Starting phenix.real_space_refine
on Tue Jan 13 18:29:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqn_42475/01_2026/8uqn_42475.map"
  }
  resolution = 3.4
  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=   0.069
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: 10
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Al      1      5.89       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      42      5.16       5
     C    5449      2.51       5
     N    1444      2.21       5
     O    1606      1.98       5
     F       4      1.80       5
     H       2      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8552
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2558
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 11, 'TRANS': 303}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 5956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 754, 5956
          Classifications: {'peptide': 754}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 48, 'TRANS': 705}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 89
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Unusual residues: {' MG': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 2.42, per 1000 atoms: 0.28
  Number of scatterers: 8552
  At special positions: 0
  Unit cell: (81.383, 97.324, 118.299, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 10
    Type Number    sf(0)
     Ca      1     19.99
     S      42     16.00
     P       2     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1606      8.00
     N    1444      7.00
     C    5449      6.00
     H       2      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM 8550  O   HOH A 501 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 346.3 milliseconds
  

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 11 sheets defined
      37.5% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 68 through 74
      removed outlier: 3.687A  pdb=" N   ARG A  73 " --> pdb=" O   ASP A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 97
      removed outlier: 3.721A  pdb=" N   TYR A  80 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ASP A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   THR A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.508A  pdb=" N   LYS A 107 " --> pdb=" O   TYR A 103 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 108'
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 125 through 137
      removed outlier: 3.515A  pdb=" N   ILE A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 147
    Processing helix  chain 'A' and resid 148 through 151
      removed outlier: 3.825A  pdb=" N   TYR A 151 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 151'
    Processing helix  chain 'A' and resid 156 through 161
      removed outlier: 3.811A  pdb=" N   TYR A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 161 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 156 through 161'
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 215 through 220
      removed outlier: 3.648A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 247 through 259
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.672A  pdb=" N   GLU A 281 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 315
      removed outlier: 3.622A  pdb=" N   ASP A 315 " --> pdb=" O   LYS A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 352
      removed outlier: 4.167A  pdb=" N   VAL A 340 " --> pdb=" O   ASN A 336 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA A 343 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 25
      removed outlier: 3.931A  pdb=" N   GLY B  25 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    Processing helix  chain 'B' and resid 83 through 91
      removed outlier: 3.906A  pdb=" N   VAL B  89 " --> pdb=" O   LYS B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 101
      removed outlier: 3.828A  pdb=" N   GLU B 100 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.911A  pdb=" N   PHE B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 146
      removed outlier: 3.568A  pdb=" N   GLN B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 163
      removed outlier: 3.572A  pdb=" N   PHE B 152 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 179
      removed outlier: 3.875A  pdb=" N   MET B 178 " --> pdb=" O   ASN B 174 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 179 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.633A  pdb=" N   CYS B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 225 through 231
    Processing helix  chain 'B' and resid 243 through 251
      removed outlier: 3.793A  pdb=" N   ASP B 248 " --> pdb=" O   GLU B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 274
      removed outlier: 3.901A  pdb=" N   ARG B 273 " --> pdb=" O   SER B 270 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU B 274 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 270 through 274'
    Processing helix  chain 'B' and resid 275 through 280
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 292 through 300
      removed outlier: 3.617A  pdb=" N   ARG B 298 " --> pdb=" O   GLU B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.569A  pdb=" N   ALA B 312 " --> pdb=" O   PRO B 309 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B 313 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 313'
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 347 through 355
      removed outlier: 3.928A  pdb=" N   ARG B 351 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 399
    Processing helix  chain 'B' and resid 421 through 433
      removed outlier: 3.631A  pdb=" N   MET B 425 " --> pdb=" O   GLN B 421 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   CYS B 429 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG B 430 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE B 433 " --> pdb=" O   CYS B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 437
      removed outlier: 3.572A  pdb=" N   LEU B 437 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 434 through 437'
    Processing helix  chain 'B' and resid 605 through 611
      removed outlier: 3.540A  pdb=" N   ARG B 611 " --> pdb=" O   ALA B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 632
      removed outlier: 3.808A  pdb=" N   GLU B 627 " --> pdb=" O   THR B 623 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR B 630 " --> pdb=" O   MET B 626 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER B 632 " --> pdb=" O   GLN B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 641
      removed outlier: 3.637A  pdb=" N   VAL B 637 " --> pdb=" O   PRO B 633 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   GLU B 638 " --> pdb=" O   MET B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 666
      removed outlier: 3.705A  pdb=" N   ASN B 666 " --> pdb=" O   GLN B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 687
    Processing helix  chain 'B' and resid 691 through 696
      removed outlier: 4.381A  pdb=" N   SER B 696 " --> pdb=" O   TYR B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 856 through 861
      removed outlier: 3.863A  pdb=" N   ILE B 860 " --> pdb=" O   ALA B 856 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN B 861 " --> pdb=" O   GLU B 857 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 856 through 861'
    Processing helix  chain 'B' and resid 861 through 875
      removed outlier: 3.881A  pdb=" N   ASP B 870 " --> pdb=" O   VAL B 866 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN B 871 " --> pdb=" O   SER B 867 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195
      removed outlier: 6.734A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 9.550A  pdb=" N   SER A 225 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LYS A  41 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   MET A 227 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A  43 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   LEU A 229 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   LEU A  45 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   ALA A 231 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A 325 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65
      removed outlier: 3.839A  pdb=" N   ASN B  39 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B  26 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 170 through 171
    Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 242
    Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 328
    Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 388
      removed outlier: 3.785A  pdb=" N   PHE B 376 " --> pdb=" O   TRP B 366 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 361 " --> pdb=" O   SER B 411 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   GLU B 413 " --> pdb=" O   VAL B 361 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU B 363 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 598 through 599
      removed outlier: 5.838A  pdb=" N   GLU B 598 " --> pdb=" O   MET B 617 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 620 through 621
    Processing sheet with id=AA9, first strand: chain 'B' and resid 781 through 786
      removed outlier: 4.310A  pdb=" N   LYS B 785 " --> pdb=" O   ASN B 726 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ASN B 726 " --> pdb=" O   LYS B 785 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LEU B 839 " --> pdb=" O   ILE B 733 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLY B 735 " --> pdb=" O   ALA B 837 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ALA B 837 " --> pdb=" O   GLY B 735 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU B 825 " --> pdb=" O   PRO B 836 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL B 823 " --> pdb=" O   LEU B 838 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR B 842 " --> pdb=" O   GLY B 819 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 781 through 786
      removed outlier: 4.310A  pdb=" N   LYS B 785 " --> pdb=" O   ASN B 726 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ASN B 726 " --> pdb=" O   LYS B 785 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER B 845 " --> pdb=" O   ALA B 727 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 762 through 763
      removed outlier: 5.930A  pdb=" N   GLU B 800 " --> pdb=" O   PHE B 805 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   PHE B 805 " --> pdb=" O   GLU B 800 " (cutoff:3.500A)

