Starting phenix.real_space_refine
on Wed Mar  4 10:10:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a6f_11672/03_2026/7a6f_11672.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      50      5.16       5
     C    8193      2.51       5
     N    2092      2.21       5
     O    2316      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12655
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1164, 9050
          Classifications: {'peptide': 1164}
          Link IDs: {'PTRANS': 27, 'TRANS': 1136}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1656
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'CYS%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 1647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1647
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PRO%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 302
          Unusual residues: {'CLR': 8, 'ZQU': 2}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 3.06, per 1000 atoms: 0.24
  Number of scatterers: 12655
  At special positions: 0
  Unit cell: (103.32, 208.32, 100.8, 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      50     16.00
     F       4      9.00
     O    2316      8.00
     N    2092      7.00
     C    8193      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  93 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 199 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS C 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.65
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 201 " distance=2.09

  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: 1.08
  Conformation dependent library (CDL) restraints added in 605.4 milliseconds
  

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2940

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 14 sheets defined
      48.5% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 62
      removed outlier: 3.552A  pdb=" N   VAL A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 80
      removed outlier: 3.747A  pdb=" N   LEU A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASP A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 157
      removed outlier: 3.560A  pdb=" N   ALA A 140 " --> pdb=" O   TRP A 136 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   HIS A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG A 157 " --> pdb=" O   HIS A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 174
    Processing helix  chain 'A' and resid 175 through 187
    Processing helix  chain 'A' and resid 187 through 211
      removed outlier: 4.316A  pdb=" N   GLY A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLY A 211 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.757A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 237
    Processing helix  chain 'A' and resid 246 through 260
      removed outlier: 4.263A  pdb=" N   ALA A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA A 252 " --> pdb=" O   ALA A 248 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A 260 " --> pdb=" O   GLU A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 268
    Processing helix  chain 'A' and resid 269 through 323
      removed outlier: 3.803A  pdb=" N   GLU A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   THR A 319 " --> pdb=" O   TRP A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 345
      removed outlier: 3.523A  pdb=" N   VAL A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 371
      removed outlier: 4.631A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 3.822A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 469
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 3.623A  pdb=" N   MET A 514 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 547
      removed outlier: 3.608A  pdb=" N   ARG A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 575
    Processing helix  chain 'A' and resid 588 through 592
      removed outlier: 3.546A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 588 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 592 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 588 through 592'
    Processing helix  chain 'A' and resid 611 through 619
      removed outlier: 3.635A  pdb=" N   LEU A 615 " --> pdb=" O   ASN A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 707 through 741
      removed outlier: 3.646A  pdb=" N   PHE A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   GLN A 725 " --> pdb=" O   ASN A 721 " (cutoff:3.500A)
      Proline residue:  A 726  - end of helix
      removed outlier: 4.460A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 797
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 810 through 852
      removed outlier: 3.569A  pdb=" N   ALA A 822 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   ARG A 832 " --> pdb=" O   ALA A 828 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 829 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 852 " --> pdb=" O   ILE A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 862
      removed outlier: 3.550A  pdb=" N   THR A 858 " --> pdb=" O   GLY A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 880
    Processing helix  chain 'A' and resid 887 through 903
      removed outlier: 3.570A  pdb=" N   GLY A 892 " --> pdb=" O   LYS A 888 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 893 " --> pdb=" O   GLU A 889 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN A 903 " --> pdb=" O   GLU A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 909
      removed outlier: 3.790A  pdb=" N   SER A 909 " --> pdb=" O   ARG A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 965
