Starting phenix.real_space_refine
on Sat Jun 28 02:21:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ixo_35800/06_2025/8ixo_35800.cif"
  }
  resolution = 4.0
  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=   0.107 sd=   1.308
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      15      5.49       5
     S     168      5.16       5
     C   21108      2.51       5
     N    5265      2.21       5
     O    5580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 1.16s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 32136
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10449
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1395, 10441
          Classifications: {'peptide': 1395}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 272}
          Link IDs: {'PTRANS': 54, 'TRANS': 1340}
          Chain breaks: 13
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1092
          Unresolved non-hydrogen angles: 1410
          Unresolved non-hydrogen dihedrals: 930
          Unresolved non-hydrogen chiralities: 106
          Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 5, 'TYR:plan': 16, 'ASN:plan1': 7, 'TRP:plan': 6, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 15, 'ARG:plan': 28}
          Unresolved non-hydrogen planarities: 612
      Conformer: "B"
        Number of residues, atoms: 1395, 10441
          Classifications: {'peptide': 1395}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 272}
          Link IDs: {'PTRANS': 54, 'TRANS': 1340}
          Chain breaks: 13
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1092
          Unresolved non-hydrogen angles: 1410
          Unresolved non-hydrogen dihedrals: 930
          Unresolved non-hydrogen chiralities: 106
          Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 5, 'TYR:plan': 16, 'ASN:plan1': 7, 'TRP:plan': 6, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 15, 'ARG:plan': 28}
          Unresolved non-hydrogen planarities: 612
          bond proxies already assigned to first conformer: 10663
    Chain: "A"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 263
          Unusual residues: {'PEE': 1, 'PLX': 2}
          Classifications: {'peptide': 2, 'undetermined': 3}
          Link IDs: {'TRANS': 1, None: 3}
            Not linked:
              pdbres="PLX A2601 "
              pdbres="PLX A2602 "
            Not linked:
              pdbres="PLX A2602 "
              pdbres="P5S A2603 "
            Not linked:
              pdbres="P5S A2604 "
              pdbres="PEE A2605 "
          Chain breaks: 1
  Restraints were copied for chains:
    B, F
  Time building chain proxies: 38.39, per 1000 atoms: 1.19
  Number of scatterers: 32136
  At special positions: 0
  Unit cell: (240.44, 225.07, 144.923, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     168     16.00
     P      15     15.00
     O    5580      8.00
     N    5265      7.00
     C   21108      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 994 " - pdb=" SG  CYS F1103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F1232 " - pdb=" SG  CYS F1253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F2437 " - pdb=" SG  CYS F2441 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 8.54
  Conformation dependent library (CDL) restraints added in 7.5 seconds
  

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  8052

  Finding SS restraints...
    Secondary structure from input PDB file:
      198 helices and 9 sheets defined
      69.6% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.58
  Creating SS restraints...
    Processing helix  chain 'F' and resid 576 through 585
    Processing helix  chain 'F' and resid 586 through 596
    Processing helix  chain 'F' and resid 608 through 625
    Processing helix  chain 'F' and resid 631 through 650
    Processing helix  chain 'F' and resid 691 through 706
    Processing helix  chain 'F' and resid 708 through 715
    Processing helix  chain 'F' and resid 785 through 804
      removed outlier: 3.600A  pdb=" N   SER F 789 " --> pdb=" O   ASP F 785 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 804 through 818
      removed outlier: 3.931A  pdb=" N   HIS F 808 " --> pdb=" O   LEU F 804 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 829 through 838
    Processing helix  chain 'F' and resid 842 through 844
      No H-bonds generated for 'chain 'F' and resid 842 through 844'
    Processing helix  chain 'F' and resid 845 through 868
    Processing helix  chain 'F' and resid 924 through 950
    Processing helix  chain 'F' and resid 967 through 971
      removed outlier: 3.975A  pdb=" N   ASP F 971 " --> pdb=" O   GLN F 968 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 973 through 1006
      removed outlier: 6.564A  pdb=" N   PHE F 986 " --> pdb=" O   ILE F 982 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   TYR F 987 " --> pdb=" O   ASN F 983 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LYS F 988 " --> pdb=" O   PHE F 984 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE F 989 " --> pdb=" O   PHE F 985 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LEU F 991 " --> pdb=" O   TYR F 987 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   GLU F 992 " --> pdb=" O   LYS F 988 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1007 through 1023
      removed outlier: 4.212A  pdb=" N   ARG F1023 " --> pdb=" O   ALA F1019 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1025 through 1052
      Proline residue:  F1034  - end of helix
    Processing helix  chain 'F' and resid 1073 through 1080
    Processing helix  chain 'F' and resid 1093 through 1113
      removed outlier: 3.582A  pdb=" N   ASP F1097 " --> pdb=" O   ASN F1093 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1138 through 1145
      removed outlier: 4.167A  pdb=" N   ASN F1142 " --> pdb=" O   ASN F1138 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   HIS F1145 " --> pdb=" O   PRO F1141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1149 through 1159
      removed outlier: 3.602A  pdb=" N   LEU F1153 " --> pdb=" O   TYR F1149 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1161 through 1175
      removed outlier: 3.781A  pdb=" N   LEU F1166 " --> pdb=" O   PHE F1162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1178 through 1194
    Processing helix  chain 'F' and resid 1194 through 1200
    Processing helix  chain 'F' and resid 1202 through 1233
      removed outlier: 4.268A  pdb=" N   LEU F1229 " --> pdb=" O   ASN F1225 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LEU F1230 " --> pdb=" O   MET F1226 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1234 through 1242
    Processing helix  chain 'F' and resid 1243 through 1249
      removed outlier: 3.742A  pdb=" N   PHE F1249 " --> pdb=" O   VAL F1245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1280 through 1297
      removed outlier: 3.612A  pdb=" N   SER F1284 " --> pdb=" O   ILE F1280 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1300 through 1315
      removed outlier: 4.049A  pdb=" N   HIS F1304 " --> pdb=" O   HIS F1300 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL F1305 " --> pdb=" O   TYR F1301 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1318 through 1363
    Processing helix  chain 'F' and resid 1402 through 1408
    Processing helix  chain 'F' and resid 1411 through 1415
    Processing helix  chain 'F' and resid 1506 through 1524
    Processing helix  chain 'F' and resid 1524 through 1544
    Processing helix  chain 'F' and resid 1656 through 1669
      removed outlier: 3.619A  pdb=" N   GLN F1669 " --> pdb=" O   PHE F1665 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1672 through 1687
    Processing helix  chain 'F' and resid 1688 through 1702
      removed outlier: 4.070A  pdb=" N   TYR F1692 " --> pdb=" O   GLU F1688 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1708 through 1717
    Processing helix  chain 'F' and resid 1728 through 1748
    Processing helix  chain 'F' and resid 1771 through 1775
    Processing helix  chain 'F' and resid 1785 through 1803
    Processing helix  chain 'F' and resid 1957 through 1966
      removed outlier: 3.519A  pdb=" N   LEU F1966 " --> pdb=" O   PHE F1962 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 1977 through 1994
    Processing helix  chain 'F' and resid 1995 through 1999
    Processing helix  chain 'F' and resid 2006 through 2013
