Starting phenix.real_space_refine
on Wed Feb  4 00:54:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ltz_63385/02_2026/9ltz_63385.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    5031      2.51       5
     N    1443      2.21       5
     O    1465      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7962
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 2266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2266
          Classifications: {'peptide': 357}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 195}
          Link IDs: {'PTRANS': 9, 'TRANS': 347}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 730
          Unresolved non-hydrogen angles: 937
          Unresolved non-hydrogen dihedrals: 603
          Unresolved non-hydrogen chiralities: 63
          Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 16, 'ARG:plan': 18, 'GLN:plan1': 12, 'PHE:plan': 14, 'ASN:plan1': 8, 'ASP:plan': 14, 'TYR:plan': 8, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 461
    Chain: "S"
      Number of atoms: 4766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 745, 4766
          Classifications: {'peptide': 745}
          Incomplete info: {'truncation_to_alanine': 319}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 718}
          Chain breaks: 9
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1146
          Unresolved non-hydrogen angles: 1434
          Unresolved non-hydrogen dihedrals: 941
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLN:plan1': 21, 'ASN:plan1': 16, 'GLU:plan': 49, 'ARG:plan': 18, 'ASP:plan': 26, 'PHE:plan': 15, 'TYR:plan': 8, 'HIS:plan': 7, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 695
    Chain: "A"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 732
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 113}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 129}
          Unresolved non-hydrogen bonds: 414
          Unresolved non-hydrogen angles: 535
          Unresolved non-hydrogen dihedrals: 346
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 6, 'TRP:plan': 3, 'PHE:plan': 5, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 233
    Chain: "F"
      Number of atoms: 198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 198
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 29}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 41
  Time building chain proxies: 2.13, per 1000 atoms: 0.27
  Number of scatterers: 7962
  At special positions: 0
  Unit cell: (119, 107.95, 108.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1465      8.00
     N    1443      7.00
     C    5031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  18 " - pdb=" SG  CYS S 313 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 377.1 milliseconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2396

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 29 sheets defined
      13.9% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'R' and resid 18 through 26
      removed outlier: 4.038A  pdb=" N   LEU R  22 " --> pdb=" O   VAL R  18 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 34 through 41
    Processing helix  chain 'R' and resid 42 through 45
    Processing helix  chain 'R' and resid 110 through 124
      removed outlier: 3.797A  pdb=" N   VAL R 114 " --> pdb=" O   ASP R 110 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   PHE R 121 " --> pdb=" O   ARG R 117 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   GLU R 122 " --> pdb=" O   GLY R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 220
    Processing helix  chain 'R' and resid 266 through 271
      removed outlier: 3.887A  pdb=" N   ALA R 270 " --> pdb=" O   THR R 267 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL R 271 " --> pdb=" O   VAL R 268 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 293 through 306
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 458 through 462
      removed outlier: 3.568A  pdb=" N   LEU R 461 " --> pdb=" O   SER R 458 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 381 through 385
    Processing helix  chain 'S' and resid 985 through 990
    Processing helix  chain 'S' and resid 1044 through 1059
    Processing helix  chain 'S' and resid 1069 through 1073
    Processing helix  chain 'S' and resid 1091 through 1097
    Processing helix  chain 'S' and resid 1101 through 1109
    Processing helix  chain 'S' and resid 1127 through 1131
      removed outlier: 3.568A  pdb=" N   LYS S1131 " --> pdb=" O   ASP S1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 152 through 166
    Processing helix  chain 'A' and resid 174 through 184
    Processing helix  chain 'A' and resid 184 through 199
    Processing sheet with id=AA1, first strand: chain 'R' and resid 51 through 52
      removed outlier: 7.618A  pdb=" N   THR R  51 " --> pdb=" O   LEU R 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'R' and resid 61 through 65
      removed outlier: 4.556A  pdb=" N   ARG R  63 " --> pdb=" O   ILE R  73 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ILE R  73 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   PHE R  72 " --> pdb=" O   TYR R  85 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   GLU R  86 " --> pdb=" O   LEU R 127 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   LEU R 127 " --> pdb=" O   GLU R  86 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'R' and resid 153 through 160