      removed outlier: 3.932A  pdb=" N   MET A 919 " --> pdb=" O   LYS A 915 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER A 923 " --> pdb=" O   MET A 919 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   VAL A 926 " --> pdb=" O   GLN A 922 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 3.528A  pdb=" N   HIS A 936 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLY A 939 " --> pdb=" O   ALA A 935 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER A 943 " --> pdb=" O   GLY A 939 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR A 950 " --> pdb=" O   GLN A 946 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR A 953 " --> pdb=" O   MET A 949 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ALA A 954 " --> pdb=" O   TYR A 950 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   PHE A 957 " --> pdb=" O   TYR A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 993
      removed outlier: 3.979A  pdb=" N   PHE A 983 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLY A 984 " --> pdb=" O   ALA A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1013
    Processing helix  chain 'A' and resid 1075 through 1084
      removed outlier: 3.772A  pdb=" N   VAL A1079 " --> pdb=" O   GLY A1075 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL A1080 " --> pdb=" O   LYS A1076 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLN A1081 " --> pdb=" O   SER A1077 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A1082 " --> pdb=" O   THR A1078 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A1083 " --> pdb=" O   VAL A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1113
    Processing helix  chain 'A' and resid 1126 through 1134
    Processing helix  chain 'A' and resid 1141 through 1152
      removed outlier: 3.619A  pdb=" N   ILE A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1161
      removed outlier: 3.674A  pdb=" N   SER A1160 " --> pdb=" O   ALA A1156 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A1161 " --> pdb=" O   PHE A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1191
      removed outlier: 3.929A  pdb=" N   ARG A1183 " --> pdb=" O   GLY A1179 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE A1184 " --> pdb=" O   GLN A1180 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ILE A1186 " --> pdb=" O   GLN A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1220
      removed outlier: 3.718A  pdb=" N   ALA A1217 " --> pdb=" O   VAL A1213 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU A1218 " --> pdb=" O   VAL A1214 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A1220 " --> pdb=" O   GLU A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1262
    Processing helix  chain 'A' and resid 1265 through 1271
      removed outlier: 3.682A  pdb=" N   SER A1269 " --> pdb=" O   GLY A1265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 133
    Processing helix  chain 'B' and resid 187 through 193
      removed outlier: 3.551A  pdb=" N   ARG B 193 " --> pdb=" O   ASP B 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.812A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 3.970A  pdb=" N   ASP C 136 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 417
      removed outlier: 3.828A  pdb=" N   ARG A 395 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   MET A 450 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399
      removed outlier: 4.085A  pdb=" N   PHE A 399 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 410 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473
      removed outlier: 6.904A  pdb=" N   GLY A 471 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU A 552 " --> pdb=" O   ILE A 583 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ILE A 585 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU A 554 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 423 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR A 422 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ALA A 599 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ALA A 424 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   PHE A 601 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   VAL A 426 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   GLY A 600 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1053 through 1060
      removed outlier: 7.878A  pdb=" N   GLN A1054 " --> pdb=" O   VAL A1041 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A1041 " --> pdb=" O   GLN A1054 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   LEU A1056 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1228 through 1230
      removed outlier: 5.703A  pdb=" N   LEU A1066 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1246 through 1247
      removed outlier: 3.567A  pdb=" N   GLN A1247 " --> pdb=" O   ARG A1250 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A1250 " --> pdb=" O   GLN A1247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 24
    Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 160
    Processing sheet with id=AB1, first strand: chain 'B' and resid 167 through 168
    Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59
      removed outlier: 6.162A  pdb=" N   LEU C  45 " --> pdb=" O   THR C  40 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   THR C  40 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 126 through 130
      removed outlier: 3.632A  pdb=" N   LYS C 149 " --> pdb=" O   SER C 126 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU C 130 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU C 144 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   TYR C 181 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160
      removed outlier: 3.882A  pdb=" N   ILE C 199 " --> pdb=" O   ILE C 216 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1779 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: 2.17

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3945
        1.34 -     1.46: 2864
        1.46 -     1.58: 6030
        1.58 -     1.71: 15
        1.71 -     1.83: 83
  Bond restraints: 12937
  Sorted by residual:
  bond pdb=" C32 ZQU A1301 "
       pdb=" N03 ZQU A1301 "
    ideal  model  delta    sigma   weight residual
    1.316  1.496 -0.180 2.00e-02 2.50e+03 8.13e+01
  bond pdb=" C32 ZQU A1302 "
       pdb=" N03 ZQU A1302 "
    ideal  model  delta    sigma   weight residual
    1.316  1.490 -0.174 2.00e-02 2.50e+03 7.58e+01
  bond pdb=" C17 ZQU A1301 "
       pdb=" C19 ZQU A1301 "
    ideal  model  delta    sigma   weight residual
    1.390  1.561 -0.171 2.00e-02 2.50e+03 7.30e+01
  bond pdb=" C17 ZQU A1302 "
       pdb=" C19 ZQU A1302 "
    ideal  model  delta    sigma   weight residual
    1.390  1.561 -0.171 2.00e-02 2.50e+03 7.28e+01
  bond pdb=" C07 ZQU A1301 "
       pdb=" C13 ZQU A1301 "
    ideal  model  delta    sigma   weight residual
    1.393  1.557 -0.164 2.00e-02 2.50e+03 6.72e+01
  ... (remaining 12932 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 17349
        3.75 -     7.50: 202
        7.50 -    11.25: 16
       11.25 -    15.01: 4
       15.01 -    18.76: 2
  Bond angle restraints: 17573
  Sorted by residual:
  angle pdb=" C03 ZQU A1301 "
        pdb=" C01 ZQU A1301 "
        pdb=" C04 ZQU A1301 "
      ideal   model   delta    sigma   weight residual
     121.18  139.94  -18.76 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" C03 ZQU A1302 "
        pdb=" C01 ZQU A1302 "
        pdb=" C04 ZQU A1302 "
      ideal   model   delta    sigma   weight residual
     121.18  138.12  -16.94 3.00e+00 1.11e-01 3.19e+01
  angle pdb=" C   ALA A 883 "
        pdb=" N   LEU A 884 "
        pdb=" CA  LEU A 884 "
      ideal   model   delta    sigma   weight residual
     121.54  130.56   -9.02 1.91e+00 2.74e-01 2.23e+01
  angle pdb=" F01 ZQU A1302 "
        pdb=" C03 ZQU A1302 "
        pdb=" F02 ZQU A1302 "
      ideal   model   delta    sigma   weight residual
     108.18  122.26  -14.08 3.00e+00 1.11e-01 2.20e+01
  angle pdb=" N   LYS A1014 "
        pdb=" CA  LYS A1014 "
        pdb=" C   LYS A1014 "
      ideal   model   delta    sigma   weight residual
     110.35  116.63   -6.28 1.36e+00 5.41e-01 2.13e+01
  ... (remaining 17568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.14: 7652
       31.14 -    62.29: 402
       62.29 -    93.43: 31
       93.43 -   124.58: 3
      124.58 -   155.72: 18
  Dihedral angle restraints: 8106
    sinusoidal: 3520
      harmonic: 4586
  Sorted by residual:
  dihedral pdb=" CA  ALA C 104 "
           pdb=" C   ALA C 104 "
           pdb=" N   TRP C 105 "
           pdb=" CA  TRP C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.16  -25.84     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  PHE A1123 "
           pdb=" C   PHE A1123 "
           pdb=" N   ASP A1124 "
           pdb=" CA  ASP A1124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.32   25.68     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  TYR A 853 "
           pdb=" C   TYR A 853 "
           pdb=" N   GLY A 854 "
           pdb=" CA  GLY A 854 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.74   25.26     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 8103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.004: 2028
       1.004 -    2.009: 0
       2.009 -    3.013: 0
       3.013 -    4.017: 0
       4.017 -    5.022: 2
  Chirality restraints: 2030
  Sorted by residual:
  chirality pdb=" C06 ZQU A1302 "
            pdb=" C07 ZQU A1302 "
            pdb=" C08 ZQU A1302 "
            pdb=" N01 ZQU A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42   -2.60    5.02 2.00e-01 2.50e+01 6.30e+02
  chirality pdb=" C06 ZQU A1301 "
            pdb=" C07 ZQU A1301 "
            pdb=" C08 ZQU A1301 "
            pdb=" N01 ZQU A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42   -2.52    4.94 2.00e-01 2.50e+01 6.10e+02
  chirality pdb=" C17 CLR A1308 "
            pdb=" C13 CLR A1308 "
            pdb=" C16 CLR A1308 "
            pdb=" C20 CLR A1308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.99   -0.43 2.00e-01 2.50e+01 4.68e+00
  ... (remaining 2027 not shown)

  Planarity restraints: 2162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 428 "    0.020 2.00e-02 2.50e+03   3.83e-02 1.47e+01
        pdb=" C   ASN A 428 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ASN A 428 "    0.025 2.00e-02 2.50e+03
        pdb=" N   SER A 429 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1119 "   -0.036 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO A1120 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A1120 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1120 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 222 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO A 223 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2159 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 14
        2.25 -     2.92: 5751
        2.92 -     3.58: 17801
        3.58 -     4.24: 28244
        4.24 -     4.90: 48296
  Nonbonded interactions: 100106
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 425 "
            pdb=" CE1 PHE A 601 "
     model   vdw
     1.592 3.760
  nonbonded pdb=" O   SER A1020 "
            pdb=" CD  GLN A1107 "
     model   vdw
     2.062 3.270
  nonbonded pdb=" CB  ALA A  58 "
            pdb=" OE1 GLN A 132 "
     model   vdw
     2.122 3.460
  nonbonded pdb=" N   ASP A 744 "
            pdb=" OD1 ASP A 744 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" O   THR A 898 "
            pdb=" CG2 ILE A 901 "
     model   vdw
     2.172 3.460
  ... (remaining 100101 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.020
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
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      :  0.014   0.616  12942  Z= 0.694
  Angle     :  1.136  26.622  17583  Z= 0.646
  Chirality :  0.169   5.022   2030
  Planarity :  0.005   0.071   2162
  Dihedral  : 19.432 155.722   5151
  Min Nonbonded Distance : 1.592

Molprobity Statistics.
