 1499 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6406 (mp)
  outliers start: 33
  outliers final: 14
  residues processed: 149
  average time/residue: 1.3009
  time to fit residues: 208.7387
Evaluate side-chains
  142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1394 ASN
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1113 GLU
Chi-restraints excluded: chain B residue 1156 GLN
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1408 THR
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1277 GLU
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1465 LYS
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1499 LEU
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 125 optimal weight:    0.1980
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 120 optimal weight:    0.0970
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A1378 HIS
A1546 GLN
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.127414 restraints weight = 11616.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.65
r_work: 0.3320 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  11238  Z= 0.136
  Angle     :  0.632  16.231  15255  Z= 0.326
  Chirality :  0.045   0.276   1720
  Planarity :  0.004   0.046   1921
  Dihedral  :  5.410  25.668   1477
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.16 %
    Favored  : 80.73 %
  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: -0.60 (0.23), residues: 1383
  helix:  0.63 (1.11), residues: 33
  sheet:  0.60 (0.22), residues: 625
  loop : -1.40 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.018   0.002   PHE A1216 
 TYR   0.022   0.001   TYR A1358 
 ARG   0.001   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03245 (  258)
  hydrogen bonds       : angle       5.18599 (  684)
  SS BOND              : bond        0.00439 (   35)
  SS BOND              : angle       1.78415 (   70)
  covalent geometry    : bond        0.00333 (11203)
  covalent geometry    : angle       0.62149 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1140 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8619 (tp)
REVERT: A 1232 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8009 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7755 (m-40) cc_final: 0.7258 (t0)
REVERT: A 1387 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8867 (mt)
REVERT: A 1412 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7587 (p0)
REVERT: A 1486 ASP cc_start: 0.7625 (m-30) cc_final: 0.7215 (t0)
REVERT: A 1545 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7841 (mt-10)
REVERT: B 1113 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7811 (mt-10)
REVERT: B 1156 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7641 (mp10)
REVERT: B 1306 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8278 (mtpm)
REVERT: C 1138 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8409 (ttp)
REVERT: C 1465 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7784 (mptt)
REVERT: C 1499 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6543 (mp)
  outliers start: 39
  outliers final: 15
  residues processed: 159
  average time/residue: 1.2836
  time to fit residues: 220.1113
Evaluate side-chains
  149 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1394 ASN
Chi-restraints excluded: chain A residue 1412 ASP
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1081 VAL
Chi-restraints excluded: chain B residue 1113 GLU
Chi-restraints excluded: chain B residue 1131 LYS
Chi-restraints excluded: chain B residue 1156 GLN
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1277 GLU
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1465 LYS
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1499 LEU
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 112 optimal weight:    0.0870
   chunk 65 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 114 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 57 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 133 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
A1378 HIS
A1546 GLN
C1394 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.153832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122526 restraints weight = 10732.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.62
r_work: 0.3215 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  11238  Z= 0.115
  Angle     :  0.622  16.161  15255  Z= 0.319
  Chirality :  0.044   0.254   1720
  Planarity :  0.004   0.046   1921
  Dihedral  :  5.298  36.778   1477
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.12 %
    Favored  : 80.25 %
  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 (0.23), residues: 1383
  helix:  0.73 (1.11), residues: 33
  sheet:  0.59 (0.22), residues: 619
  loop : -1.33 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.014   0.001   PHE A1216 
 TYR   0.023   0.001   TYR A1358 
 ARG   0.002   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03030 (  258)
  hydrogen bonds       : angle       5.10570 (  684)
  SS BOND              : bond        0.00441 (   35)
  SS BOND              : angle       2.00021 (   70)
  covalent geometry    : bond        0.00276 (11203)
  covalent geometry    : angle       0.60888 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1140 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8625 (tp)
REVERT: A 1232 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8026 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7532 (m-40) cc_final: 0.7100 (t0)
REVERT: A 1387 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8831 (mt)
REVERT: A 1486 ASP cc_start: 0.7631 (m-30) cc_final: 0.7171 (t0)
REVERT: A 1545 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7684 (tt0)
REVERT: B 1156 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7607 (mp10)
REVERT: B 1306 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8214 (mtpm)
REVERT: C 1138 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8493 (ttp)
REVERT: C 1465 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7743 (mptt)
REVERT: C 1499 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6440 (mp)
  outliers start: 33
  outliers final: 12
  residues processed: 154
  average time/residue: 1.2657
  time to fit residues: 210.0334
Evaluate side-chains
  142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1394 ASN
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1156 GLN
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1277 GLU
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1465 LYS
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1499 LEU
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0030
   chunk 108 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.0792

