Starting phenix.real_space_refine
on Tue Aug 26 17:19:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cq9_45812/08_2025/9cq9_45812.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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
     S     108      5.16       5
     C   12328      2.51       5
     N    3418      2.21       5
     O    3650      1.98       5
     H   19370      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 38874
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 19437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1256, 19437
          Classifications: {'peptide': 1256}
          Link IDs: {'PTRANS': 54, 'TRANS': 1201}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Restraints were copied for chains:
    B
  Time building chain proxies: 35.02, per 1000 atoms: 0.90
  Number of scatterers: 38874
  At special positions: 0
  Unit cell: (197.69, 156.35, 94.34, 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     108     16.00
     O    3650      8.00
     N    3418      7.00
     C   12328      6.00
     H   19370      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.17
  Conformation dependent library (CDL) restraints added in 772.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4652

  Finding SS restraints...
    Secondary structure from input PDB file:
      94 helices and 19 sheets defined
      40.2% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 894 through 900
      removed outlier: 3.501A  pdb=" N   ARG A 897 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TYR A 898 " --> pdb=" O   PRO A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 927
      removed outlier: 3.542A  pdb=" N   CYS A 915 " --> pdb=" O   PRO A 911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1008
      No H-bonds generated for 'chain 'A' and resid 1006 through 1008'
    Processing helix  chain 'A' and resid 1013 through 1024
      removed outlier: 3.694A  pdb=" N   LEU A1020 " --> pdb=" O   VAL A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1067
      removed outlier: 3.602A  pdb=" N   PHE A1055 " --> pdb=" O   ARG A1051 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG A1067 " --> pdb=" O   ASP A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1186
    Processing helix  chain 'A' and resid 1194 through 1207
    Processing helix  chain 'A' and resid 1218 through 1232
      removed outlier: 3.576A  pdb=" N   GLN A1232 " --> pdb=" O   ILE A1228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1241 through 1251
    Processing helix  chain 'A' and resid 1257 through 1275
      removed outlier: 3.664A  pdb=" N   THR A1261 " --> pdb=" O   GLY A1257 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   TYR A1271 " --> pdb=" O   HIS A1267 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   ASP A1272 " --> pdb=" O   HIS A1268 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ASP A1275 " --> pdb=" O   TYR A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1282
      removed outlier: 3.620A  pdb=" N   ALA A1281 " --> pdb=" O   LEU A1278 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   VAL A1282 " --> pdb=" O   MET A1279 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1278 through 1282'
    Processing helix  chain 'A' and resid 1284 through 1298
    Processing helix  chain 'A' and resid 1310 through 1315
    Processing helix  chain 'A' and resid 1316 through 1325
      Proline residue:  A1322  - end of helix
    Processing helix  chain 'A' and resid 1343 through 1348
      removed outlier: 4.331A  pdb=" N   GLU A1348 " --> pdb=" O   ASP A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1386 through 1398
    Processing helix  chain 'A' and resid 1413 through 1424
      removed outlier: 6.458A  pdb=" N   VAL A1419 " --> pdb=" O   THR A1415 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   VAL A1422 " --> pdb=" O   ALA A1418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1441 through 1452
      removed outlier: 3.507A  pdb=" N   HIS A1452 " --> pdb=" O   LEU A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1491 through 1502
      removed outlier: 3.960A  pdb=" N   GLU A1495 " --> pdb=" O   CYS A1491 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER A1502 " --> pdb=" O   LYS A1498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1502 through 1507
      removed outlier: 3.866A  pdb=" N   ALA A1506 " --> pdb=" O   SER A1502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1534
      removed outlier: 3.706A  pdb=" N   PHE A1527 " --> pdb=" O   GLY A1523 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLN A1533 " --> pdb=" O   ASN A1529 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLU A1534 " --> pdb=" O   CYS A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1557 through 1565
    Processing helix  chain 'A' and resid 1619 through 1623
    Processing helix  chain 'A' and resid 1643 through 1652
      removed outlier: 3.500A  pdb=" N   LEU A1647 " --> pdb=" O   VAL A1643 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A1652 " --> pdb=" O   ALA A1648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1659
    Processing helix  chain 'A' and resid 1679 through 1681
      No H-bonds generated for 'chain 'A' and resid 1679 through 1681'
    Processing helix  chain 'A' and resid 1712 through 1717
      removed outlier: 3.561A  pdb=" N   ALA A1717 " --> pdb=" O   LEU A1713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1721 through 1731
    Processing helix  chain 'A' and resid 1749 through 1763
    Processing helix  chain 'A' and resid 1773 through 1783
    Processing helix  chain 'A' and resid 1798 through 1807
    Processing helix  chain 'A' and resid 1821 through 1829
    Processing helix  chain 'A' and resid 1851 through 1855
    Processing helix  chain 'A' and resid 1866 through 1873
      removed outlier: 3.774A  pdb=" N   LEU A1870 " --> pdb=" O   ASN A1866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1875 through 1891
      removed outlier: 3.629A  pdb=" N   THR A1879 " --> pdb=" O   GLY A1875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1906 through 1917
    Processing helix  chain 'A' and resid 1965 through 1978
      removed outlier: 3.897A  pdb=" N   GLU A1969 " --> pdb=" O   GLY A1965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1992 through 2005
      removed outlier: 3.845A  pdb=" N   THR A1996 " --> pdb=" O   THR A1992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2018 through 2033
    Processing helix  chain 'A' and resid 2049 through 2053
    Processing helix  chain 'A' and resid 2054 through 2063
    Processing helix  chain 'A' and resid 2065 through 2077
    Processing helix  chain 'A' and resid 2081 through 2085
    Processing helix  chain 'A' and resid 2095 through 2097
      No H-bonds generated for 'chain 'A' and resid 2095 through 2097'
    Processing helix  chain 'A' and resid 2103 through 2124
    Processing helix  chain 'A' and resid 2139 through 2145
    Processing helix  chain 'A' and resid 2158 through 2170
      removed outlier: 4.054A  pdb=" N   SER A2170 " --> pdb=" O   ASP A2166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 900
      removed outlier: 3.501A  pdb=" N   ARG B 897 " --> pdb=" O   SER B 894 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   TYR B 898 " --> pdb=" O   PRO B 895 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 911 through 927
      removed outlier: 3.542A  pdb=" N   CYS B 915 " --> pdb=" O   PRO B 911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1006 through 1008
      No H-bonds generated for 'chain 'B' and resid 1006 through 1008'
    Processing helix  chain 'B' and resid 1013 through 1024
      removed outlier: 3.693A  pdb=" N   LEU B1020 " --> pdb=" O   VAL B1016 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1051 through 1067
      removed outlier: 3.602A  pdb=" N   PHE B1055 " --> pdb=" O   ARG B1051 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG B1067 " --> pdb=" O   ASP B1063 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1164 through 1186
    Processing helix  chain 'B' and resid 1194 through 1207
    Processing helix  chain 'B' and resid 1218 through 1232
      removed outlier: 3.577A  pdb=" N   GLN B1232 " --> pdb=" O   ILE B1228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1241 through 1251
    Processing helix  chain 'B' and resid 1257 through 1275