  All-atom Clashscore : 32.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 28.39 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.13 (0.18), residues: 1584
  helix: -2.25 (0.16), residues: 705
  sheet: -2.59 (0.30), residues: 264
  loop : -3.22 (0.20), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 101 
 TYR   0.019   0.002   TYR A 310 
 PHE   0.030   0.002   PHE B  94 
 TRP   0.021   0.002   TRP A 708 
 HIS   0.005   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.01248 (12937)
  covalent geometry    : angle       1.10605 (17573)
  SS BOND              : bond        0.27682 (    5)
  SS BOND              : angle      10.98463 (   10)
  hydrogen bonds       : bond        0.21691 (  617)
  hydrogen bonds       : angle       8.58010 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  105 MET cc_start: 0.7287 (ttt) cc_final: 0.6591 (tpp)
REVERT: A  276 ARG cc_start: 0.6823 (mtp180) cc_final: 0.6616 (mtp180)
REVERT: A  616 MET cc_start: 0.3092 (mtt) cc_final: 0.2578 (mtm)
REVERT: A  628 MET cc_start: 0.1775 (tpp) cc_final: 0.1491 (ttt)
REVERT: A 1133 TYR cc_start: 0.6890 (t80) cc_final: 0.6647 (t80)
REVERT: C  154 GLU cc_start: 0.6801 (tp30) cc_final: 0.6564 (tp30)
  outliers start: 20
  outliers final: 11
  residues processed: 144
  average time/residue: 0.1318
  time to fit residues: 26.8742
Evaluate side-chains
  113 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue  744 ASP
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue 1014 LYS
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue  101 ARG
Chi-restraints excluded: chain C residue  117 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  61 HIS
A 166 HIS
A 280 ASN
A 347 GLN
A 629 GLN
A 750 GLN
A 809 ASN
A 842 ASN
A 925 GLN
A 990 GLN
A1112 HIS
A1180 GLN
A1193 GLN
A1254 HIS
A1274 GLN
** B  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN
B 212 ASN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 170 HIS
C 202 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.210155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.176887 restraints weight = 16857.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.170823 restraints weight = 46341.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.166211 restraints weight = 25316.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.165652 restraints weight = 27219.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.165189 restraints weight = 17483.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  12942  Z= 0.244
  Angle     :  0.775   8.536  17583  Z= 0.396
  Chirality :  0.048   0.373   2030
  Planarity :  0.005   0.053   2162
  Dihedral  : 16.236 139.040   2343
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.74 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 25.47 %
    Favored  : 66.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.19), residues: 1584
  helix: -0.93 (0.18), residues: 717
  sheet: -2.10 (0.30), residues: 268
  loop : -2.47 (0.23), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 148 
 TYR   0.017   0.002   TYR C 100 
 PHE   0.022   0.002   PHE B  94 
 TRP   0.019   0.002   TRP A 708 
 HIS   0.006   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (12937)
  covalent geometry    : angle       0.77362 (17573)
  SS BOND              : bond        0.00885 (    5)
  SS BOND              : angle       1.88634 (   10)
  hydrogen bonds       : bond        0.07778 (  617)
  hydrogen bonds       : angle       5.73956 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 101
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  702 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6720 (tttt)
REVERT: A  876 MET cc_start: 0.8263 (tpt) cc_final: 0.7845 (tpt)
REVERT: A  913 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6859 (mp0)
REVERT: A 1133 TYR cc_start: 0.6902 (t80) cc_final: 0.6686 (t80)
REVERT: C   62 ASP cc_start: 0.7378 (m-30) cc_final: 0.7054 (m-30)
  outliers start: 102
  outliers final: 71
  residues processed: 194
  average time/residue: 0.1009
  time to fit residues: 29.4681
Evaluate side-chains
  164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 91
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  490 TYR
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  702 LYS
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  842 ASN
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  937 ILE
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1204 SER
Chi-restraints excluded: chain A residue 1214 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 134 optimal weight:   20.0000
   chunk 125 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 127 optimal weight:    0.0670
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:   20.0000
   chunk 131 optimal weight:   20.0000
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 936 HIS
A 946 GLN
B  43 GLN
C  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.215674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.183045 restraints weight = 16951.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.178045 restraints weight = 45131.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.173217 restraints weight = 25510.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.172782 restraints weight = 27851.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172394 restraints weight = 16412.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12942  Z= 0.141
  Angle     :  0.640   8.638  17583  Z= 0.326
  Chirality :  0.043   0.291   2030
  Planarity :  0.004   0.048   2162
  Dihedral  : 15.777 137.181   2327
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 25.92 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.20), residues: 1584