      removed outlier: 3.602A  pdb=" N   SER F2010 " --> pdb=" O   ASP F2006 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2017 through 2041
    Processing helix  chain 'F' and resid 2043 through 2061
      removed outlier: 3.616A  pdb=" N   VAL F2055 " --> pdb=" O   VAL F2051 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2063 through 2069
      removed outlier: 3.614A  pdb=" N   THR F2069 " --> pdb=" O   LEU F2065 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2077 through 2100
      removed outlier: 4.064A  pdb=" N   LEU F2081 " --> pdb=" O   ALA F2077 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2115 through 2128
      removed outlier: 3.537A  pdb=" N   VAL F2128 " --> pdb=" O   GLY F2124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2130 through 2143
    Processing helix  chain 'F' and resid 2148 through 2175
      removed outlier: 3.569A  pdb=" N   TYR F2175 " --> pdb=" O   THR F2171 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2184 through 2214
      Proline residue:  F2206  - end of helix
    Processing helix  chain 'F' and resid 2244 through 2246
      No H-bonds generated for 'chain 'F' and resid 2244 through 2246'
    Processing helix  chain 'F' and resid 2252 through 2263
      removed outlier: 3.535A  pdb=" N   PHE F2263 " --> pdb=" O   LEU F2259 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2266 through 2275
    Processing helix  chain 'F' and resid 2276 through 2279
      removed outlier: 6.291A  pdb=" N   GLU F2279 " --> pdb=" O   TYR F2276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 2276 through 2279'
    Processing helix  chain 'F' and resid 2297 through 2311
    Processing helix  chain 'F' and resid 2348 through 2359
    Processing helix  chain 'F' and resid 2422 through 2424
      No H-bonds generated for 'chain 'F' and resid 2422 through 2424'
    Processing helix  chain 'F' and resid 2458 through 2463
    Processing helix  chain 'F' and resid 2465 through 2473
    Processing helix  chain 'F' and resid 2473 through 2484
    Processing helix  chain 'F' and resid 2489 through 2493
      removed outlier: 4.399A  pdb=" N   MET F2493 " --> pdb=" O   HIS F2490 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2500 through 2517
      removed outlier: 3.592A  pdb=" N   GLU F2515 " --> pdb=" O   PHE F2511 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2518 through 2535
    Processing helix  chain 'F' and resid 2535 through 2543
    Processing helix  chain 'A' and resid 577 through 585
    Processing helix  chain 'A' and resid 586 through 596
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 631 through 650
    Processing helix  chain 'A' and resid 691 through 706
    Processing helix  chain 'A' and resid 708 through 715
    Processing helix  chain 'A' and resid 785 through 804
      removed outlier: 3.600A  pdb=" N   SER A 789 " --> pdb=" O   ASP A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 818
      removed outlier: 3.931A  pdb=" N   HIS A 808 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 838
    Processing helix  chain 'A' and resid 842 through 844
      No H-bonds generated for 'chain 'A' and resid 842 through 844'
    Processing helix  chain 'A' and resid 845 through 868
    Processing helix  chain 'A' and resid 924 through 950
    Processing helix  chain 'A' and resid 967 through 971
      removed outlier: 3.975A  pdb=" N   ASP A 971 " --> pdb=" O   GLN A 968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 1006
      removed outlier: 6.564A  pdb=" N   PHE A 986 " --> pdb=" O   ILE A 982 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   TYR A 987 " --> pdb=" O   ASN A 983 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LYS A 988 " --> pdb=" O   PHE A 984 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE A 989 " --> pdb=" O   PHE A 985 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU A 991 " --> pdb=" O   TYR A 987 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   GLU A 992 " --> pdb=" O   LYS A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1023
      removed outlier: 4.212A  pdb=" N   ARG A1023 " --> pdb=" O   ALA A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1052
      Proline residue:  A1034  - end of helix
    Processing helix  chain 'A' and resid 1073 through 1080
    Processing helix  chain 'A' and resid 1093 through 1113
      removed outlier: 3.582A  pdb=" N   ASP A1097 " --> pdb=" O   ASN A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1145
      removed outlier: 4.167A  pdb=" N   ASN A1142 " --> pdb=" O   ASN A1138 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   HIS A1145 " --> pdb=" O   PRO A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1159
      removed outlier: 3.603A  pdb=" N   LEU A1153 " --> pdb=" O   TYR A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1175
      removed outlier: 3.781A  pdb=" N   LEU A1166 " --> pdb=" O   PHE A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1194 through 1200
    Processing helix  chain 'A' and resid 1202 through 1233
      removed outlier: 4.268A  pdb=" N   LEU A1229 " --> pdb=" O   ASN A1225 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU A1230 " --> pdb=" O   MET A1226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1242
    Processing helix  chain 'A' and resid 1243 through 1249
      removed outlier: 3.742A  pdb=" N   PHE A1249 " --> pdb=" O   VAL A1245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1280 through 1297
      removed outlier: 3.612A  pdb=" N   SER A1284 " --> pdb=" O   ILE A1280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1315
      removed outlier: 4.049A  pdb=" N   HIS A1304 " --> pdb=" O   HIS A1300 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL A1305 " --> pdb=" O   TYR A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1318 through 1363
    Processing helix  chain 'A' and resid 1402 through 1408
    Processing helix  chain 'A' and resid 1411 through 1415
    Processing helix  chain 'A' and resid 1506 through 1524
    Processing helix  chain 'A' and resid 1524 through 1544
    Processing helix  chain 'A' and resid 1656 through 1669
      removed outlier: 3.620A  pdb=" N   GLN A1669 " --> pdb=" O   PHE A1665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1672 through 1687
    Processing helix  chain 'A' and resid 1688 through 1702
      removed outlier: 4.070A  pdb=" N   TYR A1692 " --> pdb=" O   GLU A1688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1708 through 1717
    Processing helix  chain 'A' and resid 1728 through 1748
    Processing helix  chain 'A' and resid 1771 through 1775
    Processing helix  chain 'A' and resid 1785 through 1803
    Processing helix  chain 'A' and resid 1957 through 1966
      removed outlier: 3.519A  pdb=" N   LEU A1966 " --> pdb=" O   PHE A1962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1977 through 1994
    Processing helix  chain 'A' and resid 1995 through 1999
    Processing helix  chain 'A' and resid 2006 through 2013
      removed outlier: 3.602A  pdb=" N   SER A2010 " --> pdb=" O   ASP A2006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2017 through 2041
    Processing helix  chain 'A' and resid 2043 through 2061
      removed outlier: 3.617A  pdb=" N   VAL A2055 " --> pdb=" O   VAL A2051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2063 through 2069
      removed outlier: 3.614A  pdb=" N   THR A2069 " --> pdb=" O   LEU A2065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2077 through 2100
      removed outlier: 4.063A  pdb=" N   LEU A2081 " --> pdb=" O   ALA A2077 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2115 through 2128
      removed outlier: 3.537A  pdb=" N   VAL A2128 " --> pdb=" O   GLY A2124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2130 through 2143
    Processing helix  chain 'A' and resid 2148 through 2175
      removed outlier: 3.570A  pdb=" N   TYR A2175 " --> pdb=" O   THR A2171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2184 through 2214
      Proline residue:  A2206  - end of helix
    Processing helix  chain 'A' and resid 2244 through 2246
      No H-bonds generated for 'chain 'A' and resid 2244 through 2246'
    Processing helix  chain 'A' and resid 2252 through 2263
      removed outlier: 3.536A  pdb=" N   PHE A2263 " --> pdb=" O   LEU A2259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2266 through 2275
    Processing helix  chain 'A' and resid 2276 through 2279