      removed outlier: 3.663A  pdb=" N   THR B1261 " --> pdb=" O   GLY B1257 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   TYR B1271 " --> pdb=" O   HIS B1267 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   ASP B1272 " --> pdb=" O   HIS B1268 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ASP B1275 " --> pdb=" O   TYR B1271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1278 through 1282
      removed outlier: 3.620A  pdb=" N   ALA B1281 " --> pdb=" O   LEU B1278 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   VAL B1282 " --> pdb=" O   MET B1279 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1278 through 1282'
    Processing helix  chain 'B' and resid 1284 through 1298
    Processing helix  chain 'B' and resid 1310 through 1315
    Processing helix  chain 'B' and resid 1316 through 1325
      Proline residue:  B1322  - end of helix
    Processing helix  chain 'B' and resid 1343 through 1348
      removed outlier: 4.331A  pdb=" N   GLU B1348 " --> pdb=" O   ASP B1345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1386 through 1398
    Processing helix  chain 'B' and resid 1413 through 1424
      removed outlier: 6.457A  pdb=" N   VAL B1419 " --> pdb=" O   THR B1415 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL B1422 " --> pdb=" O   ALA B1418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1441 through 1452
      removed outlier: 3.507A  pdb=" N   HIS B1452 " --> pdb=" O   LEU B1448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1491 through 1502
      removed outlier: 3.960A  pdb=" N   GLU B1495 " --> pdb=" O   CYS B1491 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   SER B1502 " --> pdb=" O   LYS B1498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1502 through 1507
      removed outlier: 3.866A  pdb=" N   ALA B1506 " --> pdb=" O   SER B1502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1523 through 1534
      removed outlier: 3.707A  pdb=" N   PHE B1527 " --> pdb=" O   GLY B1523 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   GLN B1533 " --> pdb=" O   ASN B1529 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLU B1534 " --> pdb=" O   CYS B1530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1557 through 1565
    Processing helix  chain 'B' and resid 1619 through 1623
    Processing helix  chain 'B' and resid 1643 through 1652
      removed outlier: 3.574A  pdb=" N   GLY B1652 " --> pdb=" O   ALA B1648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1655 through 1659
    Processing helix  chain 'B' and resid 1679 through 1681
      No H-bonds generated for 'chain 'B' and resid 1679 through 1681'
    Processing helix  chain 'B' and resid 1712 through 1717
      removed outlier: 3.561A  pdb=" N   ALA B1717 " --> pdb=" O   LEU B1713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1721 through 1731
    Processing helix  chain 'B' and resid 1749 through 1763
    Processing helix  chain 'B' and resid 1773 through 1783
    Processing helix  chain 'B' and resid 1798 through 1807
    Processing helix  chain 'B' and resid 1821 through 1829
    Processing helix  chain 'B' and resid 1851 through 1855
    Processing helix  chain 'B' and resid 1866 through 1873
      removed outlier: 3.773A  pdb=" N   LEU B1870 " --> pdb=" O   ASN B1866 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1875 through 1891
      removed outlier: 3.629A  pdb=" N   THR B1879 " --> pdb=" O   GLY B1875 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1906 through 1917
    Processing helix  chain 'B' and resid 1965 through 1978
      removed outlier: 3.896A  pdb=" N   GLU B1969 " --> pdb=" O   GLY B1965 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1992 through 2005
      removed outlier: 3.846A  pdb=" N   THR B1996 " --> pdb=" O   THR B1992 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2018 through 2033
    Processing helix  chain 'B' and resid 2049 through 2053
    Processing helix  chain 'B' and resid 2054 through 2063
    Processing helix  chain 'B' and resid 2065 through 2077
    Processing helix  chain 'B' and resid 2081 through 2085
    Processing helix  chain 'B' and resid 2095 through 2097
      No H-bonds generated for 'chain 'B' and resid 2095 through 2097'
    Processing helix  chain 'B' and resid 2103 through 2124
    Processing helix  chain 'B' and resid 2139 through 2145
    Processing helix  chain 'B' and resid 2158 through 2170
      removed outlier: 4.054A  pdb=" N   SER B2170 " --> pdb=" O   ASP B2166 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 886 through 889
      removed outlier: 3.751A  pdb=" N   GLY A 980 " --> pdb=" O   PHE A 968 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   GLU A 972 " --> pdb=" O   LEU A 976 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   LEU A 976 " --> pdb=" O   GLU A 972 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   LEU A 977 " --> pdb=" O   ILE A 943 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ILE A 943 " --> pdb=" O   LEU A 977 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   SER A 979 " --> pdb=" O   VAL A 941 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL A 941 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A1080 " --> pdb=" O   ARG A1120 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU A1043 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A1036 " --> pdb=" O   GLU A1045 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 902 through 904
      removed outlier: 3.596A  pdb=" N   GLN A 903 " --> pdb=" O   GLU A1026 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1074 through 1077
      removed outlier: 5.785A  pdb=" N   ILE A1125 " --> pdb=" O   PRO A1075 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1482 through 1485
      removed outlier: 6.021A  pdb=" N   THR A1482 " --> pdb=" O   TRP A1514 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL A1516 " --> pdb=" O   THR A1482 " (cutoff:3.500A)
      removed outlier: 5.684A  pdb=" N   LEU A1484 " --> pdb=" O   VAL A1516 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LEU A1513 " --> pdb=" O   ARG A1541 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL A1543 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU A1515 " --> pdb=" O   VAL A1543 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL A1545 " --> pdb=" O   LEU A1515 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY A1517 " --> pdb=" O   VAL A1545 " (cutoff:3.500A)
      removed outlier: 8.638A  pdb=" N   ASN A1571 " --> pdb=" O   VAL A1540 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   CYS A1542 " --> pdb=" O   ASN A1571 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   HIS A1573 " --> pdb=" O   CYS A1542 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLN A1544 " --> pdb=" O   HIS A1573 " (cutoff:3.500A)
      removed outlier: 8.509A  pdb=" N   PHE A1570 " --> pdb=" O   TYR A1581 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   TYR A1581 " --> pdb=" O   PHE A1570 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   HIS A2179 " --> pdb=" O   VAL A1137 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   VAL A2175 " --> pdb=" O   TYR A1141 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   SER A2129 " --> pdb=" O   VAL A2176 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   CYS A2178 " --> pdb=" O   SER A2129 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN A2131 " --> pdb=" O   CYS A2178 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   GLY A2036 " --> pdb=" O   HIS A2087 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   VAL A2089 " --> pdb=" O   GLY A2036 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   VAL A2038 " --> pdb=" O   VAL A2089 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   PHE A2091 " --> pdb=" O   VAL A2038 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ASN A2040 " --> pdb=" O   PHE A2091 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   SER A2093 " --> pdb=" O   ASN A2040 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   SER A1956 " --> pdb=" O   GLY A2037 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   PHE A2039 " --> pdb=" O   SER A1956 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL A1958 " --> pdb=" O   PHE A2039 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1352 through 1353
      removed outlier: 3.791A  pdb=" N   LYS A1352 " --> pdb=" O   TYR A1335 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   VAL A1304 " --> pdb=" O   ARG A1334 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   THR A1336 " --> pdb=" O   VAL A1304 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL A1306 " --> pdb=" O   THR A1336 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   GLY A1338 " --> pdb=" O   VAL A1306 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   GLU A1308 " --> pdb=" O   GLY A1338 " (cutoff:3.500A)