  helix:  0.05 (0.19), residues: 739
  sheet: -1.63 (0.32), residues: 245
  loop : -2.09 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  66 
 TYR   0.013   0.001   TYR C 100 
 PHE   0.013   0.001   PHE A 512 
 TRP   0.016   0.001   TRP A 708 
 HIS   0.006   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12937)
  covalent geometry    : angle       0.63763 (17573)
  SS BOND              : bond        0.00520 (    5)
  SS BOND              : angle       2.40545 (   10)
  hydrogen bonds       : bond        0.05985 (  617)
  hydrogen bonds       : angle       4.99408 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 97
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  227 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7453 (tt)
REVERT: A  616 MET cc_start: 0.3156 (mtt) cc_final: 0.2655 (mtm)
REVERT: A  733 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8804 (m)
REVERT: A  876 MET cc_start: 0.8179 (tpt) cc_final: 0.7840 (tpt)
REVERT: C   62 ASP cc_start: 0.7401 (m-30) cc_final: 0.6946 (m-30)
  outliers start: 88
  outliers final: 60
  residues processed: 176
  average time/residue: 0.1069
  time to fit residues: 28.3136
Evaluate side-chains
  149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 87
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  943 SER
Chi-restraints excluded: chain A residue  946 GLN
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1204 SER
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  192 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9980
   chunk 139 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 145 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 143 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1034 ASN
A1064 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.215845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183252 restraints weight = 16912.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.177345 restraints weight = 44288.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.171359 restraints weight = 24845.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.171142 restraints weight = 28202.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.170551 restraints weight = 20071.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12942  Z= 0.140
  Angle     :  0.622   9.682  17583  Z= 0.315
  Chirality :  0.043   0.267   2030
  Planarity :  0.004   0.042   2162
  Dihedral  : 15.628 137.434   2325
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 26.89 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.21), residues: 1584
  helix:  0.34 (0.19), residues: 740
  sheet: -1.40 (0.31), residues: 249
  loop : -1.88 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.018   0.001   TYR A 950 
 PHE   0.015   0.001   PHE A 942 
 TRP   0.012   0.001   TRP A 708 
 HIS   0.006   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12937)
  covalent geometry    : angle       0.62055 (17573)
  SS BOND              : bond        0.00656 (    5)
  SS BOND              : angle       1.94969 (   10)
  hydrogen bonds       : bond        0.05765 (  617)
  hydrogen bonds       : angle       4.78621 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 92
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  616 MET cc_start: 0.2831 (mtt) cc_final: 0.2584 (mtm)
REVERT: A  876 MET cc_start: 0.8201 (tpt) cc_final: 0.7831 (tpt)
REVERT: B  190 GLU cc_start: 0.4885 (mp0) cc_final: 0.4229 (tt0)
REVERT: C   62 ASP cc_start: 0.7436 (m-30) cc_final: 0.6953 (m-30)
  outliers start: 86
  outliers final: 65
  residues processed: 164
  average time/residue: 0.0984
  time to fit residues: 24.6713
Evaluate side-chains
  153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 88
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  943 SER
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1204 SER
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue    4 MET
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  111 ILE
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  192 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 112 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 141 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 105 optimal weight:   20.0000
   chunk 116 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 128 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 946 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.212455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.179188 restraints weight = 16967.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.173282 restraints weight = 45490.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.167992 restraints weight = 23811.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.167265 restraints weight = 31367.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.167237 restraints weight = 16447.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12942  Z= 0.210
  Angle     :  0.680   8.241  17583  Z= 0.345
  Chirality :  0.045   0.283   2030
  Planarity :  0.004   0.040   2162
  Dihedral  : 15.709 137.851   2325
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  7.34 %
    Allowed  : 26.07 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.21), residues: 1584
  helix:  0.24 (0.19), residues: 727
  sheet: -1.39 (0.31), residues: 249
  loop : -1.82 (0.24), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 787 
 TYR   0.021   0.002   TYR A1133 
 PHE   0.020   0.002   PHE B  94 
 TRP   0.012   0.001   TRP A 708 
 HIS   0.005   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (12937)
  covalent geometry    : angle       0.67808 (17573)