      removed outlier: 3.765A  pdb=" N   SER R 158 " --> pdb=" O   SER R 192 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER R 192 " --> pdb=" O   SER R 158 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA R 160 " --> pdb=" O   ASP R 190 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASP R 190 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TYR R 191 " --> pdb=" O   LYS R 210 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   LYS R 210 " --> pdb=" O   TYR R 191 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   LEU R 193 " --> pdb=" O   THR R 208 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   THR R 208 " --> pdb=" O   LEU R 193 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   ILE R 195 " --> pdb=" O   THR R 206 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   THR R 206 " --> pdb=" O   ILE R 195 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 222 through 225
      removed outlier: 3.517A  pdb=" N   TYR R 223 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   ILE R 239 " --> pdb=" O   THR R 255 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   THR R 255 " --> pdb=" O   ILE R 239 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   VAL R 241 " --> pdb=" O   VAL R 253 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL R 253 " --> pdb=" O   VAL R 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'R' and resid 341 through 346
      removed outlier: 3.764A  pdb=" N   LEU R 342 " --> pdb=" O   TYR R 368 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TYR R 368 " --> pdb=" O   LEU R 342 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE R 364 " --> pdb=" O   TYR R 346 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 466 through 467
    Processing sheet with id=AA7, first strand: chain 'R' and resid 519 through 521
      removed outlier: 4.139A  pdb=" N   ALA R 519 " --> pdb=" O   VAL R 532 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL R 532 " --> pdb=" O   ALA R 519 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL R 540 " --> pdb=" O   GLN R 533 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 1007 through 1009
      removed outlier: 3.698A  pdb=" N   SER S1027 " --> pdb=" O   VAL S1040 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL S1040 " --> pdb=" O   SER S1027 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU S1029 " --> pdb=" O   GLY S1038 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLY S1038 " --> pdb=" O   LEU S1029 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE S1037 " --> pdb=" O   ALA S   9 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR S1041 " --> pdb=" O   TYR S   5 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TYR S   5 " --> pdb=" O   THR S1041 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ASN S   4 " --> pdb=" O   ILE S1089 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 17 through 21
      removed outlier: 3.550A  pdb=" N   LEU S  39 " --> pdb=" O   VAL S  55 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL S  55 " --> pdb=" O   LEU S  39 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS S  53 " --> pdb=" O   ILE S  41 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 66 through 67
    Processing sheet with id=AB2, first strand: chain 'S' and resid 87 through 88
      removed outlier: 3.894A  pdb=" N   ALA S 104 " --> pdb=" O   ILE S  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 91 through 92
      removed outlier: 3.855A  pdb=" N   LYS S  92 " --> pdb=" O   ASP S  99 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 121 through 124
      removed outlier: 3.562A  pdb=" N   ILE S 121 " --> pdb=" O   ARG S 134 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 164 through 169
      removed outlier: 6.669A  pdb=" N   VAL S 181 " --> pdb=" O   ILE S 165 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL S 167 " --> pdb=" O   CYS S 179 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS S 179 " --> pdb=" O   VAL S 167 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   PHE S 169 " --> pdb=" O   THR S 177 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   THR S 177 " --> pdb=" O   PHE S 169 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU S 194 " --> pdb=" O   ASN S 203 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 164 through 169
      removed outlier: 6.669A  pdb=" N   VAL S 181 " --> pdb=" O   ILE S 165 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL S 167 " --> pdb=" O   CYS S 179 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS S 179 " --> pdb=" O   VAL S 167 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   PHE S 169 " --> pdb=" O   THR S 177 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   THR S 177 " --> pdb=" O   PHE S 169 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG S 188 " --> pdb=" O   VAL S 212 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   VAL S 190 " --> pdb=" O   GLU S 210 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLU S 210 " --> pdb=" O   VAL S 190 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 218 through 221
    Processing sheet with id=AB8, first strand: chain 'S' and resid 270 through 272