      removed outlier: 8.779A  pdb=" N   LEU A1374 " --> pdb=" O   ILE A1303 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASN A1305 " --> pdb=" O   LEU A1374 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL A1376 " --> pdb=" O   ASN A1305 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU A1307 " --> pdb=" O   VAL A1376 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   LYS A1378 " --> pdb=" O   LEU A1307 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   ALA A1309 " --> pdb=" O   LYS A1378 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU A1375 " --> pdb=" O   LEU A1405 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   GLN A1407 " --> pdb=" O   LEU A1375 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   LEU A1377 " --> pdb=" O   GLN A1407 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   PHE A1409 " --> pdb=" O   LEU A1377 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   ALA A1466 " --> pdb=" O   SER A1461 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   SER A1461 " --> pdb=" O   ALA A1466 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   MET A1468 " --> pdb=" O   HIS A1459 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   HIS A1459 " --> pdb=" O   MET A1468 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU A1470 " --> pdb=" O   VAL A1457 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1595 through 1597
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1600 through 1604
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1697 through 1699
      removed outlier: 3.598A  pdb=" N   ARG A1677 " --> pdb=" O   THR A1636 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1639 through 1642
      removed outlier: 4.649A  pdb=" N   LEU A1923 " --> pdb=" O   VAL A1642 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR A1902 " --> pdb=" O   LYS A1926 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1791 through 1793
      removed outlier: 8.315A  pdb=" N   CYS A1792 " --> pdb=" O   ILE A1766 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   ILE A1768 " --> pdb=" O   CYS A1792 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL A1742 " --> pdb=" O   PHE A1767 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   SER A1769 " --> pdb=" O   VAL A1742 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL A1744 " --> pdb=" O   SER A1769 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   THR A1741 " --> pdb=" O   ASP A1813 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   ILE A1815 " --> pdb=" O   THR A1741 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU A1743 " --> pdb=" O   ILE A1815 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   VAL A1812 " --> pdb=" O   ALA A1832 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ARG A1834 " --> pdb=" O   VAL A1812 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE A1814 " --> pdb=" O   ARG A1834 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ARG A1836 " --> pdb=" O   ILE A1814 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   LEU A1816 " --> pdb=" O   ARG A1836 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU A1838 " --> pdb=" O   LEU A1816 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   THR A1860 " --> pdb=" O   ASP B1864 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP B1864 " --> pdb=" O   THR A1860 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP A1864 " --> pdb=" O   THR B1860 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   THR B1860 " --> pdb=" O   ASP A1864 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   VAL B1812 " --> pdb=" O   ALA B1832 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ARG B1834 " --> pdb=" O   VAL B1812 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ILE B1814 " --> pdb=" O   ARG B1834 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ARG B1836 " --> pdb=" O   ILE B1814 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   LEU B1816 " --> pdb=" O   ARG B1836 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   LEU B1838 " --> pdb=" O   LEU B1816 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   THR B1741 " --> pdb=" O   ASP B1813 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   ILE B1815 " --> pdb=" O   THR B1741 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU B1743 " --> pdb=" O   ILE B1815 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL B1742 " --> pdb=" O   PHE B1767 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   SER B1769 " --> pdb=" O   VAL B1742 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   VAL B1744 " --> pdb=" O   SER B1769 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   CYS B1792 " --> pdb=" O   ILE B1766 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   ILE B1768 " --> pdb=" O   CYS B1792 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 886 through 889
      removed outlier: 3.750A  pdb=" N   GLY B 980 " --> pdb=" O   PHE B 968 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   GLU B 972 " --> pdb=" O   LEU B 976 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   LEU B 976 " --> pdb=" O   GLU B 972 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   LEU B 977 " --> pdb=" O   ILE B 943 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   ILE B 943 " --> pdb=" O   LEU B 977 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   SER B 979 " --> pdb=" O   VAL B 941 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 941 " --> pdb=" O   SER B 979 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER B1080 " --> pdb=" O   ARG B1120 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU B1043 " --> pdb=" O   SER B1038 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG B1036 " --> pdb=" O   GLU B1045 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 902 through 904
      removed outlier: 3.596A  pdb=" N   GLN B 903 " --> pdb=" O   GLU B1026 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1074 through 1077
      removed outlier: 5.785A  pdb=" N   ILE B1125 " --> pdb=" O   PRO B1075 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 1482 through 1485
      removed outlier: 6.021A  pdb=" N   THR B1482 " --> pdb=" O   TRP B1514 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B1516 " --> pdb=" O   THR B1482 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   LEU B1484 " --> pdb=" O   VAL B1516 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LEU B1513 " --> pdb=" O   ARG B1541 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL B1543 " --> pdb=" O   LEU B1513 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU B1515 " --> pdb=" O   VAL B1543 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL B1545 " --> pdb=" O   LEU B1515 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY B1517 " --> pdb=" O   VAL B1545 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   ASN B1571 " --> pdb=" O   VAL B1540 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   CYS B1542 " --> pdb=" O   ASN B1571 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   HIS B1573 " --> pdb=" O   CYS B1542 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLN B1544 " --> pdb=" O   HIS B1573 " (cutoff:3.500A)
      removed outlier: 8.509A  pdb=" N   PHE B1570 " --> pdb=" O   TYR B1581 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   TYR B1581 " --> pdb=" O   PHE B1570 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   HIS B2179 " --> pdb=" O   VAL B1137 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   VAL B2175 " --> pdb=" O   TYR B1141 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   SER B2129 " --> pdb=" O   VAL B2176 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   CYS B2178 " --> pdb=" O   SER B2129 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN B2131 " --> pdb=" O   CYS B2178 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   GLY B2036 " --> pdb=" O   HIS B2087 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   VAL B2089 " --> pdb=" O   GLY B2036 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   VAL B2038 " --> pdb=" O   VAL B2089 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   PHE B2091 " --> pdb=" O   VAL B2038 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ASN B2040 " --> pdb=" O   PHE B2091 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   SER B2093 " --> pdb=" O   ASN B2040 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   SER B1956 " --> pdb=" O   GLY B2037 " (cutoff:3.500A)