  SS BOND              : bond        0.00923 (    5)
  SS BOND              : angle       2.05854 (   10)
  hydrogen bonds       : bond        0.06514 (  617)
  hydrogen bonds       : angle       4.92231 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 95
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6618 (mmm) cc_final: 0.6249 (mmm)
REVERT: A  616 MET cc_start: 0.2770 (mtt) cc_final: 0.2529 (mtm)
REVERT: A  876 MET cc_start: 0.8203 (tpt) cc_final: 0.7804 (tpt)
REVERT: B  190 GLU cc_start: 0.4905 (mp0) cc_final: 0.4268 (tt0)
REVERT: C   62 ASP cc_start: 0.7348 (m-30) cc_final: 0.6868 (m-30)
  outliers start: 98
  outliers final: 74
  residues processed: 179
  average time/residue: 0.0990
  time to fit residues: 26.6942
Evaluate side-chains
  166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 92
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  283 GLU
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  931 SER
Chi-restraints excluded: chain A residue  937 ILE
Chi-restraints excluded: chain A residue  943 SER
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  986 MET
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue  101 ARG
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  187 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0470
   chunk 137 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 142 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 35 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.215915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.183295 restraints weight = 16767.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.176979 restraints weight = 43042.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.171195 restraints weight = 24871.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.170923 restraints weight = 28062.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.170404 restraints weight = 17730.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12942  Z= 0.132
  Angle     :  0.600   8.702  17583  Z= 0.303
  Chirality :  0.042   0.262   2030
  Planarity :  0.003   0.040   2162
  Dihedral  : 15.525 137.316   2325
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 27.42 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.21), residues: 1584
  helix:  0.68 (0.19), residues: 722
  sheet: -1.27 (0.31), residues: 259
  loop : -1.66 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.021   0.001   TYR A1133 
 PHE   0.015   0.001   PHE C 172 
 TRP   0.024   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12937)
  covalent geometry    : angle       0.59909 (17573)
  SS BOND              : bond        0.00661 (    5)
  SS BOND              : angle       1.50215 (   10)
  hydrogen bonds       : bond        0.05512 (  617)
  hydrogen bonds       : angle       4.60715 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 101
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6240 (mmm) cc_final: 0.5914 (mmm)
REVERT: A  242 LYS cc_start: 0.5822 (mttt) cc_final: 0.5606 (mttp)
REVERT: A  876 MET cc_start: 0.8166 (tpt) cc_final: 0.7814 (tpt)
REVERT: C   62 ASP cc_start: 0.7402 (m-30) cc_final: 0.6948 (m-30)
  outliers start: 80
  outliers final: 61
  residues processed: 173
  average time/residue: 0.1071
  time to fit residues: 27.9174
Evaluate side-chains
  157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 96
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 117 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 149 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 570 GLN
A 629 GLN
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.215468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.183496 restraints weight = 16714.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.176636 restraints weight = 43109.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.171962 restraints weight = 26098.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171225 restraints weight = 29350.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.171124 restraints weight = 16430.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12942  Z= 0.141
  Angle     :  0.613   8.511  17583  Z= 0.307
  Chirality :  0.043   0.270   2030
  Planarity :  0.003   0.039   2162
  Dihedral  : 15.501 137.405   2325
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 27.49 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.21), residues: 1584
  helix:  0.75 (0.19), residues: 727
  sheet: -1.17 (0.31), residues: 251
  loop : -1.60 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 442 
 TYR   0.024   0.001   TYR A1133 
 PHE   0.015   0.001   PHE B  94 
 TRP   0.013   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (12937)
  covalent geometry    : angle       0.61116 (17573)
  SS BOND              : bond        0.00771 (    5)
  SS BOND              : angle       1.91789 (   10)
  hydrogen bonds       : bond        0.05513 (  617)
  hydrogen bonds       : angle       4.56449 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 97
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6283 (mmm) cc_final: 0.5945 (mmm)
REVERT: A  242 LYS cc_start: 0.5793 (mttt) cc_final: 0.5585 (mttp)
REVERT: A  876 MET cc_start: 0.8155 (tpt) cc_final: 0.7796 (tpt)
REVERT: A 1021 TYR cc_start: 0.4202 (OUTLIER) cc_final: 0.2018 (t80)
REVERT: B  190 GLU cc_start: 0.4577 (mp0) cc_final: 0.4228 (mt-10)
REVERT: C   33 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8684 (m)
REVERT: C   62 ASP cc_start: 0.7433 (m-30) cc_final: 0.6977 (m-30)
  outliers start: 78
  outliers final: 69
  residues processed: 165
  average time/residue: 0.1002
  time to fit residues: 25.0951