      removed outlier: 3.861A  pdb=" N   TYR S 271 " --> pdb=" O   LEU S 283 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU S 283 " --> pdb=" O   TYR S 271 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU S 280 " --> pdb=" O   LEU S 304 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LEU S 304 " --> pdb=" O   LEU S 280 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   MET S 282 " --> pdb=" O   VAL S 302 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL S 302 " --> pdb=" O   MET S 282 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   LEU S 284 " --> pdb=" O   LEU S 300 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU S 300 " --> pdb=" O   LEU S 284 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   GLU S 286 " --> pdb=" O   LYS S 298 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'S' and resid 313 through 314
      removed outlier: 3.691A  pdb=" N   CYS S 313 " --> pdb=" O   GLY S 325 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'S' and resid 378 through 379
    Processing sheet with id=AC2, first strand: chain 'S' and resid 726 through 727
      removed outlier: 3.804A  pdb=" N   GLU S 741 " --> pdb=" O   VAL S 786 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   VAL S 786 " --> pdb=" O   GLU S 741 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   HIS S 789 " --> pdb=" O   GLN S 806 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLN S 806 " --> pdb=" O   HIS S 789 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   LEU S 791 " --> pdb=" O   ALA S 804 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   ALA S 804 " --> pdb=" O   LEU S 791 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE S 793 " --> pdb=" O   LEU S 802 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   SER S 764 " --> pdb=" O   GLN S 806 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'S' and resid 811 through 817
      removed outlier: 3.556A  pdb=" N   TYR S 812 " --> pdb=" O   ALA S 834 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA S 834 " --> pdb=" O   TYR S 812 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY S 832 " --> pdb=" O   LEU S 814 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU S 816 " --> pdb=" O   ILE S 830 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE S 830 " --> pdb=" O   LEU S 816 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'S' and resid 845 through 847
    Processing sheet with id=AC5, first strand: chain 'S' and resid 850 through 853
      removed outlier: 7.036A  pdb=" N   VAL S 850 " --> pdb=" O   VAL S 861 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'S' and resid 870 through 876
      removed outlier: 5.180A  pdb=" N   SER S 872 " --> pdb=" O   SER S 883 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'S' and resid 913 through 917
      removed outlier: 3.512A  pdb=" N   TYR S 913 " --> pdb=" O   GLY S 924 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   VAL S 930 " --> pdb=" O   ARG S 947 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ARG S 947 " --> pdb=" O   VAL S 930 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LEU S 932 " --> pdb=" O   ILE S 945 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'S' and resid 964 through 965
      removed outlier: 6.520A  pdb=" N   VAL S 976 " --> pdb=" O   VAL S 995 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'S' and resid 1076 through 1078
    Processing sheet with id=AD1, first strand: chain 'S' and resid 1114 through 1115
      removed outlier: 3.856A  pdb=" N   TYR S1114 " --> pdb=" O   ARG S1122 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 75 through 79

    260 hydrogen bonds defined for protein.
    672 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: 1.51

  Time building geometry restraints manager: 0.90 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: 2783
        1.34 -     1.46: 1728
        1.46 -     1.58: 3532
        1.58 -     1.70: 2
        1.70 -     1.82: 35
  Bond restraints: 8080
  Sorted by residual:
  bond pdb=" N   PRO R  59 "
       pdb=" CD  PRO R  59 "
    ideal  model  delta    sigma   weight residual
    1.473  1.585 -0.112 1.40e-02 5.10e+03 6.44e+01
  bond pdb=" N   PRO R 524 "
       pdb=" CD  PRO R 524 "
    ideal  model  delta    sigma   weight residual
    1.473  1.550 -0.077 1.40e-02 5.10e+03 3.06e+01
  bond pdb=" CA  PRO S 250 "
       pdb=" C   PRO S 250 "
    ideal  model  delta    sigma   weight residual
    1.517  1.547 -0.030 9.30e-03 1.16e+04 1.01e+01
  bond pdb=" CA  GLU S1002 "
       pdb=" CB  GLU S1002 "
    ideal  model  delta    sigma   weight residual
    1.535  1.486  0.049 1.90e-02 2.77e+03 6.76e+00
  bond pdb=" CG  GLU S1002 "
       pdb=" CD  GLU S1002 "
    ideal  model  delta    sigma   weight residual
    1.516  1.457  0.059 2.50e-02 1.60e+03 5.48e+00
  ... (remaining 8075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11010
        2.32 -     4.63: 92
        4.63 -     6.95: 11
        6.95 -     9.27: 3
        9.27 -    11.58: 1
  Bond angle restraints: 11117
  Sorted by residual:
  angle pdb=" CA  PRO R  59 "
        pdb=" N   PRO R  59 "
        pdb=" CD  PRO R  59 "
      ideal   model   delta    sigma   weight residual
     112.00  100.42   11.58 1.40e+00 5.10e-01 6.84e+01
  angle pdb=" CA  PRO R 524 "