      removed outlier: 8.540A  pdb=" N   PHE B2039 " --> pdb=" O   SER B1956 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL B1958 " --> pdb=" O   PHE B2039 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 1352 through 1353
      removed outlier: 3.791A  pdb=" N   LYS B1352 " --> pdb=" O   TYR B1335 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   VAL B1304 " --> pdb=" O   ARG B1334 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR B1336 " --> pdb=" O   VAL B1304 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL B1306 " --> pdb=" O   THR B1336 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   GLY B1338 " --> pdb=" O   VAL B1306 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   GLU B1308 " --> pdb=" O   GLY B1338 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   LEU B1374 " --> pdb=" O   ILE B1303 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASN B1305 " --> pdb=" O   LEU B1374 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL B1376 " --> pdb=" O   ASN B1305 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU B1307 " --> pdb=" O   VAL B1376 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LYS B1378 " --> pdb=" O   LEU B1307 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ALA B1309 " --> pdb=" O   LYS B1378 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU B1375 " --> pdb=" O   LEU B1405 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   GLN B1407 " --> pdb=" O   LEU B1375 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   LEU B1377 " --> pdb=" O   GLN B1407 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   PHE B1409 " --> pdb=" O   LEU B1377 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   ALA B1466 " --> pdb=" O   SER B1461 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   SER B1461 " --> pdb=" O   ALA B1466 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   MET B1468 " --> pdb=" O   HIS B1459 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   HIS B1459 " --> pdb=" O   MET B1468 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU B1470 " --> pdb=" O   VAL B1457 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1595 through 1597
    Processing sheet with id=AB8, first strand: chain 'B' and resid 1600 through 1604
    Processing sheet with id=AB9, first strand: chain 'B' and resid 1697 through 1699
      removed outlier: 3.598A  pdb=" N   ARG B1677 " --> pdb=" O   THR B1636 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 1639 through 1642
      removed outlier: 4.649A  pdb=" N   LEU B1923 " --> pdb=" O   VAL B1642 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR B1902 " --> pdb=" O   LYS B1926 " (cutoff:3.500A)

    789 hydrogen bonds defined for protein.
    2193 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: 8.88

  Time building geometry restraints manager: 4.18 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 19310
        1.03 -     1.23: 62
        1.23 -     1.42: 8292
        1.42 -     1.61: 11450
        1.61 -     1.81: 156
  Bond restraints: 39270
  Sorted by residual:
  bond pdb=" C   GLU B1658 "
       pdb=" N   LEU B1659 "
    ideal  model  delta    sigma   weight residual
    1.330  1.365 -0.035 1.47e-02 4.63e+03 5.76e+00
  bond pdb=" C   GLU A1658 "
       pdb=" N   LEU A1659 "
    ideal  model  delta    sigma   weight residual
    1.331  1.365 -0.034 1.48e-02 4.57e+03 5.30e+00
  bond pdb=" CA  LYS A1518 "
       pdb=" CB  LYS A1518 "
    ideal  model  delta    sigma   weight residual
    1.527  1.574 -0.047 2.48e-02 1.63e+03 3.56e+00
  bond pdb=" CA  LYS B1518 "
       pdb=" CB  LYS B1518 "
    ideal  model  delta    sigma   weight residual
    1.527  1.574 -0.046 2.48e-02 1.63e+03 3.48e+00
  bond pdb=" N   VAL A1137 "
       pdb=" CA  VAL A1137 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.22e+00
  ... (remaining 39265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 68161
        1.29 -     2.58: 2527
        2.58 -     3.87: 224
        3.87 -     5.16: 34
        5.16 -     6.45: 8
  Bond angle restraints: 70954
  Sorted by residual:
  angle pdb=" N   ASP B1462 "
        pdb=" CA  ASP B1462 "
        pdb=" C   ASP B1462 "
      ideal   model   delta    sigma   weight residual
     114.39  108.97    5.42 1.45e+00 4.76e-01 1.40e+01
  angle pdb=" N   ASP A1462 "
        pdb=" CA  ASP A1462 "
        pdb=" C   ASP A1462 "
      ideal   model   delta    sigma   weight residual
     114.39  108.98    5.41 1.45e+00 4.76e-01 1.39e+01
  angle pdb=" N   VAL A1137 "
        pdb=" CA  VAL A1137 "
        pdb=" C   VAL A1137 "
      ideal   model   delta    sigma   weight residual
     106.21  110.17   -3.96 1.07e+00 8.73e-01 1.37e+01
  angle pdb=" N   VAL B1137 "
        pdb=" CA  VAL B1137 "
        pdb=" C   VAL B1137 "
      ideal   model   delta    sigma   weight residual
     106.21  110.15   -3.94 1.07e+00 8.73e-01 1.36e+01
  angle pdb=" N   GLY B1686 "
        pdb=" CA  GLY B1686 "
        pdb=" C   GLY B1686 "
      ideal   model   delta    sigma   weight residual
     110.56  115.43   -4.87 1.36e+00 5.41e-01 1.28e+01
  ... (remaining 70949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 16425
       17.94 -    35.87: 1377
       35.87 -    53.81: 478
       53.81 -    71.74: 126
       71.74 -    89.68: 24
  Dihedral angle restraints: 18430
    sinusoidal: 10036
      harmonic: 8394
  Sorted by residual:
  dihedral pdb=" CA  CYS B1491 "
           pdb=" C   CYS B1491 "
           pdb=" N   SER B1492 "
           pdb=" CA  SER B1492 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  CYS A1491 "
           pdb=" C   CYS A1491 "
           pdb=" N   SER A1492 "
           pdb=" CA  SER A1492 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  LEU B1416 "
           pdb=" C   LEU B1416 "
           pdb=" N   LEU B1417 "
           pdb=" CA  LEU B1417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 18427 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 2149
       0.036 -    0.071: 634
       0.071 -    0.107: 181
       0.107 -    0.143: 68
       0.143 -    0.178: 2
  Chirality restraints: 3034
  Sorted by residual:
  chirality pdb=" CB  VAL B1721 "
            pdb=" CA  VAL B1721 "
            pdb=" CG1 VAL B1721 "
            pdb=" CG2 VAL B1721 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CB  VAL A1721 "
            pdb=" CA  VAL A1721 "
            pdb=" CG1 VAL A1721 "
            pdb=" CG2 VAL A1721 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  ILE A2100 "
            pdb=" N   ILE A2100 "
            pdb=" C   ILE A2100 "
            pdb=" CB  ILE A2100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 3031 not shown)

  Planarity restraints: 5884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1416 "    0.010 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" C   LEU A1416 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU A1416 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A1417 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B1416 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" C   LEU B1416 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LEU B1416 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B1417 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1789 "   -0.137 9.50e-02 1.11e+02   4.60e-02 2.54e+00
        pdb=" NE  ARG A1789 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1789 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1789 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1789 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A1789 "    0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG A1789 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A1789 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A1789 "    0.000 2.00e-02 2.50e+03
  ... (remaining 5881 not shown)

  Histogram of nonbonded interaction distances:
        1.24 -     1.91: 198
        1.91 -     2.58: 41308
        2.58 -     3.25: 118606
        3.25 -     3.93: 148509
        3.93 -     4.60: 235631
  Nonbonded interactions: 544252
  Sorted by model distance:
  nonbonded pdb=" HB2 ALA A1311 "
            pdb="HG13 VAL A1337 "
     model   vdw
     1.237 2.440
  nonbonded pdb=" HB2 ALA B1311 "
            pdb="HG13 VAL B1337 "
     model   vdw
     1.238 2.440