      removed outlier: 6.291A  pdb=" N   GLU A2279 " --> pdb=" O   TYR A2276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2276 through 2279'
    Processing helix  chain 'A' and resid 2297 through 2311
    Processing helix  chain 'A' and resid 2348 through 2359
    Processing helix  chain 'A' and resid 2422 through 2424
      No H-bonds generated for 'chain 'A' and resid 2422 through 2424'
    Processing helix  chain 'A' and resid 2458 through 2463
    Processing helix  chain 'A' and resid 2465 through 2473
    Processing helix  chain 'A' and resid 2473 through 2484
    Processing helix  chain 'A' and resid 2489 through 2493
      removed outlier: 4.398A  pdb=" N   MET A2493 " --> pdb=" O   HIS A2490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2500 through 2517
      removed outlier: 3.591A  pdb=" N   GLU A2515 " --> pdb=" O   PHE A2511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2518 through 2535
    Processing helix  chain 'A' and resid 2535 through 2543
    Processing helix  chain 'B' and resid 577 through 585
    Processing helix  chain 'B' and resid 586 through 596
    Processing helix  chain 'B' and resid 608 through 625
    Processing helix  chain 'B' and resid 631 through 650
    Processing helix  chain 'B' and resid 691 through 706
    Processing helix  chain 'B' and resid 708 through 715
    Processing helix  chain 'B' and resid 785 through 804
      removed outlier: 3.601A  pdb=" N   SER B 789 " --> pdb=" O   ASP B 785 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 818
      removed outlier: 3.931A  pdb=" N   HIS B 808 " --> pdb=" O   LEU B 804 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 829 through 838
    Processing helix  chain 'B' and resid 842 through 844
      No H-bonds generated for 'chain 'B' and resid 842 through 844'
    Processing helix  chain 'B' and resid 845 through 868
    Processing helix  chain 'B' and resid 924 through 950
    Processing helix  chain 'B' and resid 967 through 971
      removed outlier: 3.974A  pdb=" N   ASP B 971 " --> pdb=" O   GLN B 968 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 1006
      removed outlier: 6.563A  pdb=" N   PHE B 986 " --> pdb=" O   ILE B 982 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   TYR B 987 " --> pdb=" O   ASN B 983 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LYS B 988 " --> pdb=" O   PHE B 984 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B 989 " --> pdb=" O   PHE B 985 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LEU B 991 " --> pdb=" O   TYR B 987 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   GLU B 992 " --> pdb=" O   LYS B 988 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1007 through 1023
      removed outlier: 4.212A  pdb=" N   ARG B1023 " --> pdb=" O   ALA B1019 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1025 through 1052
      Proline residue:  B1034  - end of helix
    Processing helix  chain 'B' and resid 1073 through 1080
    Processing helix  chain 'B' and resid 1093 through 1113
      removed outlier: 3.582A  pdb=" N   ASP B1097 " --> pdb=" O   ASN B1093 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1138 through 1145
      removed outlier: 4.168A  pdb=" N   ASN B1142 " --> pdb=" O   ASN B1138 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   HIS B1145 " --> pdb=" O   PRO B1141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1149 through 1159
      removed outlier: 3.602A  pdb=" N   LEU B1153 " --> pdb=" O   TYR B1149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1161 through 1175
      removed outlier: 3.781A  pdb=" N   LEU B1166 " --> pdb=" O   PHE B1162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1178 through 1194
    Processing helix  chain 'B' and resid 1194 through 1200
    Processing helix  chain 'B' and resid 1202 through 1233
      removed outlier: 4.269A  pdb=" N   LEU B1229 " --> pdb=" O   ASN B1225 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU B1230 " --> pdb=" O   MET B1226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1234 through 1242
    Processing helix  chain 'B' and resid 1243 through 1249
      removed outlier: 3.741A  pdb=" N   PHE B1249 " --> pdb=" O   VAL B1245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1280 through 1297
      removed outlier: 3.613A  pdb=" N   SER B1284 " --> pdb=" O   ILE B1280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1300 through 1315
      removed outlier: 3.998A  pdb=" N   HIS B1304 " --> pdb=" O   HIS B1300 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL B1305 " --> pdb=" O   TYR B1301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1318 through 1363
    Processing helix  chain 'B' and resid 1402 through 1408
    Processing helix  chain 'B' and resid 1411 through 1415
    Processing helix  chain 'B' and resid 1506 through 1524
    Processing helix  chain 'B' and resid 1524 through 1544
    Processing helix  chain 'B' and resid 1656 through 1669
      removed outlier: 3.620A  pdb=" N   GLN B1669 " --> pdb=" O   PHE B1665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1672 through 1687
    Processing helix  chain 'B' and resid 1688 through 1702
      removed outlier: 4.071A  pdb=" N   TYR B1692 " --> pdb=" O   GLU B1688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1708 through 1717
    Processing helix  chain 'B' and resid 1728 through 1748
    Processing helix  chain 'B' and resid 1771 through 1775
    Processing helix  chain 'B' and resid 1785 through 1803
    Processing helix  chain 'B' and resid 1957 through 1966
      removed outlier: 3.519A  pdb=" N   LEU B1966 " --> pdb=" O   PHE B1962 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1977 through 1994
    Processing helix  chain 'B' and resid 1995 through 1999
    Processing helix  chain 'B' and resid 2006 through 2013
      removed outlier: 3.601A  pdb=" N   SER B2010 " --> pdb=" O   ASP B2006 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2017 through 2041
    Processing helix  chain 'B' and resid 2043 through 2061
      removed outlier: 3.616A  pdb=" N   VAL B2055 " --> pdb=" O   VAL B2051 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2063 through 2069
      removed outlier: 3.614A  pdb=" N   THR B2069 " --> pdb=" O   LEU B2065 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2077 through 2100
      removed outlier: 4.062A  pdb=" N   LEU B2081 " --> pdb=" O   ALA B2077 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2115 through 2128
      removed outlier: 3.537A  pdb=" N   VAL B2128 " --> pdb=" O   GLY B2124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2130 through 2143
    Processing helix  chain 'B' and resid 2148 through 2175
      removed outlier: 3.571A  pdb=" N   TYR B2175 " --> pdb=" O   THR B2171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2184 through 2214
      Proline residue:  B2206  - end of helix
    Processing helix  chain 'B' and resid 2244 through 2246
      No H-bonds generated for 'chain 'B' and resid 2244 through 2246'
    Processing helix  chain 'B' and resid 2252 through 2263
      removed outlier: 3.536A  pdb=" N   PHE B2263 " --> pdb=" O   LEU B2259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2266 through 2275
    Processing helix  chain 'B' and resid 2276 through 2279
      removed outlier: 6.291A  pdb=" N   GLU B2279 " --> pdb=" O   TYR B2276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 2276 through 2279'
    Processing helix  chain 'B' and resid 2297 through 2311
    Processing helix  chain 'B' and resid 2348 through 2359
    Processing helix  chain 'B' and resid 2422 through 2424
      No H-bonds generated for 'chain 'B' and resid 2422 through 2424'
    Processing helix  chain 'B' and resid 2458 through 2463
    Processing helix  chain 'B' and resid 2465 through 2473
    Processing helix  chain 'B' and resid 2473 through 2484
    Processing helix  chain 'B' and resid 2489 through 2493
      removed outlier: 4.399A  pdb=" N   MET B2493 " --> pdb=" O   HIS B2490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2500 through 2517
      removed outlier: 3.592A  pdb=" N   GLU B2515 " --> pdb=" O   PHE B2511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2518 through 2535
    Processing helix  chain 'B' and resid 2535 through 2543
    Processing sheet with id=AA1, first strand: chain 'F' and resid 2237 through 2241
      removed outlier: 7.014A  pdb=" N   LEU F2232 " --> pdb=" O   PRO F2237 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP F2225 " --> pdb=" O   GLN F2324 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR F2336 " --> pdb=" O   PHE F2323 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 2248 through 2250