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

Flipped N/Q/H residues before XYZ refinement:
A1322 HIS
A1378 HIS
A1546 GLN
B1156 GLN
C1394 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.155582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.126017 restraints weight = 11485.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.63
r_work: 0.3295 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  11238  Z= 0.184
  Angle     :  0.714  17.914  15255  Z= 0.366
  Chirality :  0.047   0.288   1720
  Planarity :  0.005   0.048   1921
  Dihedral  :  5.792  36.338   1477
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.83 %
    Favored  : 79.94 %
  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: -0.63 (0.23), residues: 1383
  helix:  0.59 (1.11), residues: 33
  sheet:  0.50 (0.22), residues: 609
  loop : -1.30 (0.21), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A1197 
 HIS   0.007   0.001   HIS A1378 
 PHE   0.018   0.002   PHE A1216 
 TYR   0.024   0.002   TYR A1358 
 ARG   0.004   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03549 (  258)
  hydrogen bonds       : angle       5.27151 (  684)
  SS BOND              : bond        0.00504 (   35)
  SS BOND              : angle       2.17446 (   70)
  covalent geometry    : bond        0.00449 (11203)
  covalent geometry    : angle       0.70057 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1140 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8645 (tp)
REVERT: A 1232 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7998 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7848 (m-40) cc_final: 0.7350 (t0)
REVERT: A 1387 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8886 (mt)
REVERT: A 1486 ASP cc_start: 0.7662 (m-30) cc_final: 0.7208 (t0)
REVERT: A 1545 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7743 (tt0)
REVERT: B 1306 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (mtpm)
REVERT: B 1433 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8677 (mtm)
REVERT: C 1138 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8422 (ttp)
REVERT: C 1499 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6531 (mp)
  outliers start: 28
  outliers final: 14
  residues processed: 147
  average time/residue: 1.3083
  time to fit residues: 207.7267
Evaluate side-chains
  139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1394 ASN
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1433 MET
Chi-restraints excluded: chain B residue 1462 ILE
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1499 LEU
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 115 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 119 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1322 HIS
A1378 HIS
A1546 GLN
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.156966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.127426 restraints weight = 11442.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.64
r_work: 0.3314 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  11238  Z= 0.144
  Angle     :  0.662  16.762  15255  Z= 0.340
  Chirality :  0.045   0.271   1720
  Planarity :  0.004   0.048   1921
  Dihedral  :  5.575  36.736   1477
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.07 %
    Favored  : 79.70 %
  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: -0.65 (0.23), residues: 1383
  helix:  0.64 (1.11), residues: 33
  sheet:  0.49 (0.22), residues: 627
  loop : -1.37 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.013   0.002   PHE C1216 
 TYR   0.026   0.002   TYR A1358 
 ARG   0.003   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03277 (  258)
  hydrogen bonds       : angle       5.19690 (  684)
  SS BOND              : bond        0.00476 (   35)
  SS BOND              : angle       1.97400 (   70)
  covalent geometry    : bond        0.00352 (11203)
  covalent geometry    : angle       0.64949 (15185)

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

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

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2766 Ramachandran restraints generated.
    1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1129 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4533 (pp20)
REVERT: A 1140 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8628 (tp)
REVERT: A 1232 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7978 (mt-10)
REVERT: A 1333 ASN cc_start: 0.7770 (m-40) cc_final: 0.7286 (t0)
REVERT: A 1387 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8890 (mt)
REVERT: A 1486 ASP cc_start: 0.7625 (m-30) cc_final: 0.7227 (t0)
REVERT: A 1545 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7826 (tt0)
REVERT: B 1156 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7685 (mp10)
REVERT: B 1306 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8299 (mtpm)
REVERT: C 1138 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8387 (ttp)
REVERT: C 1465 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7786 (mptt)
REVERT: C 1499 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6493 (mp)
  outliers start: 28
  outliers final: 14
  residues processed: 142
  average time/residue: 1.2569
  time to fit residues: 192.9154
Evaluate side-chains
  142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1129 GLU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1226 VAL
Chi-restraints excluded: chain A residue 1232 GLU
Chi-restraints excluded: chain A residue 1387 ILE
Chi-restraints excluded: chain A residue 1394 ASN
Chi-restraints excluded: chain A residue 1539 CYS
Chi-restraints excluded: chain A residue 1552 ILE
Chi-restraints excluded: chain B residue 1156 GLN
Chi-restraints excluded: chain B residue 1193 CYS
Chi-restraints excluded: chain B residue 1215 LEU
Chi-restraints excluded: chain B residue 1302 SER
Chi-restraints excluded: chain B residue 1306 LYS
Chi-restraints excluded: chain B residue 1462 ILE
Chi-restraints excluded: chain C residue 1102 VAL
Chi-restraints excluded: chain C residue 1138 MET
Chi-restraints excluded: chain C residue 1369 THR
Chi-restraints excluded: chain C residue 1392 THR
Chi-restraints excluded: chain C residue 1465 LYS
Chi-restraints excluded: chain C residue 1480 VAL
Chi-restraints excluded: chain C residue 1499 LEU
Chi-restraints excluded: chain C residue 1531 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 133 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 28 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0980
   chunk 11 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A1378 HIS
A1546 GLN
C1296 GLN
C1394 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.128168 restraints weight = 11373.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.63
r_work: 0.3330 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  11238  Z= 0.136
  Angle     :  0.650  16.340  15255  Z= 0.334
  Chirality :  0.045   0.263   1720
  Planarity :  0.004   0.048   1921
  Dihedral  :  5.466  36.390   1477
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.15 %
    Favored  : 79.86 %
  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: -0.62 (0.23), residues: 1383
  helix:  0.67 (1.11), residues: 33
  sheet:  0.53 (0.22), residues: 621
  loop : -1.35 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A1197 
 HIS   0.005   0.001   HIS A1378 
 PHE   0.013   0.002   PHE B1507 
 TYR   0.025   0.002   TYR A1358 
 ARG   0.003   0.000   ARG C1115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  258)
  hydrogen bonds       : angle       5.15944 (  684)
  SS BOND              : bond        0.00460 (   35)
  SS BOND              : angle       1.89518 (   70)
  covalent geometry    : bond        0.00331 (11203)
  covalent geometry    : angle       0.63818 (15185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7902.15 seconds
wall clock time: 136 minutes 58.68 seconds (8218.68 seconds total)