  nonbonded pdb=" OD1 ASP A1859 "
            pdb="HH12 ARG B1733 "
     model   vdw
     1.536 2.450
  nonbonded pdb=" OE1 GLU B1136 "
            pdb=" H   GLU B1136 "
     model   vdw
     1.536 2.450
  nonbonded pdb=" OE1 GLU A1136 "
            pdb=" H   GLU A1136 "
     model   vdw
     1.536 2.450
  ... (remaining 544247 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.370
  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:             0.240
  Extract box with map and model:          0.900
  Check model and map are aligned:         0.110
  Set scattering table:                    0.090
  Process input model:                     61.630
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  19900  Z= 0.199
  Angle     :  0.618   6.449  26956  Z= 0.361
  Chirality :  0.039   0.178   3034
  Planarity :  0.004   0.061   3494
  Dihedral  : 15.899  89.678   7288
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.10 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.17), residues: 2480
  helix:  0.66 (0.18), residues: 882
  sheet: -1.96 (0.26), residues: 400
  loop : -1.78 (0.17), residues: 1198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1789 
 TYR   0.014   0.002   TYR A1017 
 PHE   0.010   0.001   PHE A1316 
 TRP   0.012   0.001   TRP A1274 
 HIS   0.010   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (19900)
  covalent geometry    : angle       0.61814 (26956)
  hydrogen bonds       : bond        0.12821 (  789)
  hydrogen bonds       : angle       6.30110 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 203
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1094 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6383 (mm-30)
REVERT: A 1484 LEU cc_start: 0.8252 (tp) cc_final: 0.8029 (tp)
REVERT: B 1094 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6399 (mm-30)
REVERT: B 1484 LEU cc_start: 0.8228 (tp) cc_final: 0.8014 (tp)
  outliers start: 33
  outliers final: 30
  residues processed: 234
  average time/residue: 0.3043
  time to fit residues: 109.8914
Evaluate side-chains
  215 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1530 CYS
Chi-restraints excluded: chain A residue 1534 GLU
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1587 THR
Chi-restraints excluded: chain A residue 1625 SER
Chi-restraints excluded: chain A residue 1669 THR
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1740 ASP
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain B residue 1095 ASP
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1530 CYS
Chi-restraints excluded: chain B residue 1534 GLU
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1587 THR
Chi-restraints excluded: chain B residue 1625 SER
Chi-restraints excluded: chain B residue 1669 THR
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1740 ASP
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2149 VAL
Chi-restraints excluded: chain B residue 2175 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 216 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 194 optimal weight:    0.6980
   chunk 227 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 247 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A1079 GLN
B1079 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.119827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.098355 restraints weight = 108363.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.102434 restraints weight = 42029.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.104943 restraints weight = 23627.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.106486 restraints weight = 16292.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.107461 restraints weight = 12748.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.0682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  19900  Z= 0.126
  Angle     :  0.511   5.062  26956  Z= 0.266
  Chirality :  0.039   0.165   3034
  Planarity :  0.004   0.039   3494
  Dihedral  :  5.000  49.208   2757
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.19 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.17), residues: 2480
  helix:  0.79 (0.18), residues: 894
  sheet: -1.88 (0.25), residues: 422
  loop : -1.60 (0.18), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1789 
 TYR   0.011   0.001   TYR A1017 
 PHE   0.018   0.001   PHE B1449 
 TRP   0.008   0.001   TRP B1274 
 HIS   0.007   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (19900)
  covalent geometry    : angle       0.51136 (26956)
  hydrogen bonds       : bond        0.03998 (  789)
  hydrogen bonds       : angle       5.22930 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1015 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7705 (mt-10)
REVERT: A 1094 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6305 (mm-30)
REVERT: A 1484 LEU cc_start: 0.8243 (tp) cc_final: 0.8033 (tp)
REVERT: B 1015 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7697 (mt-10)
REVERT: B 1094 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6340 (mm-30)
REVERT: B 1484 LEU cc_start: 0.8243 (tp) cc_final: 0.8033 (tp)
REVERT: B 1560 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7946 (t80)
  outliers start: 40
  outliers final: 32
  residues processed: 224
  average time/residue: 0.3417
  time to fit residues: 118.4330
Evaluate side-chains
  219 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1489 LEU
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1534 GLU
Chi-restraints excluded: chain A residue 1699 CYS
Chi-restraints excluded: chain A residue 1702 SER
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2058 TYR
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue 1015 GLU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1534 GLU
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1699 CYS
Chi-restraints excluded: chain B residue 1702 SER
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2058 TYR
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 230 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 235 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 165 optimal weight:    7.9990
   chunk 167 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 188 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 227 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A2105 ASN
B2105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.117740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.096387 restraints weight = 109313.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.100341 restraints weight = 42984.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.102765 restraints weight = 24352.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.104265 restraints weight = 16875.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.105219 restraints weight = 13258.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  19900  Z= 0.217
  Angle     :  0.541   5.477  26956  Z= 0.287
  Chirality :  0.040   0.190   3034
  Planarity :  0.004   0.033   3494
  Dihedral  :  4.811  48.393   2730
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.10 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.17), residues: 2480
  helix:  0.67 (0.18), residues: 894
  sheet: -2.13 (0.25), residues: 418
  loop : -1.68 (0.17), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1789 
 TYR   0.012   0.002   TYR B2167 
 PHE   0.010   0.001   PHE B1055 
 TRP   0.009   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (19900)
  covalent geometry    : angle       0.54094 (26956)
  hydrogen bonds       : bond        0.04194 (  789)
  hydrogen bonds       : angle       5.25337 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 189
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1094 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6354 (mm-30)
REVERT: A 1446 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7357 (mpp80)
REVERT: A 1450 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8575 (ttt-90)
REVERT: A 1484 LEU cc_start: 0.8378 (tp) cc_final: 0.8157 (tp)
REVERT: B 1094 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6345 (mm-30)
REVERT: B 1446 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7365 (mpp80)
REVERT: B 1484 LEU cc_start: 0.8374 (tp) cc_final: 0.8159 (tp)
REVERT: B 1560 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8030 (t80)
  outliers start: 52
  outliers final: 39
  residues processed: 232
  average time/residue: 0.3684
  time to fit residues: 131.0025
Evaluate side-chains
  216 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1446 ARG