      removed outlier: 3.510A  pdb=" N   ASN F2385 " --> pdb=" O   ARG F2377 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 2366 through 2372
      removed outlier: 3.589A  pdb=" N   VAL F2366 " --> pdb=" O   ILE F2403 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   HIS F2370 " --> pdb=" O   LEU F2399 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU F2399 " --> pdb=" O   HIS F2370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2237 through 2241
      removed outlier: 7.014A  pdb=" N   LEU A2232 " --> pdb=" O   PRO A2237 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP A2225 " --> pdb=" O   GLN A2324 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR A2336 " --> pdb=" O   PHE A2323 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2248 through 2250
      removed outlier: 3.510A  pdb=" N   ASN A2385 " --> pdb=" O   ARG A2377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2366 through 2372
      removed outlier: 3.589A  pdb=" N   VAL A2366 " --> pdb=" O   ILE A2403 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   HIS A2370 " --> pdb=" O   LEU A2399 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU A2399 " --> pdb=" O   HIS A2370 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2237 through 2241
      removed outlier: 7.015A  pdb=" N   LEU B2232 " --> pdb=" O   PRO B2237 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP B2225 " --> pdb=" O   GLN B2324 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR B2336 " --> pdb=" O   PHE B2323 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 2248 through 2250
      removed outlier: 3.510A  pdb=" N   ASN B2385 " --> pdb=" O   ARG B2377 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 2366 through 2372
      removed outlier: 3.590A  pdb=" N   VAL B2366 " --> pdb=" O   ILE B2403 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   HIS B2370 " --> pdb=" O   LEU B2399 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LEU B2399 " --> pdb=" O   HIS B2370 " (cutoff:3.500A)

    2140 hydrogen bonds defined for protein.
    6363 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: 13.25

  Time building geometry restraints manager: 9.69 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 5492
        1.33 -     1.45: 8452
        1.45 -     1.58: 18582
        1.58 -     1.70: 33
        1.70 -     1.82: 258
  Bond restraints: 32817
  Sorted by residual:
  bond pdb=" C18 PEE F2605 "
       pdb=" C19 PEE F2605 "
    ideal  model  delta    sigma   weight residual
    1.523  1.307  0.216 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" C18 PEE B2605 "
       pdb=" C19 PEE B2605 "
    ideal  model  delta    sigma   weight residual
    1.523  1.307  0.216 2.00e-02 2.50e+03 1.17e+02
  bond pdb=" C18 PEE A2605 "
       pdb=" C19 PEE A2605 "
    ideal  model  delta    sigma   weight residual
    1.523  1.307  0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C38 PEE F2605 "
       pdb=" C39 PEE F2605 "
    ideal  model  delta    sigma   weight residual
    1.523  1.310  0.213 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C38 PEE A2605 "
       pdb=" C39 PEE A2605 "
    ideal  model  delta    sigma   weight residual
    1.523  1.310  0.213 2.00e-02 2.50e+03 1.14e+02
  ... (remaining 32812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 44007
        2.97 -     5.93: 444
        5.93 -     8.90: 69
        8.90 -    11.87: 12
       11.87 -    14.84: 12
  Bond angle restraints: 44544
  Sorted by residual:
  angle pdb=" C38 PEE A2605 "
        pdb=" C39 PEE A2605 "
        pdb=" C40 PEE A2605 "
      ideal   model   delta    sigma   weight residual
     112.47  127.31  -14.84 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" C38 PEE B2605 "
        pdb=" C39 PEE B2605 "
        pdb=" C40 PEE B2605 "
      ideal   model   delta    sigma   weight residual
     112.47  127.30  -14.83 3.00e+00 1.11e-01 2.44e+01
  angle pdb=" C38 PEE F2605 "
        pdb=" C39 PEE F2605 "
        pdb=" C40 PEE F2605 "
      ideal   model   delta    sigma   weight residual
     112.47  127.29  -14.82 3.00e+00 1.11e-01 2.44e+01
  angle pdb=" O3P PEE F2605 "
        pdb=" P   PEE F2605 "
        pdb=" O4P PEE F2605 "
      ideal   model   delta    sigma   weight residual
      92.91  106.26  -13.35 3.00e+00 1.11e-01 1.98e+01
  angle pdb=" O3P PEE B2605 "
        pdb=" P   PEE B2605 "
        pdb=" O4P PEE B2605 "
      ideal   model   delta    sigma   weight residual
      92.91  106.25  -13.34 3.00e+00 1.11e-01 1.98e+01
  ... (remaining 44539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.99: 18768
       29.99 -    59.99: 721
       59.99 -    89.98: 92
       89.98 -   119.98: 45
      119.98 -   149.97: 42
  Dihedral angle restraints: 19668
    sinusoidal: 7329
      harmonic: 12339
  Sorted by residual:
  dihedral pdb=" CB  CYS F1232 "
           pdb=" SG  CYS F1232 "
           pdb=" SG  CYS F1253 "
           pdb=" CB  CYS F1253 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.59   67.59     1      1.00e+01 1.00e-02 5.94e+01
  dihedral pdb=" CA  ARG B1147 "
           pdb=" C   ARG B1147 "
           pdb=" N   SER B1148 "
           pdb=" CA  SER B1148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.83  -24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  ARG F1147 "
           pdb=" C   ARG F1147 "
           pdb=" N   SER F1148 "
           pdb=" CA  SER F1148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.84  -24.16     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 19665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 4833
       0.077 -    0.155: 319
       0.155 -    0.232: 8
       0.232 -    0.310: 3
       0.310 -    0.387: 3
  Chirality restraints: 5166
  Sorted by residual:
  chirality pdb=" C6  PLX F2601 "
            pdb=" C7  PLX F2601 "
            pdb=" O6  PLX F2601 "
            pdb=" O7  PLX F2601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.01    2.40   -0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" C6  PLX B2601 "
            pdb=" C7  PLX B2601 "
            pdb=" O6  PLX B2601 "
            pdb=" O7  PLX B2601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.01    2.40   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" C6  PLX A2601 "
            pdb=" C7  PLX A2601 "
            pdb=" O6  PLX A2601 "
            pdb=" O7  PLX A2601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.01    2.39   -0.38 2.00e-01 2.50e+01 3.65e+00
  ... (remaining 5163 not shown)

  Planarity restraints: 5511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B2319 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.23e+00
        pdb=" C   PHE B2319 "    0.036 2.00e-02 2.50e+03
        pdb=" O   PHE B2319 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR B2320 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A2319 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.18e+00
        pdb=" C   PHE A2319 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE A2319 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   THR A2320 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F2319 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   PHE F2319 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   PHE F2319 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR F2320 "    0.012 2.00e-02 2.50e+03
  ... (remaining 5508 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 213
        2.60 -     3.18: 28128
        3.18 -     3.75: 49944
        3.75 -     4.33: 60954
        4.33 -     4.90: 102156
  Nonbonded interactions: 241395
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B2437 "
            pdb=" SG  CYS B2441 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS A2437 "
            pdb=" SG  CYS A2441 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS B1232 "
            pdb=" SG  CYS B1253 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS A1232 "
            pdb=" SG  CYS A1253 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS A 994 "
            pdb=" SG  CYS A1103 "
     model   vdw
     2.033 3.760
  ... (remaining 241390 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: 0.20
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.000
  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:             0.020
  Extract box with map and model:          1.410