        pdb=" N   PRO R 524 "
        pdb=" CD  PRO R 524 "
      ideal   model   delta    sigma   weight residual
     112.00  103.67    8.33 1.40e+00 5.10e-01 3.54e+01
  angle pdb=" N   PRO R  59 "
        pdb=" CD  PRO R  59 "
        pdb=" CG  PRO R  59 "
      ideal   model   delta    sigma   weight residual
     103.20   95.42    7.78 1.50e+00 4.44e-01 2.69e+01
  angle pdb=" C   ASN F  12 "
        pdb=" N   LYS F  13 "
        pdb=" CA  LYS F  13 "
      ideal   model   delta    sigma   weight residual
     122.44  116.80    5.64 1.19e+00 7.06e-01 2.25e+01
  angle pdb=" CA  GLU S1002 "
        pdb=" CB  GLU S1002 "
        pdb=" CG  GLU S1002 "
      ideal   model   delta    sigma   weight residual
     114.10  107.56    6.54 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 11112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4321
       17.59 -    35.19: 304
       35.19 -    52.78: 92
       52.78 -    70.37: 9
       70.37 -    87.97: 3
  Dihedral angle restraints: 4729
    sinusoidal: 1047
      harmonic: 3682
  Sorted by residual:
  dihedral pdb=" CA  LEU S 152 "
           pdb=" C   LEU S 152 "
           pdb=" N   LYS S 153 "
           pdb=" CA  LYS S 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.51  -35.49     0      5.00e+00 4.00e-02 5.04e+01
  dihedral pdb=" CA  LYS F  13 "
           pdb=" C   LYS F  13 "
           pdb=" N   SER F  14 "
           pdb=" CA  SER F  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  LEU S 890 "
           pdb=" C   LEU S 890 "
           pdb=" N   TYR S 891 "
           pdb=" CA  TYR S 891 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.64  -18.36     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1022
       0.044 -    0.087: 256
       0.087 -    0.131: 109
       0.131 -    0.174: 4
       0.174 -    0.218: 1
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CB  ILE S 884 "
            pdb=" CA  ILE S 884 "
            pdb=" CG1 ILE S 884 "
            pdb=" CG2 ILE S 884 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  MET S1036 "
            pdb=" N   MET S1036 "
            pdb=" C   MET S1036 "
            pdb=" CB  MET S1036 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  PRO R 524 "
            pdb=" N   PRO R 524 "
            pdb=" C   PRO R 524 "
            pdb=" CB  PRO R 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 5.91e-01
  ... (remaining 1389 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS R 523 "   -0.086 5.00e-02 4.00e+02   1.23e-01 2.43e+01
        pdb=" N   PRO R 524 "    0.213 5.00e-02 4.00e+02
        pdb=" CA  PRO R 524 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO R 524 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  58 "    0.061 5.00e-02 4.00e+02   8.44e-02 1.14e+01
        pdb=" N   PRO R  59 "   -0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO R  59 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R  59 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 117 "    0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO A 118 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "    0.045 5.00e-02 4.00e+02
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 63
        2.61 -     3.19: 6572
        3.19 -     3.76: 11037
        3.76 -     4.33: 13611
        4.33 -     4.90: 23282
  Nonbonded interactions: 54565
  Sorted by model distance:
  nonbonded pdb=" O   VAL R  46 "
            pdb=" OH  TYR R 460 "
     model   vdw
     2.042 3.040
  nonbonded pdb=" OE2 GLU S1002 "
            pdb=" CB  MET S1036 "
     model   vdw
     2.169 3.440
  nonbonded pdb=" O   VAL S 219 "
            pdb=" NE2 HIS S 261 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OG  SER S   2 "
            pdb=" OD1 ASN S   4 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   GLY S 119 "
            pdb=" NH1 ARG S 134 "
     model   vdw
     2.268 3.120
  ... (remaining 54560 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.690
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   8081  Z= 0.185
  Angle     :  0.569  11.582  11119  Z= 0.315
  Chirality :  0.044   0.218   1392
  Planarity :  0.005   0.123   1489
  Dihedral  : 14.512  87.966   2330
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.31 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 33.47 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.95 (0.24), residues: 1235
  helix:  1.77 (0.44), residues: 169
  sheet: -1.40 (0.29), residues: 329
  loop : -2.08 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG S 722 
 TYR   0.012   0.001   TYR S 316 
 PHE   0.010   0.001   PHE R 343 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.002   0.001   HIS S  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8080)
  covalent geometry    : angle       0.56920 (11117)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       1.11491 (    2)
  hydrogen bonds       : bond        0.09405 (  251)
  hydrogen bonds       : angle       5.76870 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.278 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0562
  time to fit residues: 5.6534
Evaluate side-chains
  58 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:    0.0040
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7072