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1534 GLU
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2030 THR
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2058 TYR
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue 1026 GLU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1446 ARG
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1534 GLU
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2030 THR
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2058 TYR
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 233 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 195 optimal weight:    1.9990
   chunk 227 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0270
   chunk 14 optimal weight:    4.9990
   chunk 232 optimal weight:    0.7980
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
B1802 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.095182 restraints weight = 108953.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.099223 restraints weight = 42820.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.101718 restraints weight = 24136.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103271 restraints weight = 16632.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.104195 restraints weight = 12980.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  19900  Z= 0.099
  Angle     :  0.481   4.673  26956  Z= 0.249
  Chirality :  0.039   0.176   3034
  Planarity :  0.003   0.040   3494
  Dihedral  :  4.552  47.641   2730
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.95 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.17), residues: 2480
  helix:  0.97 (0.18), residues: 894
  sheet: -1.79 (0.25), residues: 420
  loop : -1.51 (0.18), residues: 1166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1789 
 TYR   0.018   0.001   TYR A1168 
 PHE   0.026   0.001   PHE B1449 
 TRP   0.007   0.001   TRP A1274 
 HIS   0.008   0.001   HIS A1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (19900)
  covalent geometry    : angle       0.48135 (26956)
  hydrogen bonds       : bond        0.03371 (  789)
  hydrogen bonds       : angle       4.85476 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 182
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1015 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7660 (mt-10)
REVERT: A 1094 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6438 (mm-30)
REVERT: A 1450 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8603 (ttt-90)
REVERT: A 1484 LEU cc_start: 0.8242 (tp) cc_final: 0.8027 (tp)
REVERT: A 1529 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7385 (t0)
REVERT: B 1015 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7661 (mt-10)
REVERT: B 1094 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6435 (mm-30)
REVERT: B 1450 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8610 (ttt-90)
REVERT: B 1484 LEU cc_start: 0.8236 (tp) cc_final: 0.8016 (tp)
REVERT: B 1529 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7398 (t0)
REVERT: B 1560 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7934 (t80)
  outliers start: 49
  outliers final: 32
  residues processed: 222
  average time/residue: 0.3487
  time to fit residues: 119.5917
Evaluate side-chains
  211 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 174
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1489 LEU
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1529 ASN
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue 1015 GLU
Chi-restraints excluded: chain B residue 1022 LEU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1529 ASN
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 152 optimal weight:    8.9990
   chunk 193 optimal weight:    2.9990
   chunk 186 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 234 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.113801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.092695 restraints weight = 110130.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.096588 restraints weight = 43592.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099005 restraints weight = 24741.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100504 restraints weight = 17162.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101456 restraints weight = 13472.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  19900  Z= 0.191
  Angle     :  0.511   4.872  26956  Z= 0.270
  Chirality :  0.040   0.192   3034
  Planarity :  0.004   0.035   3494
  Dihedral  :  4.530  47.379   2722
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.05 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.17), residues: 2480
  helix:  0.94 (0.18), residues: 882
  sheet: -1.90 (0.25), residues: 422
  loop : -1.62 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1789 
 TYR   0.015   0.002   TYR A2106 
 PHE   0.035   0.001   PHE A1449 
 TRP   0.008   0.001   TRP A1274 
 HIS   0.008   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (19900)
  covalent geometry    : angle       0.51116 (26956)
  hydrogen bonds       : bond        0.03787 (  789)
  hydrogen bonds       : angle       5.00308 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 175
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1015 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7678 (mt-10)
REVERT: A 1094 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6444 (mm-30)
REVERT: A 1450 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8620 (ttt-90)
REVERT: A 1484 LEU cc_start: 0.8333 (tp) cc_final: 0.8084 (tp)
REVERT: A 2166 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8993 (t0)
REVERT: B 1094 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6438 (mm-30)
REVERT: B 1450 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8631 (ttt-90)
REVERT: B 1484 LEU cc_start: 0.8357 (tp) cc_final: 0.8120 (tp)
REVERT: B 1560 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7962 (t80)
REVERT: B 2166 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8997 (t0)
  outliers start: 60
  outliers final: 47
  residues processed: 224
  average time/residue: 0.3433
  time to fit residues: 119.9976
Evaluate side-chains
  221 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 170
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1337 VAL
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1489 LEU
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2030 THR
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2166 ASP
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1381 LEU
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2030 THR
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2166 ASP
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 148 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 132 optimal weight:   10.0000
   chunk 184 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 134 optimal weight:    0.4980
   chunk 205 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 240 optimal weight:    2.9990
   chunk 189 optimal weight:    6.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A2098 HIS
B2098 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.092988 restraints weight = 110536.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096934 restraints weight = 43816.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.099384 restraints weight = 24812.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100900 restraints weight = 17178.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.101846 restraints weight = 13454.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  19900  Z= 0.163
  Angle     :  0.499   4.813  26956  Z= 0.263
  Chirality :  0.039   0.194   3034
  Planarity :  0.003   0.036   3494
  Dihedral  :  4.523  47.351   2722
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.10 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.17), residues: 2480
  helix:  0.96 (0.18), residues: 882
  sheet: -1.92 (0.25), residues: 420
  loop : -1.57 (0.18), residues: 1178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1789 
 TYR   0.012   0.001   TYR B2106 
 PHE   0.027   0.001   PHE B1449 
 TRP   0.008   0.001   TRP B1274 
 HIS   0.008   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (19900)
  covalent geometry    : angle       0.49858 (26956)
  hydrogen bonds       : bond        0.03658 (  789)
  hydrogen bonds       : angle       4.93858 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 173