Evaluate side-chains
  165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 94
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  697 PHE
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  923 SER
Chi-restraints excluded: chain A residue  931 SER
Chi-restraints excluded: chain A residue  948 MET
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1021 TYR
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 127 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 112 optimal weight:   20.0000
   chunk 115 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 508 ASN
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.215373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.176687 restraints weight = 16730.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.177537 restraints weight = 44212.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.173714 restraints weight = 20182.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.172860 restraints weight = 23873.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.172790 restraints weight = 15156.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12942  Z= 0.148
  Angle     :  0.616   8.793  17583  Z= 0.309
  Chirality :  0.043   0.270   2030
  Planarity :  0.003   0.040   2162
  Dihedral  : 15.487 137.451   2325
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 27.49 %
    Favored  : 66.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.21), residues: 1584
  helix:  0.79 (0.19), residues: 727
  sheet: -1.06 (0.32), residues: 251
  loop : -1.53 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 276 
 TYR   0.022   0.001   TYR A1133 
 PHE   0.015   0.001   PHE B  94 
 TRP   0.015   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12937)
  covalent geometry    : angle       0.61485 (17573)
  SS BOND              : bond        0.00756 (    5)
  SS BOND              : angle       1.86429 (   10)
  hydrogen bonds       : bond        0.05554 (  617)
  hydrogen bonds       : angle       4.55236 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 98
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6355 (mmm) cc_final: 0.6015 (mmm)
REVERT: A  876 MET cc_start: 0.8218 (tpt) cc_final: 0.7906 (tpt)
REVERT: A 1021 TYR cc_start: 0.4349 (OUTLIER) cc_final: 0.2075 (t80)
REVERT: A 1151 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4888 (tt0)
REVERT: B  190 GLU cc_start: 0.4471 (mp0) cc_final: 0.4154 (mt-10)
REVERT: C   33 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8670 (m)
REVERT: C   62 ASP cc_start: 0.7413 (m-30) cc_final: 0.6976 (m-30)
  outliers start: 81
  outliers final: 69
  residues processed: 169
  average time/residue: 0.1007
  time to fit residues: 25.8351
Evaluate side-chains
  166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 94
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  454 ASP
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  931 SER
Chi-restraints excluded: chain A residue  948 MET
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1021 TYR
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  188 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 155 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 153 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:   20.0000
   chunk 156 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.215105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.182377 restraints weight = 16791.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.175341 restraints weight = 43507.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.169595 restraints weight = 25083.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.168874 restraints weight = 27757.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.168737 restraints weight = 14460.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12942  Z= 0.151
  Angle     :  0.619   9.336  17583  Z= 0.310
  Chirality :  0.043   0.270   2030
  Planarity :  0.003   0.040   2162
  Dihedral  : 15.472 137.463   2325
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 27.42 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.21), residues: 1584
  helix:  0.77 (0.19), residues: 735
  sheet: -0.96 (0.32), residues: 248
  loop : -1.50 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 276 
 TYR   0.023   0.001   TYR A1133 
 PHE   0.017   0.001   PHE C 172 
 TRP   0.015   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12937)
  covalent geometry    : angle       0.61826 (17573)
  SS BOND              : bond        0.00752 (    5)
  SS BOND              : angle       1.75397 (   10)
  hydrogen bonds       : bond        0.05560 (  617)
  hydrogen bonds       : angle       4.51585 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 98
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6386 (mmm) cc_final: 0.6050 (mmm)
REVERT: A  876 MET cc_start: 0.8177 (tpt) cc_final: 0.7824 (tpt)
REVERT: A 1021 TYR cc_start: 0.4341 (OUTLIER) cc_final: 0.2114 (t80)
REVERT: A 1151 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4918 (tt0)
REVERT: B  190 GLU cc_start: 0.4477 (mp0) cc_final: 0.4210 (mt-10)
REVERT: C   33 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (m)
  outliers start: 80
  outliers final: 73
  residues processed: 169
  average time/residue: 0.0932
  time to fit residues: 24.1905
Evaluate side-chains
  169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 93
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  923 SER
Chi-restraints excluded: chain A residue  931 SER
Chi-restraints excluded: chain A residue  948 MET
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1021 TYR