  Check model and map are aligned:         0.220
  Set scattering table:                    0.260
  Process input model:                     96.600
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.150
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  105.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.005   0.216  32820  Z= 0.253
  Angle     :  0.755  14.837  44550  Z= 0.358
  Chirality :  0.042   0.387   5166
  Planarity :  0.004   0.048   5511
  Dihedral  : 18.882 149.971  11607
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.71 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  7.38 %
    Favored  : 92.51 %
  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:  0.57 (0.14), residues: 4104
  helix:  1.67 (0.10), residues: 2748
  sheet: -1.01 (0.32), residues: 282
  loop : -2.78 (0.18), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 836 
 HIS   0.006   0.001   HIS A1403 
 PHE   0.022   0.001   PHE A2062 
 TYR   0.011   0.001   TYR F2470 
 ARG   0.011   0.000   ARG A1724 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11959 ( 2140)
  hydrogen bonds       : angle       5.26395 ( 6363)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.86677 (    6)
  covalent geometry    : bond        0.00512 (32817)
  covalent geometry    : angle       0.75524 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 223
  time to evaluate  : 3.464 
Fit side-chains
REVERT: F 1152 MET cc_start: 0.8558 (mtt) cc_final: 0.8345 (mtt)
REVERT: F 2241 MET cc_start: 0.8421 (tpp) cc_final: 0.8127 (tpt)
REVERT: B 1072 MET cc_start: 0.7290 (ptp) cc_final: 0.7072 (ptt)
REVERT: B 1215 LEU cc_start: 0.8791 (tt) cc_final: 0.8285 (mt)
REVERT: B 1349 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7584 (tpp)
REVERT: B 2509 ASP cc_start: 0.8200 (m-30) cc_final: 0.7855 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 223
  average time/residue: 0.3449
  time to fit residues: 138.5831
Evaluate side-chains
  221 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 218
  time to evaluate  : 3.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1349 MET
Chi-restraints excluded: chain A residue 1349 MET
Chi-restraints excluded: chain B residue 1349 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 352 optimal weight:    0.6980
   chunk 316 optimal weight:    6.9990
   chunk 175 optimal weight:    0.2980
   chunk 107 optimal weight:    9.9990
   chunk 213 optimal weight:    0.2980
   chunk 168 optimal weight:    0.9980
   chunk 326 optimal weight:    6.9990
   chunk 126 optimal weight:    6.9990
   chunk 198 optimal weight:    2.9990
   chunk 243 optimal weight:    3.9990
   chunk 378 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
F1304 HIS
F2118 ASN
F2244 GLN
A1304 HIS
A2118 ASN
A2151 ASN
B1304 HIS
B2118 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.081235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.067202 restraints weight = 140594.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.069124 restraints weight = 67219.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.070412 restraints weight = 41685.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.0763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  32820  Z= 0.130
  Angle     :  0.580   7.189  44550  Z= 0.296
  Chirality :  0.039   0.153   5166
  Planarity :  0.004   0.045   5511
  Dihedral  : 17.726 159.678   5286
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.21 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.14), residues: 4104
  helix:  1.89 (0.10), residues: 2790
  sheet: -0.83 (0.32), residues: 282
  loop : -2.63 (0.19), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B2142 
 HIS   0.006   0.001   HIS A1403 
 PHE   0.021   0.001   PHE A2062 
 TYR   0.015   0.001   TYR B2470 
 ARG   0.003   0.000   ARG B1295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 ( 2140)
  hydrogen bonds       : angle       4.24694 ( 6363)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.66102 (    6)
  covalent geometry    : bond        0.00286 (32817)
  covalent geometry    : angle       0.57990 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 4.314 
Fit side-chains
REVERT: F 1226 MET cc_start: 0.8468 (tpp) cc_final: 0.8193 (mmm)
REVERT: F 2053 LEU cc_start: 0.8940 (tp) cc_final: 0.8684 (tp)
REVERT: F 2241 MET cc_start: 0.8328 (tpp) cc_final: 0.8126 (tpt)
REVERT: A 2031 MET cc_start: 0.8299 (mtm) cc_final: 0.8078 (mtp)
REVERT: B 1072 MET cc_start: 0.7288 (ptp) cc_final: 0.7058 (ptt)
REVERT: B 1731 MET cc_start: 0.9024 (tpp) cc_final: 0.8799 (mmp)
REVERT: B 2509 ASP cc_start: 0.8180 (m-30) cc_final: 0.7848 (m-30)
  outliers start: 29
  outliers final: 18
  residues processed: 236
  average time/residue: 0.3893
  time to fit residues: 166.6061
Evaluate side-chains
  226 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 208
  time to evaluate  : 4.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1676 LEU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 2304 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 367 optimal weight:    2.9990
   chunk 355 optimal weight:    0.9980
   chunk 203 optimal weight:    0.7980
   chunk 323 optimal weight:    0.4980
   chunk 227 optimal weight:    0.9990
   chunk 255 optimal weight:    4.9990
   chunk 254 optimal weight:    0.7980
   chunk 209 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0020
   chunk 411 optimal weight:    2.9990
   chunk 387 optimal weight:    1.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
F2151 ASN
A1225 ASN
B2151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.082140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068289 restraints weight = 163912.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.070736 restraints weight = 72550.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.072094 restraints weight = 38691.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  32820  Z= 0.106
  Angle     :  0.535  12.723  44550  Z= 0.270
  Chirality :  0.038   0.148   5166
  Planarity :  0.004   0.037   5511
  Dihedral  : 16.042 162.847   5277
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.39 %
    Favored  : 88.62 %
  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:  1.16 (0.14), residues: 4104
  helix:  2.03 (0.10), residues: 2814
  sheet: -0.72 (0.32), residues: 276
  loop : -2.56 (0.19), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 836 
 HIS   0.008   0.001   HIS F1304 
 PHE   0.020   0.001   PHE A2062 
 TYR   0.023   0.001   TYR B1046 
 ARG   0.003   0.000   ARG B2098 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 ( 2140)
  hydrogen bonds       : angle       3.95402 ( 6363)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       0.64107 (    6)
  covalent geometry    : bond        0.00227 (32817)
  covalent geometry    : angle       0.53498 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 227
  time to evaluate  : 7.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 1226 MET cc_start: 0.8534 (tpp) cc_final: 0.8282 (mmm)
REVERT: F 2053 LEU cc_start: 0.8850 (tp) cc_final: 0.8629 (tp)
REVERT: F 2263 PHE cc_start: 0.8478 (m-80) cc_final: 0.8228 (m-80)
REVERT: A 2263 PHE cc_start: 0.8224 (m-80) cc_final: 0.7804 (m-80)
REVERT: A 2270 MET cc_start: 0.7925 (mmm) cc_final: 0.7716 (mmm)
REVERT: B 1215 LEU cc_start: 0.8764 (tt) cc_final: 0.8312 (mm)
REVERT: B 2309 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7766 (m-10)
REVERT: B 2408 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: B 2509 ASP cc_start: 0.8252 (m-30) cc_final: 0.7831 (m-30)
  outliers start: 29
  outliers final: 21
  residues processed: 245
  average time/residue: 0.5632
  time to fit residues: 250.2312
Evaluate side-chains
  234 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 7.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1245 VAL
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 2309 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 252 optimal weight:    0.4980
   chunk 341 optimal weight:    0.6980
   chunk 133 optimal weight:    0.1980
   chunk 104 optimal weight:    3.9990
   chunk 337 optimal weight:    0.9980
   chunk 323 optimal weight:    4.9990
   chunk 288 optimal weight:   30.0000
   chunk 301 optimal weight:    6.9990
   chunk 329 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
F1047 GLN
** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F2356 GLN
A1047 GLN
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1304 HIS
A2356 GLN
B1047 GLN
** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B2356 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.081451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.067747 restraints weight = 152966.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.070068 restraints weight = 70455.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.071150 restraints weight = 39025.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  32820  Z= 0.110
  Angle     :  0.517   9.902  44550  Z= 0.263
  Chirality :  0.038   0.146   5166
  Planarity :  0.003   0.036   5511
  Dihedral  : 15.281 156.124   5277
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.52 %
    Favored  : 87.18 %
  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:  1.32 (0.14), residues: 4104
  helix:  2.13 (0.10), residues: 2820
  sheet: -0.59 (0.32), residues: 276
  loop : -2.50 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 836 
 HIS   0.004   0.001   HIS B1403 
 PHE   0.023   0.001   PHE B1143 
 TYR   0.022   0.001   TYR B1046 
 ARG   0.002   0.000   ARG B2098 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 ( 2140)
  hydrogen bonds       : angle       3.85834 ( 6363)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       0.60524 (    6)
  covalent geometry    : bond        0.00245 (32817)
  covalent geometry    : angle       0.51727 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 4.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 2053 LEU cc_start: 0.8890 (tp) cc_final: 0.8647 (tp)
REVERT: A 2263 PHE cc_start: 0.8259 (m-80) cc_final: 0.7837 (m-80)
REVERT: B 2270 MET cc_start: 0.8677 (mmm) cc_final: 0.8084 (mmm)
REVERT: B 2309 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7822 (m-10)
REVERT: B 2509 ASP cc_start: 0.8255 (m-30) cc_final: 0.7847 (m-30)
  outliers start: 38
  outliers final: 24
  residues processed: 240
  average time/residue: 0.4853
  time to fit residues: 210.2559
Evaluate side-chains
  231 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 3.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2493 MET
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 2002 SER
Chi-restraints excluded: chain B residue 2309 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 199 optimal weight:    4.9990
   chunk 151 optimal weight:    9.9990
   chunk 223 optimal weight:    0.8980
   chunk 162 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 232 optimal weight:    0.3980
   chunk 233 optimal weight:    0.7980
   chunk 330 optimal weight:    1.9990
   chunk 189 optimal weight:    9.9990
   chunk 387 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
F1225 ASN
** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1669 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.079848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.065944 restraints weight = 161127.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068245 restraints weight = 74381.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.069485 restraints weight = 40398.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  32820  Z= 0.143
  Angle     :  0.540   7.574  44550  Z= 0.278
  Chirality :  0.039   0.157   5166
  Planarity :  0.004   0.036   5511
  Dihedral  : 14.867 155.007   5277
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.69 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.14), residues: 4104
  helix:  2.15 (0.10), residues: 2811
  sheet: -0.52 (0.32), residues: 276
  loop : -2.54 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 836 
 HIS   0.008   0.001   HIS A1304 
 PHE   0.018   0.001   PHE A1143 
 TYR   0.018   0.001   TYR B 842 
 ARG   0.004   0.000   ARG B2407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03591 ( 2140)
  hydrogen bonds       : angle       3.90330 ( 6363)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       0.62914 (    6)
  covalent geometry    : bond        0.00329 (32817)
  covalent geometry    : angle       0.54041 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 203
  time to evaluate  : 5.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 2121 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8728 (tp)
REVERT: A 1700 MET cc_start: 0.8577 (mtp) cc_final: 0.8251 (mtp)
REVERT: A 2121 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8770 (tp)
REVERT: A 2263 PHE cc_start: 0.8242 (m-80) cc_final: 0.7934 (m-80)
REVERT: B 1238 MET cc_start: 0.7009 (tpp) cc_final: 0.6751 (tpt)
REVERT: B 2121 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8748 (tp)
REVERT: B 2270 MET cc_start: 0.8591 (mmm) cc_final: 0.8043 (mmm)
REVERT: B 2509 ASP cc_start: 0.8136 (m-30) cc_final: 0.7929 (m-30)
  outliers start: 55
  outliers final: 35
  residues processed: 242
  average time/residue: 0.4771
  time to fit residues: 208.4619
Evaluate side-chains
  238 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 3.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  836 TRP
Chi-restraints excluded: chain F residue 1011 ILE
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1726 SER
Chi-restraints excluded: chain F residue 1739 VAL
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2493 MET
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2493 MET
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue  836 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1245 VAL
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2002 SER
Chi-restraints excluded: chain B residue 2121 LEU
Chi-restraints excluded: chain B residue 2194 LEU
Chi-restraints excluded: chain B residue 2304 MET
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 386 optimal weight:    2.9990
   chunk 249 optimal weight:    4.9990
   chunk 171 optimal weight:    0.9980
   chunk 330 optimal weight:    1.9990
   chunk 262 optimal weight:    6.9990
   chunk 231 optimal weight:    1.9990
   chunk 139 optimal weight:   40.0000
   chunk 86 optimal weight:    5.9990
   chunk 194 optimal weight:    1.9990
   chunk 96 optimal weight:    0.2980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1225 ASN
** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.080121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.066405 restraints weight = 137840.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.068570 restraints weight = 68939.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.069450 restraints weight = 37529.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  32820  Z= 0.122
  Angle     :  0.519   8.013  44550  Z= 0.266
  Chirality :  0.038   0.146   5166
  Planarity :  0.003   0.037   5511
  Dihedral  : 14.482 149.183   5277
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.17 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.14), residues: 4104
  helix:  2.21 (0.10), residues: 2814
  sheet: -0.39 (0.32), residues: 276
  loop : -2.50 (0.19), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 836 
 HIS   0.005   0.001   HIS A1304 
 PHE   0.020   0.001   PHE B1143 
 TYR   0.026   0.001   TYR B1046 
 ARG   0.002   0.000   ARG A2407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 ( 2140)
  hydrogen bonds       : angle       3.83351 ( 6363)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       0.60118 (    6)
  covalent geometry    : bond        0.00277 (32817)
  covalent geometry    : angle       0.51877 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 205
  time to evaluate  : 3.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 2121 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8698 (tp)
REVERT: A 1226 MET cc_start: 0.8464 (mmm) cc_final: 0.8259 (mmm)
REVERT: A 1700 MET cc_start: 0.8620 (mtp) cc_final: 0.8336 (mtp)
REVERT: A 2121 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8749 (tp)
REVERT: A 2263 PHE cc_start: 0.8185 (m-80) cc_final: 0.7979 (m-80)
REVERT: A 2309 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7407 (t80)
REVERT: B 2121 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (tp)
REVERT: B 2270 MET cc_start: 0.8603 (mmm) cc_final: 0.8028 (mmm)
REVERT: B 2509 ASP cc_start: 0.8110 (m-30) cc_final: 0.7879 (m-30)
  outliers start: 53
  outliers final: 34
  residues processed: 238
  average time/residue: 0.3582
  time to fit residues: 153.1365
Evaluate side-chains
  237 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 199
  time to evaluate  : 3.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  836 TRP
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1222 ILE
Chi-restraints excluded: chain F residue 1505 LEU
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1726 SER