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1015 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7665 (mt-10)
REVERT: A 1094 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6440 (mm-30)
REVERT: A 1450 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8621 (ttt-90)
REVERT: A 1484 LEU cc_start: 0.8308 (tp) cc_final: 0.8077 (tp)
REVERT: A 2166 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8970 (t0)
REVERT: B 1015 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7653 (mt-10)
REVERT: B 1094 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6441 (mm-30)
REVERT: B 1450 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8628 (ttt-90)
REVERT: B 1484 LEU cc_start: 0.8330 (tp) cc_final: 0.8099 (tp)
REVERT: B 1560 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7915 (t80)
REVERT: B 2166 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8969 (t0)
  outliers start: 60
  outliers final: 45
  residues processed: 223
  average time/residue: 0.3452
  time to fit residues: 121.3257
Evaluate side-chains
  218 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 168
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2166 ASP
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1015 GLU
Chi-restraints excluded: chain B residue 1022 LEU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1198 LEU
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1271 TYR
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1381 LEU
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2166 ASP
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 146 optimal weight:    1.9990
   chunk 154 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 249 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 175 optimal weight:    4.9990
   chunk 132 optimal weight:    7.9990
   chunk 159 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.113036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091924 restraints weight = 110571.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.095809 restraints weight = 43943.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098214 restraints weight = 24963.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.099706 restraints weight = 17329.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.100658 restraints weight = 13601.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  19900  Z= 0.205
  Angle     :  0.524   5.252  26956  Z= 0.278
  Chirality :  0.040   0.202   3034
  Planarity :  0.004   0.036   3494
  Dihedral  :  4.626  47.351   2722
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.90 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.17), residues: 2480
  helix:  0.89 (0.18), residues: 878
  sheet: -2.22 (0.23), residues: 460
  loop : -1.54 (0.18), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1789 
 TYR   0.013   0.002   TYR B2106 
 PHE   0.019   0.001   PHE A1449 
 TRP   0.010   0.001   TRP B1274 
 HIS   0.008   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (19900)
  covalent geometry    : angle       0.52355 (26956)
  hydrogen bonds       : bond        0.03867 (  789)
  hydrogen bonds       : angle       5.03728 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 173
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1015 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7639 (mt-10)
REVERT: A 1094 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6440 (mm-30)
REVERT: A 1450 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8627 (ttt-90)
REVERT: A 1484 LEU cc_start: 0.8377 (tp) cc_final: 0.8132 (tp)
REVERT: B 1015 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7636 (mt-10)
REVERT: B 1094 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6453 (mm-30)
REVERT: B 1450 ARG cc_start: 0.8898 (ttp80) cc_final: 0.8643 (ttt-90)
REVERT: B 1484 LEU cc_start: 0.8386 (tp) cc_final: 0.8146 (tp)
REVERT: B 1560 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7922 (t80)
  outliers start: 65
  outliers final: 53
  residues processed: 225
  average time/residue: 0.3224
  time to fit residues: 115.2915
Evaluate side-chains
  223 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 167
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1381 LEU
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1452 HIS
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2030 THR
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2149 VAL
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  961 VAL
Chi-restraints excluded: chain B residue  975 ASN
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1015 GLU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1198 LEU
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1381 LEU
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1452 HIS
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2030 THR
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 167 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 134 optimal weight:    8.9990
   chunk 224 optimal weight:    4.9990
   chunk 109 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 190 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 210 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.114336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.093189 restraints weight = 109553.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.097134 restraints weight = 43483.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.099579 restraints weight = 24612.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.101112 restraints weight = 17013.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.102031 restraints weight = 13281.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  19900  Z= 0.133
  Angle     :  0.491   4.765  26956  Z= 0.257
  Chirality :  0.039   0.192   3034
  Planarity :  0.003   0.037   3494
  Dihedral  :  4.517  47.616   2722
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.48 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.17), residues: 2480
  helix:  1.04 (0.18), residues: 878
  sheet: -2.08 (0.24), residues: 468
  loop : -1.46 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1789 
 TYR   0.011   0.001   TYR B2167 
 PHE   0.017   0.001   PHE A1449 
 TRP   0.009   0.001   TRP A1274 
 HIS   0.009   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (19900)
  covalent geometry    : angle       0.49071 (26956)
  hydrogen bonds       : bond        0.03537 (  789)
  hydrogen bonds       : angle       4.86955 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 175
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1094 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6446 (mm-30)
REVERT: A 1484 LEU cc_start: 0.8353 (tp) cc_final: 0.8111 (tp)
REVERT: B 1094 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6441 (mm-30)
REVERT: B 1450 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8642 (ttt-90)
REVERT: B 1484 LEU cc_start: 0.8360 (tp) cc_final: 0.8020 (tp)
REVERT: B 1560 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7870 (t80)
  outliers start: 61
  outliers final: 51
  residues processed: 226
  average time/residue: 0.3383
  time to fit residues: 120.1722
Evaluate side-chains
  219 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 167
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1271 TYR
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2149 VAL
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  961 VAL
Chi-restraints excluded: chain B residue  975 ASN
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1022 LEU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1198 LEU
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1381 LEU
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1489 LEU
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2149 VAL
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 176 optimal weight:    0.4980
   chunk 178 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 240 optimal weight:    3.9990
   chunk 147 optimal weight:    2.9990
   chunk 153 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 166 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.113898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.092933 restraints weight = 109886.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096850 restraints weight = 43364.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.099275 restraints weight = 24510.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.100783 restraints weight = 16950.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.101731 restraints weight = 13240.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  19900  Z= 0.153