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.167857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.142956 restraints weight = 25999.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.4254 rms_B_bonded: 5.25
r_work: 0.4191 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.0500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063   8081  Z= 0.097
  Angle     :  0.481   6.705  11119  Z= 0.250
  Chirality :  0.044   0.183   1392
  Planarity :  0.004   0.068   1489
  Dihedral  :  3.912  35.339   1311
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 31.83 %
    Favored  : 64.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.80 (0.24), residues: 1235
  helix:  2.08 (0.44), residues: 163
  sheet: -1.25 (0.29), residues: 324
  loop : -2.02 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 134 
 TYR   0.013   0.001   TYR S 316 
 PHE   0.009   0.001   PHE R 343 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.004   0.001   HIS S 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8080)
  covalent geometry    : angle       0.48044 (11117)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.75754 (    2)
  hydrogen bonds       : bond        0.02561 (  251)
  hydrogen bonds       : angle       4.76254 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.306 
Fit side-chains
  outliers start: 17
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0644
  time to fit residues: 8.2549
Evaluate side-chains
  72 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   42 PHE
Chi-restraints excluded: chain R residue   47 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  531 SER
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  985 THR
Chi-restraints excluded: chain S residue 1006 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0570
   chunk 8 optimal weight:    8.9990
   chunk 105 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 125 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 103 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.1904

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

Flipped N/Q/H residues before XYZ refinement:
S  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.165232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.139886 restraints weight = 25526.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 5.23
r_work: 0.4151 rms_B_bonded: 5.00 restraints_weight: 2.0000
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.0762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8081  Z= 0.131
  Angle     :  0.511   6.587  11119  Z= 0.266
  Chirality :  0.044   0.222   1392
  Planarity :  0.004   0.063   1489
  Dihedral  :  4.063  34.077   1311
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 31.21 %
    Favored  : 63.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.86 (0.24), residues: 1235
  helix:  2.00 (0.44), residues: 163
  sheet: -1.19 (0.30), residues: 306
  loop : -2.10 (0.22), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 546 
 TYR   0.016   0.001   TYR S 316 
 PHE   0.009   0.001   PHE S1030 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.004   0.001   HIS S 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8080)
  covalent geometry    : angle       0.51036 (11117)
  SS BOND              : bond        0.00650 (    1)
  SS BOND              : angle       1.83306 (    2)
  hydrogen bonds       : bond        0.02814 (  251)
  hydrogen bonds       : angle       4.73876 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.309 
Fit side-chains
  outliers start: 26
  outliers final: 20
  residues processed: 82
  average time/residue: 0.0508
  time to fit residues: 7.0636
Evaluate side-chains
  81 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  531 SER
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue    6 VAL
Chi-restraints excluded: chain S residue   15 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   79 ILE
Chi-restraints excluded: chain S residue  121 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  195 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  764 SER
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  985 THR
Chi-restraints excluded: chain S residue 1006 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 117 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 122 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0070
   chunk 103 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   overall best weight:    2.1000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.160306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.133717 restraints weight = 25784.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 5.09
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8081  Z= 0.214
  Angle     :  0.609   7.104  11119  Z= 0.320
  Chirality :  0.046   0.146   1392
  Planarity :  0.004   0.067   1489
  Dihedral  :  4.822  36.173   1311
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.79 %
    Favored  : 87.21 %
  Rotamer:
    Outliers :  8.42 %
    Allowed  : 30.80 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.29 (0.24), residues: 1235
  helix:  1.33 (0.43), residues: 169
  sheet: -1.10 (0.31), residues: 286
  loop : -2.50 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 546 
 TYR   0.023   0.002   TYR S 316 