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  188 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 139 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 155 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0170
   chunk 120 optimal weight:    0.0970
   overall best weight:    1.2222

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.217346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.187841 restraints weight = 16831.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.180556 restraints weight = 43241.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.176387 restraints weight = 27185.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.175870 restraints weight = 28253.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.175290 restraints weight = 17700.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12942  Z= 0.154
  Angle     :  0.622  10.125  17583  Z= 0.310
  Chirality :  0.043   0.270   2030
  Planarity :  0.003   0.039   2162
  Dihedral  : 15.463 137.507   2325
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 27.49 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.21), residues: 1584
  helix:  0.83 (0.19), residues: 733
  sheet: -0.94 (0.32), residues: 248
  loop : -1.52 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 276 
 TYR   0.023   0.001   TYR A1133 
 PHE   0.016   0.001   PHE B  94 
 TRP   0.016   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12937)
  covalent geometry    : angle       0.62031 (17573)
  SS BOND              : bond        0.00780 (    5)
  SS BOND              : angle       1.75076 (   10)
  hydrogen bonds       : bond        0.05639 (  617)
  hydrogen bonds       : angle       4.50971 ( 1779)

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

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

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3168 Ramachandran restraints generated.
    1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 97
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "CYS B 214 " (corrupted residue). Skipping it.
REVERT: A  111 MET cc_start: 0.6352 (mmm) cc_final: 0.6016 (mmm)
REVERT: A  876 MET cc_start: 0.8182 (tpt) cc_final: 0.7866 (tpt)
REVERT: A 1021 TYR cc_start: 0.4436 (OUTLIER) cc_final: 0.2150 (t80)
REVERT: A 1151 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4915 (tt0)
REVERT: B  190 GLU cc_start: 0.4579 (mp0) cc_final: 0.4310 (mt-10)
REVERT: C   33 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8726 (m)
  outliers start: 80
  outliers final: 71
  residues processed: 168
  average time/residue: 0.0962
  time to fit residues: 24.3874
Evaluate side-chains
  167 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 93
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  770 PHE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  800 ASP
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  865 VAL
Chi-restraints excluded: chain A residue  904 PHE
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  923 SER
Chi-restraints excluded: chain A residue  931 SER
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  972 GLU
Chi-restraints excluded: chain A residue  975 LEU
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue  993 SER
Chi-restraints excluded: chain A residue 1021 TYR
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1074 CYS
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1127 ILE
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1151 GLU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1226 THR
Chi-restraints excluded: chain A residue 1244 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   96 CYS
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  127 VAL
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  157 THR
Chi-restraints excluded: chain C residue  159 THR
Chi-restraints excluded: chain C residue  170 HIS
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 SER
Chi-restraints excluded: chain C residue  188 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 139 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 141 optimal weight:    0.9990
   chunk 148 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.218951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.189777 restraints weight = 16679.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.180896 restraints weight = 41897.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.175575 restraints weight = 31892.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.175621 restraints weight = 29372.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.175055 restraints weight = 17096.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12942  Z= 0.126
  Angle     :  0.593   8.731  17583  Z= 0.296
  Chirality :  0.042   0.266   2030
  Planarity :  0.003   0.040   2162
  Dihedral  : 15.393 137.266   2325
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.91 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.21), residues: 1584
  helix:  0.99 (0.19), residues: 734
  sheet: -0.89 (0.32), residues: 248
  loop : -1.40 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.021   0.001   TYR A1133 
 PHE   0.016   0.001   PHE C 172 
 TRP   0.016   0.001   TRP C 160 
 HIS   0.005   0.001   HIS C 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12937)
  covalent geometry    : angle       0.59181 (17573)
  SS BOND              : bond        0.00659 (    5)
  SS BOND              : angle       1.52019 (   10)
  hydrogen bonds       : bond        0.05190 (  617)
  hydrogen bonds       : angle       4.40424 ( 1779)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1930.86 seconds
wall clock time: 34 minutes 20.88 seconds (2060.88 seconds total)