  Angle     :  0.497   4.747  26956  Z= 0.262
  Chirality :  0.039   0.194   3034
  Planarity :  0.003   0.040   3494
  Dihedral  :  4.514  47.538   2722
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.62 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.17), residues: 2480
  helix:  1.02 (0.18), residues: 878
  sheet: -2.06 (0.24), residues: 464
  loop : -1.46 (0.18), residues: 1138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1450 
 TYR   0.014   0.001   TYR A2106 
 PHE   0.018   0.001   PHE A1449 
 TRP   0.011   0.001   TRP A1274 
 HIS   0.009   0.001   HIS B1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (19900)
  covalent geometry    : angle       0.49708 (26956)
  hydrogen bonds       : bond        0.03548 (  789)
  hydrogen bonds       : angle       4.85241 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 169
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1094 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6442 (mm-30)
REVERT: A 1484 LEU cc_start: 0.8378 (tp) cc_final: 0.8030 (tp)
REVERT: A 1872 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8407 (t0)
REVERT: B 1094 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6450 (mm-30)
REVERT: B 1484 LEU cc_start: 0.8385 (tp) cc_final: 0.8045 (tp)
REVERT: B 1560 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7885 (t80)
  outliers start: 58
  outliers final: 50
  residues processed: 218
  average time/residue: 0.3394
  time to fit residues: 116.5432
Evaluate side-chains
  217 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 165
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  961 VAL
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 1872 ASP
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2031 ASP
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2149 VAL
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  961 VAL
Chi-restraints excluded: chain B residue  975 ASN
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1022 LEU
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1198 LEU
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1381 LEU
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1560 PHE
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2149 VAL
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 110 optimal weight:    0.3980
   chunk 29 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 227 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 175 optimal weight:    7.9990
   chunk 81 optimal weight:    0.2980
   chunk 148 optimal weight:    0.4980
   chunk 141 optimal weight:    7.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A1802 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.094743 restraints weight = 108762.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.098734 restraints weight = 42811.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.101218 restraints weight = 24121.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.102750 restraints weight = 16592.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.103722 restraints weight = 12945.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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   0.050  19900  Z= 0.098
  Angle     :  0.474   4.711  26956  Z= 0.246
  Chirality :  0.039   0.184   3034
  Planarity :  0.003   0.039   3494
  Dihedral  :  4.369  48.090   2722
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 20.38 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.17), residues: 2480
  helix:  1.21 (0.18), residues: 878
  sheet: -1.84 (0.26), residues: 420
  loop : -1.41 (0.18), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B1450 
 TYR   0.009   0.001   TYR B1168 
 PHE   0.015   0.001   PHE A1449 
 TRP   0.010   0.001   TRP A1274 
 HIS   0.008   0.001   HIS A1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (19900)
  covalent geometry    : angle       0.47368 (26956)
  hydrogen bonds       : bond        0.03192 (  789)
  hydrogen bonds       : angle       4.63802 ( 2193)

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

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

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4960 Ramachandran restraints generated.
    2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 175
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1094 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6439 (mm-30)
REVERT: A 1484 LEU cc_start: 0.8367 (tp) cc_final: 0.8039 (tp)
REVERT: B 1094 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6413 (mm-30)
REVERT: B 1484 LEU cc_start: 0.8373 (tp) cc_final: 0.8049 (tp)
  outliers start: 46
  outliers final: 44
  residues processed: 214
  average time/residue: 0.3308
  time to fit residues: 112.3451
Evaluate side-chains
  209 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 165
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  975 ASN
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1117 VAL
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 1275 ASP
Chi-restraints excluded: chain A residue 1306 VAL
Chi-restraints excluded: chain A residue 1440 TYR
Chi-restraints excluded: chain A residue 1519 SER
Chi-restraints excluded: chain A residue 1542 CYS
Chi-restraints excluded: chain A residue 1586 ILE
Chi-restraints excluded: chain A residue 1635 CYS
Chi-restraints excluded: chain A residue 1721 VAL
Chi-restraints excluded: chain A residue 1766 ILE
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2125 LEU
Chi-restraints excluded: chain A residue 2150 ILE
Chi-restraints excluded: chain A residue 2175 VAL
Chi-restraints excluded: chain A residue 2178 CYS
Chi-restraints excluded: chain B residue  961 VAL
Chi-restraints excluded: chain B residue  975 ASN
Chi-restraints excluded: chain B residue  983 THR
Chi-restraints excluded: chain B residue  993 SER
Chi-restraints excluded: chain B residue 1117 VAL
Chi-restraints excluded: chain B residue 1133 HIS
Chi-restraints excluded: chain B residue 1198 LEU
Chi-restraints excluded: chain B residue 1247 ASN
Chi-restraints excluded: chain B residue 1275 ASP
Chi-restraints excluded: chain B residue 1306 VAL
Chi-restraints excluded: chain B residue 1440 TYR
Chi-restraints excluded: chain B residue 1519 SER
Chi-restraints excluded: chain B residue 1542 CYS
Chi-restraints excluded: chain B residue 1586 ILE
Chi-restraints excluded: chain B residue 1635 CYS
Chi-restraints excluded: chain B residue 1721 VAL
Chi-restraints excluded: chain B residue 1766 ILE
Chi-restraints excluded: chain B residue 2026 VAL
Chi-restraints excluded: chain B residue 2031 ASP
Chi-restraints excluded: chain B residue 2125 LEU
Chi-restraints excluded: chain B residue 2150 ILE
Chi-restraints excluded: chain B residue 2175 VAL
Chi-restraints excluded: chain B residue 2178 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 233 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 187 optimal weight:    6.9990
   chunk 199 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 157 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.094729 restraints weight = 109326.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.098736 restraints weight = 42730.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101223 restraints weight = 24029.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.102743 restraints weight = 16551.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.103714 restraints weight = 12907.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  19900  Z= 0.105
  Angle     :  0.473   6.755  26956  Z= 0.245
  Chirality :  0.039   0.184   3034
  Planarity :  0.003   0.040   3494
  Dihedral  :  4.302  48.634   2722
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.76 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.17), residues: 2480
  helix:  1.33 (0.18), residues: 878
  sheet: -1.81 (0.26), residues: 418
  loop : -1.34 (0.18), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1450 
 TYR   0.011   0.001   TYR A1017 
 PHE   0.015   0.001   PHE A1449 
 TRP   0.010   0.001   TRP B1274 
 HIS   0.007   0.001   HIS A1452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (19900)
  covalent geometry    : angle       0.47289 (26956)
  hydrogen bonds       : bond        0.03137 (  789)
  hydrogen bonds       : angle       4.56806 ( 2193)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7447.49 seconds
wall clock time: 127 minutes 37.93 seconds (7657.93 seconds total)