 PHE   0.011   0.002   PHE S1030 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.004   0.001   HIS S 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 8080)
  covalent geometry    : angle       0.60785 (11117)
  SS BOND              : bond        0.00579 (    1)
  SS BOND              : angle       2.58278 (    2)
  hydrogen bonds       : bond        0.03602 (  251)
  hydrogen bonds       : angle       5.49380 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 63
  time to evaluate  : 0.407 
Fit side-chains
  outliers start: 41
  outliers final: 28
  residues processed: 94
  average time/residue: 0.0631
  time to fit residues: 9.5123
Evaluate side-chains
  88 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 60
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  231 ILE
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  293 ASN
Chi-restraints excluded: chain R residue  531 SER
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue    6 VAL
Chi-restraints excluded: chain S residue   15 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   79 ILE
Chi-restraints excluded: chain S residue  121 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  195 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  764 SER
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  880 LEU
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  966 LEU
Chi-restraints excluded: chain S residue  969 GLU
Chi-restraints excluded: chain S residue  985 THR
Chi-restraints excluded: chain S residue 1006 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    0.5980
   chunk 121 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0050
   chunk 40 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.1198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.162359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.135934 restraints weight = 25587.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 5.04
r_work: 0.4127 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8081  Z= 0.124
  Angle     :  0.520   6.523  11119  Z= 0.269
  Chirality :  0.044   0.169   1392
  Planarity :  0.004   0.065   1489
  Dihedral  :  4.305  37.514   1311
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 32.24 %
    Favored  : 61.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.08 (0.24), residues: 1235
  helix:  1.75 (0.44), residues: 163
  sheet: -0.98 (0.32), residues: 267
  loop : -2.35 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 546 
 TYR   0.014   0.001   TYR S 316 
 PHE   0.010   0.001   PHE S1030 
 TRP   0.011   0.001   TRP R  36 
 HIS   0.004   0.001   HIS S 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8080)
  covalent geometry    : angle       0.51983 (11117)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       1.25363 (    2)
  hydrogen bonds       : bond        0.02743 (  251)
  hydrogen bonds       : angle       4.94222 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.284 
Fit side-chains
REVERT: S  791 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7998 (mp)
  outliers start: 32
  outliers final: 23
  residues processed: 93
  average time/residue: 0.0580
  time to fit residues: 8.7539
Evaluate side-chains
  86 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  531 SER
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue    6 VAL
Chi-restraints excluded: chain S residue   15 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   61 ILE
Chi-restraints excluded: chain S residue  121 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  195 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  764 SER
Chi-restraints excluded: chain S residue  791 LEU
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  969 GLU
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    0.1980
   chunk 15 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0970
   chunk 79 optimal weight:    0.0470
   chunk 10 optimal weight:    0.0980
   chunk 82 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 121 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0270
   overall best weight:    0.0934

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

Flipped N/Q/H residues before XYZ refinement:
** S  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.168480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.143567 restraints weight = 25870.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.4274 rms_B_bonded: 5.33
r_work: 0.4212 rms_B_bonded: 5.28 restraints_weight: 2.0000
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8081  Z= 0.077
  Angle     :  0.479   7.390  11119  Z= 0.243
  Chirality :  0.044   0.159   1392
  Planarity :  0.003   0.057   1489
  Dihedral  :  3.674  35.204   1311
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 36.55 %
    Favored  : 60.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.73 (0.24), residues: 1235
  helix:  2.03 (0.44), residues: 164
  sheet: -1.10 (0.29), residues: 325
  loop : -2.01 (0.22), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R  40 
 TYR   0.008   0.001   TYR S 271 
 PHE   0.008   0.001   PHE S 323 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.005   0.001   HIS S 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 ( 8080)
  covalent geometry    : angle       0.47870 (11117)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.95972 (    2)