Chi-restraints excluded: chain F residue 1739 VAL
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1505 LEU
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2309 TYR
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1245 VAL
Chi-restraints excluded: chain B residue 1505 LEU
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2121 LEU
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 259 optimal weight:    4.9990
   chunk 206 optimal weight:    8.9990
   chunk 281 optimal weight:    0.8980
   chunk 136 optimal weight:    0.9980
   chunk 187 optimal weight:    0.9980
   chunk 309 optimal weight:    2.9990
   chunk 389 optimal weight:    0.5980
   chunk 379 optimal weight:    6.9990
   chunk 83 optimal weight:    0.1980
   chunk 164 optimal weight:    1.9990
   chunk 402 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.081116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.066781 restraints weight = 211253.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.068940 restraints weight = 92072.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.070051 restraints weight = 48807.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  32820  Z= 0.102
  Angle     :  0.501   8.303  44550  Z= 0.256
  Chirality :  0.038   0.141   5166
  Planarity :  0.003   0.039   5511
  Dihedral  : 14.106 141.164   5277
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.65 %
    Favored  : 85.54 %
  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:  1.51 (0.14), residues: 4104
  helix:  2.26 (0.10), residues: 2811
  sheet: -0.33 (0.32), residues: 276
  loop : -2.41 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F2142 
 HIS   0.005   0.001   HIS F1699 
 PHE   0.026   0.001   PHE F2062 
 TYR   0.022   0.001   TYR B1046 
 ARG   0.002   0.000   ARG A1295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 ( 2140)
  hydrogen bonds       : angle       3.74783 ( 6363)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       0.58348 (    6)
  covalent geometry    : bond        0.00223 (32817)
  covalent geometry    : angle       0.50106 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 216
  time to evaluate  : 3.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 2121 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (tp)
REVERT: F 2263 PHE cc_start: 0.8452 (m-80) cc_final: 0.8227 (m-80)
REVERT: A 1700 MET cc_start: 0.8605 (mtp) cc_final: 0.8337 (mtp)
REVERT: A 2121 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8722 (tp)
REVERT: B 2121 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8716 (tp)
REVERT: B 2270 MET cc_start: 0.8659 (mmm) cc_final: 0.8102 (mmm)
REVERT: B 2309 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7722 (t80)
REVERT: B 2509 ASP cc_start: 0.8079 (m-30) cc_final: 0.7831 (m-30)
  outliers start: 53
  outliers final: 37
  residues processed: 254
  average time/residue: 0.3604
  time to fit residues: 162.3661
Evaluate side-chains
  242 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 201
  time to evaluate  : 3.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1011 ILE
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1505 LEU
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2493 MET
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue  836 TRP
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1505 LEU
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1245 VAL
Chi-restraints excluded: chain B residue 1348 GLN
Chi-restraints excluded: chain B residue 1505 LEU
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2121 LEU
Chi-restraints excluded: chain B residue 2194 LEU
Chi-restraints excluded: chain B residue 2309 TYR
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 376 optimal weight:    2.9990
   chunk 151 optimal weight:   10.0000
   chunk 365 optimal weight:    1.9990
   chunk 143 optimal weight:   10.0000
   chunk 102 optimal weight:    0.8980
   chunk 193 optimal weight:    0.9990
   chunk 347 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0370
   chunk 355 optimal weight:    4.9990
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
F1669 GLN
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.080681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.066811 restraints weight = 172936.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.068843 restraints weight = 74025.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.070090 restraints weight = 42092.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  32820  Z= 0.112
  Angle     :  0.509  11.418  44550  Z= 0.258
  Chirality :  0.038   0.180   5166
  Planarity :  0.003   0.038   5511
  Dihedral  : 13.976 141.153   5277
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.79 %
    Favored  : 85.33 %
  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:  1.54 (0.14), residues: 4104
  helix:  2.28 (0.10), residues: 2811
  sheet: -0.27 (0.32), residues: 276
  loop : -2.40 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A2142 
 HIS   0.005   0.001   HIS A1304 
 PHE   0.019   0.001   PHE F2062 
 TYR   0.023   0.001   TYR B1046 
 ARG   0.002   0.000   ARG A2098 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 ( 2140)
  hydrogen bonds       : angle       3.73571 ( 6363)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.57204 (    6)
  covalent geometry    : bond        0.00252 (32817)
  covalent geometry    : angle       0.50925 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 205
  time to evaluate  : 3.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 1348 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8655 (mp10)
REVERT: F 2121 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (tp)
REVERT: F 2263 PHE cc_start: 0.8454 (m-80) cc_final: 0.8223 (m-80)
REVERT: A 1348 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8689 (mt0)
REVERT: A 1700 MET cc_start: 0.8686 (mtp) cc_final: 0.8413 (mtp)
REVERT: A 2121 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (tp)
REVERT: B 2121 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8666 (tp)
REVERT: B 2270 MET cc_start: 0.8718 (mmm) cc_final: 0.8165 (mmm)
REVERT: B 2309 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7659 (t80)
REVERT: B 2509 ASP cc_start: 0.8165 (m-30) cc_final: 0.7880 (m-30)
  outliers start: 55
  outliers final: 34
  residues processed: 246
  average time/residue: 0.3706
  time to fit residues: 162.9343
Evaluate side-chains
  244 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 3.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1011 ILE
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1348 GLN
Chi-restraints excluded: chain F residue 1505 LEU
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2493 MET
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1348 GLN
Chi-restraints excluded: chain A residue 1505 LEU
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1348 GLN
Chi-restraints excluded: chain B residue 1505 LEU
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2121 LEU
Chi-restraints excluded: chain B residue 2194 LEU
Chi-restraints excluded: chain B residue 2309 TYR
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 362 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 304 optimal weight:    0.9990
   chunk 360 optimal weight:    0.3980
   chunk 361 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 226 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.080502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.066416 restraints weight = 192220.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068159 restraints weight = 87614.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.069381 restraints weight = 50963.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  32820  Z= 0.114
  Angle     :  0.509   8.163  44550  Z= 0.259
  Chirality :  0.038   0.244   5166
  Planarity :  0.003   0.038   5511
  Dihedral  : 13.888 140.869   5277
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.20 %
    Favored  : 85.30 %
  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:  1.56 (0.14), residues: 4104
  helix:  2.30 (0.10), residues: 2811
  sheet: -0.25 (0.32), residues: 276
  loop : -2.40 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A2142 
 HIS   0.005   0.001   HIS A1304 
 PHE   0.019   0.001   PHE F2062 
 TYR   0.023   0.001   TYR B1046 
 ARG   0.002   0.000   ARG A2098 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 ( 2140)
  hydrogen bonds       : angle       3.73019 ( 6363)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.58195 (    6)
  covalent geometry    : bond        0.00258 (32817)
  covalent geometry    : angle       0.50862 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 203
  time to evaluate  : 3.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 2121 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8672 (tp)
REVERT: F 2263 PHE cc_start: 0.8445 (m-80) cc_final: 0.8234 (m-80)
REVERT: F 2509 ASP cc_start: 0.8138 (m-30) cc_final: 0.7833 (m-30)
REVERT: A 1016 TRP cc_start: 0.7924 (t-100) cc_final: 0.7644 (t-100)
REVERT: A 1700 MET cc_start: 0.8655 (mtp) cc_final: 0.8323 (mtp)
REVERT: A 2121 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8724 (tp)
REVERT: A 2394 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: B 2121 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8705 (tp)
REVERT: B 2270 MET cc_start: 0.8653 (mmm) cc_final: 0.8111 (mmm)
REVERT: B 2309 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7695 (t80)
REVERT: B 2509 ASP cc_start: 0.8052 (m-30) cc_final: 0.7808 (m-30)
  outliers start: 44
  outliers final: 35
  residues processed: 234
  average time/residue: 0.3584
  time to fit residues: 151.3383
Evaluate side-chains
  240 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 201
  time to evaluate  : 3.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1011 ILE
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1505 LEU
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2493 MET
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1505 LEU
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1676 LEU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1102 LEU
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1505 LEU
Chi-restraints excluded: chain B residue 1540 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2121 LEU
Chi-restraints excluded: chain B residue 2194 LEU
Chi-restraints excluded: chain B residue 2309 TYR
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 171 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 249 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 356 optimal weight:    5.9990
   chunk 293 optimal weight:   20.0000
   chunk 182 optimal weight:    7.9990
   chunk 388 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 265 optimal weight:    4.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1669 GLN
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.078876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.064783 restraints weight = 194568.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.066761 restraints weight = 88728.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.067497 restraints weight = 49249.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  32820  Z= 0.151
  Angle     :  0.542   8.316  44550  Z= 0.277
  Chirality :  0.039   0.158   5166
  Planarity :  0.003   0.039   5511
  Dihedral  : 13.932 141.104   5277
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.33 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.14), residues: 4104
  helix:  2.26 (0.10), residues: 2814
  sheet: -0.29 (0.32), residues: 276
  loop : -2.45 (0.19), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A2142 
 HIS   0.006   0.001   HIS A1304 
 PHE   0.019   0.001   PHE A1143 
 TYR   0.023   0.001   TYR B1046 
 ARG   0.003   0.000   ARG B1353 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 ( 2140)
  hydrogen bonds       : angle       3.83439 ( 6363)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.62420 (    6)
  covalent geometry    : bond        0.00348 (32817)
  covalent geometry    : angle       0.54204 (44544)

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

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

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8208 Ramachandran restraints generated.
    4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 199
  time to evaluate  : 3.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F 1348 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8674 (mt0)
REVERT: F 2121 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8715 (tp)
REVERT: F 2263 PHE cc_start: 0.8566 (m-80) cc_final: 0.8349 (m-80)
REVERT: A 1700 MET cc_start: 0.8687 (mtp) cc_final: 0.8362 (mtp)
REVERT: A 2121 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8735 (tp)
REVERT: A 2394 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: B 2270 MET cc_start: 0.8684 (mmm) cc_final: 0.8128 (mmm)
REVERT: B 2309 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7746 (m-10)
REVERT: B 2509 ASP cc_start: 0.8137 (m-30) cc_final: 0.7898 (m-30)
  outliers start: 40
  outliers final: 34
  residues processed: 230
  average time/residue: 0.3835
  time to fit residues: 158.9790
Evaluate side-chains
  232 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 194
  time to evaluate  : 3.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 1011 ILE
Chi-restraints excluded: chain F residue 1013 HIS
Chi-restraints excluded: chain F residue 1143 PHE
Chi-restraints excluded: chain F residue 1348 GLN
Chi-restraints excluded: chain F residue 1505 LEU
Chi-restraints excluded: chain F residue 1540 LEU
Chi-restraints excluded: chain F residue 1663 GLU
Chi-restraints excluded: chain F residue 1689 LEU
Chi-restraints excluded: chain F residue 1690 LEU
Chi-restraints excluded: chain F residue 1791 MET
Chi-restraints excluded: chain F residue 2121 LEU
Chi-restraints excluded: chain F residue 2493 MET
Chi-restraints excluded: chain F residue 2542 TRP
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1505 LEU
Chi-restraints excluded: chain A residue 1540 LEU
Chi-restraints excluded: chain A residue 1663 GLU
Chi-restraints excluded: chain A residue 1690 LEU
Chi-restraints excluded: chain A residue 2121 LEU
Chi-restraints excluded: chain A residue 2197 LEU
Chi-restraints excluded: chain A residue 2542 TRP
Chi-restraints excluded: chain B residue 1009 MET
Chi-restraints excluded: chain B residue 1011 ILE
Chi-restraints excluded: chain B residue 1013 HIS
Chi-restraints excluded: chain B residue 1102 LEU
Chi-restraints excluded: chain B residue 1143 PHE
Chi-restraints excluded: chain B residue 1348 GLN
Chi-restraints excluded: chain B residue 1505 LEU
Chi-restraints excluded: chain B residue 1663 GLU
Chi-restraints excluded: chain B residue 1689 LEU
Chi-restraints excluded: chain B residue 1690 LEU
Chi-restraints excluded: chain B residue 1726 SER
Chi-restraints excluded: chain B residue 2194 LEU
Chi-restraints excluded: chain B residue 2309 TYR
Chi-restraints excluded: chain B residue 2542 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 417
   random chunks:
   chunk 299 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0970
   chunk 311 optimal weight:    0.0870
   chunk 117 optimal weight:    3.9990
   chunk 253 optimal weight:    6.9990
   chunk 143 optimal weight:    9.9990
   chunk 212 optimal weight:    0.7980
   chunk 133 optimal weight:    1.9990
   chunk 337 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 377 optimal weight:    3.9990
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.080289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.066111 restraints weight = 181352.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.068391 restraints weight = 80585.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.069322 restraints weight = 44236.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  32820  Z= 0.107
  Angle     :  0.517  10.649  44550  Z= 0.263
  Chirality :  0.038   0.144   5166
  Planarity :  0.003   0.039   5511
  Dihedral  : 13.698 142.416   5277
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.54 %
    Favored  : 85.16 %
  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:  1.57 (0.14), residues: 4104
  helix:  2.30 (0.10), residues: 2811
  sheet: -0.29 (0.32), residues: 276
  loop : -2.39 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP F2142 
 HIS   0.005   0.001   HIS A1304 
 PHE   0.019   0.001   PHE F2062 
 TYR   0.022   0.001   TYR B1046 
 ARG   0.003   0.000   ARG B2402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03257 ( 2140)
  hydrogen bonds       : angle       3.75455 ( 6363)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       0.58327 (    6)
  covalent geometry    : bond        0.00238 (32817)
  covalent geometry    : angle       0.51730 (44544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11580.79 seconds
wall clock time: 209 minutes 18.36 seconds (12558.36 seconds total)