  hydrogen bonds       : bond        0.02167 (  251)
  hydrogen bonds       : angle       4.21768 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.310 
Fit side-chains
  outliers start: 14
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0620
  time to fit residues: 8.2960
Evaluate side-chains
  77 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  124 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  913 TYR
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 52 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 77 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
S  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.161303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.135040 restraints weight = 25665.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 5.22
r_work: 0.4111 rms_B_bonded: 5.02 restraints_weight: 2.0000
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8081  Z= 0.179
  Angle     :  0.568   7.367  11119  Z= 0.294
  Chirality :  0.045   0.163   1392
  Planarity :  0.004   0.065   1489
  Dihedral  :  4.271  33.239   1311
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 34.09 %
    Favored  : 60.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.92 (0.24), residues: 1235
  helix:  1.83 (0.44), residues: 163
  sheet: -0.83 (0.32), residues: 281
  loop : -2.27 (0.21), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 119 
 TYR   0.021   0.002   TYR S 316 
 PHE   0.010   0.001   PHE R 343 
 TRP   0.011   0.001   TRP R  36 
 HIS   0.003   0.001   HIS S 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8080)
  covalent geometry    : angle       0.56554 (11117)
  SS BOND              : bond        0.01645 (    1)
  SS BOND              : angle       4.30583 (    2)
  hydrogen bonds       : bond        0.03060 (  251)
  hydrogen bonds       : angle       4.90113 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 63
  time to evaluate  : 0.359 
Fit side-chains
  outliers start: 25
  outliers final: 19
  residues processed: 83
  average time/residue: 0.0569
  time to fit residues: 7.7474
Evaluate side-chains
  80 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 PHE
Chi-restraints excluded: chain R residue  124 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue   15 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   61 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  764 SER
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 120 optimal weight:    0.0770
   chunk 19 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 91 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 118 optimal weight:    0.5980
   overall best weight:    0.6538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.165659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.140370 restraints weight = 25859.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.4229 rms_B_bonded: 5.33
r_work: 0.4155 rms_B_bonded: 5.25 restraints_weight: 2.0000
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8081  Z= 0.093
  Angle     :  0.501   7.487  11119  Z= 0.254
  Chirality :  0.044   0.145   1392
  Planarity :  0.003   0.064   1489
  Dihedral  :  3.929  35.444   1311
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 35.73 %
    Favored  : 60.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.81 (0.24), residues: 1235
  helix:  1.98 (0.44), residues: 164
  sheet: -0.89 (0.30), residues: 309
  loop : -2.19 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 546 
 TYR   0.011   0.001   TYR S 316 
 PHE   0.009   0.001   PHE S1030 
 TRP   0.011   0.001   TRP R  36 
 HIS   0.004   0.001   HIS S 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8080)
  covalent geometry    : angle       0.49984 (11117)
  SS BOND              : bond        0.00806 (    1)
  SS BOND              : angle       2.52359 (    2)
  hydrogen bonds       : bond        0.02407 (  251)
  hydrogen bonds       : angle       4.52306 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.178 
Fit side-chains
  outliers start: 20
  outliers final: 18
  residues processed: 82
  average time/residue: 0.0562
  time to fit residues: 7.3078
Evaluate side-chains
  81 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   47 PHE
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  124 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue    6 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   61 ILE
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  725 CYS
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0670
   chunk 9 optimal weight:    3.9990
   chunk 112 optimal weight:   30.0000
   chunk 35 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0040
   chunk 83 optimal weight:    0.0770
   chunk 82 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 18 optimal weight:    9.9990
   overall best weight:    0.3088

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.167836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.143019 restraints weight = 25874.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 5.34
r_work: 0.4204 rms_B_bonded: 5.05 restraints_weight: 2.0000
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8081  Z= 0.076
  Angle     :  0.481   8.297  11119  Z= 0.241
  Chirality :  0.044   0.136   1392
  Planarity :  0.003   0.060   1489
  Dihedral  :  3.559  33.248   1311
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 35.73 %
    Favored  : 60.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.60 (0.24), residues: 1235
  helix:  2.08 (0.44), residues: 164
  sheet: -0.67 (0.31), residues: 303
  loop : -2.06 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 546 
 TYR   0.007   0.001   TYR S   5 
 PHE   0.007   0.001   PHE S 323 
 TRP   0.012   0.001   TRP R  36 
 HIS   0.003   0.001   HIS S 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 8080)
  covalent geometry    : angle       0.48061 (11117)
  SS BOND              : bond        0.00560 (    1)
  SS BOND              : angle       1.53634 (    2)
  hydrogen bonds       : bond        0.02105 (  251)
  hydrogen bonds       : angle       4.13882 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.276 
Fit side-chains
  outliers start: 20
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0537
  time to fit residues: 7.3229
Evaluate side-chains
  83 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  124 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  253 VAL
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue   31 LEU
Chi-restraints excluded: chain S residue   61 ILE
Chi-restraints excluded: chain S residue  121 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  880 LEU
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 69 optimal weight:    2.9990
   chunk 112 optimal weight:   30.0000
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.165615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.140480 restraints weight = 25540.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 5.38
r_work: 0.4174 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6777
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8081  Z= 0.110
  Angle     :  0.503   8.831  11119  Z= 0.255
  Chirality :  0.044   0.180   1392
  Planarity :  0.004   0.063   1489
  Dihedral  :  3.752  32.552   1311
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 35.73 %
    Favored  : 59.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.62 (0.24), residues: 1235
  helix:  2.02 (0.44), residues: 164
  sheet: -0.78 (0.30), residues: 318
  loop : -2.04 (0.22), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 546 
 TYR   0.012   0.001   TYR S 316 
 PHE   0.008   0.001   PHE R 343 
 TRP   0.010   0.001   TRP R  36 
 HIS   0.003   0.001   HIS S 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8080)
  covalent geometry    : angle       0.50231 (11117)
  SS BOND              : bond        0.00665 (    1)
  SS BOND              : angle       1.91205 (    2)
  hydrogen bonds       : bond        0.02447 (  251)
  hydrogen bonds       : angle       4.32007 (  672)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.303 
Fit side-chains
REVERT: R  460 TYR cc_start: 0.8159 (m-80) cc_final: 0.7925 (m-80)
  outliers start: 21
  outliers final: 19
  residues processed: 83
  average time/residue: 0.0572
  time to fit residues: 7.6636
Evaluate side-chains
  83 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  124 PHE
Chi-restraints excluded: chain R residue  194 HIS
Chi-restraints excluded: chain R residue  264 ASP
Chi-restraints excluded: chain R residue  541 VAL
Chi-restraints excluded: chain S residue   61 ILE
Chi-restraints excluded: chain S residue  121 ILE
Chi-restraints excluded: chain S residue  190 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  220 ILE
Chi-restraints excluded: chain S residue  321 VAL
Chi-restraints excluded: chain S residue  725 CYS
Chi-restraints excluded: chain S residue  764 SER
Chi-restraints excluded: chain S residue  792 LEU
Chi-restraints excluded: chain S residue  830 ILE
Chi-restraints excluded: chain S residue  870 VAL
Chi-restraints excluded: chain S residue  880 LEU
Chi-restraints excluded: chain S residue  947 ARG
Chi-restraints excluded: chain S residue  985 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 99 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.166436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.141427 restraints weight = 25656.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 5.36
r_work: 0.4183 rms_B_bonded: 5.11 restraints_weight: 2.0000
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8081  Z= 0.092
  Angle     :  0.494   8.957  11119  Z= 0.249
  Chirality :  0.044   0.170   1392
  Planarity :  0.003   0.062   1489
  Dihedral  :  3.660  32.909   1311
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 34.91 %
    Favored  : 60.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.58 (0.24), residues: 1235
  helix:  2.07 (0.44), residues: 164
  sheet: -0.62 (0.31), residues: 300
  loop : -2.05 (0.22), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 546 
 TYR   0.010   0.001   TYR S 316 
 PHE   0.007   0.001   PHE R 528 
 TRP   0.011   0.001   TRP R  36 
 HIS   0.003   0.001   HIS S 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 8080)
  covalent geometry    : angle       0.49400 (11117)
  SS BOND              : bond        0.00542 (    1)
  SS BOND              : angle       1.54534 (    2)
  hydrogen bonds       : bond        0.02272 (  251)
  hydrogen bonds       : angle       4.22131 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2866.05 seconds
wall clock time: 49 minutes 26.09 seconds (2966.09 seconds total)