    247 hydrogen bonds defined for protein.
    696 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: 1.24

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        0.97 -     1.14: 2
        1.14 -     1.30: 1435
        1.30 -     1.47: 3457
        1.47 -     1.64: 3764
        1.64 -     1.81: 76
  Bond restraints: 8734
  Sorted by residual:
  bond pdb=" O   HOH A 501 "
       pdb=" H2  HOH A 501 "
    ideal  model  delta    sigma   weight residual
    0.850  0.967 -0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" O   HOH A 501 "
       pdb=" H1  HOH A 501 "
    ideal  model  delta    sigma   weight residual
    0.850  0.967 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" F2  ALF A 402 "
       pdb="AL   ALF A 402 "
    ideal  model  delta    sigma   weight residual
    1.685  1.781 -0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" F3  ALF A 402 "
       pdb="AL   ALF A 402 "
    ideal  model  delta    sigma   weight residual
    1.685  1.779 -0.094 2.00e-02 2.50e+03 2.19e+01
  bond pdb=" F1  ALF A 402 "
       pdb="AL   ALF A 402 "
    ideal  model  delta    sigma   weight residual
    1.684  1.777 -0.093 2.00e-02 2.50e+03 2.17e+01
  ... (remaining 8729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.17: 11838
       14.17 -    28.33: 4
       28.33 -    42.50: 0
       42.50 -    56.66: 0
       56.66 -    70.83: 2
  Bond angle restraints: 11844
  Sorted by residual:
  angle pdb=" F1  ALF A 402 "
        pdb="AL   ALF A 402 "
        pdb=" F2  ALF A 402 "
      ideal   model   delta    sigma   weight residual
     108.68  179.51  -70.83 3.00e+00 1.11e-01 5.57e+02
  angle pdb=" F3  ALF A 402 "
        pdb="AL   ALF A 402 "
        pdb=" F4  ALF A 402 "
      ideal   model   delta    sigma   weight residual
     109.63  178.38  -68.75 3.00e+00 1.11e-01 5.25e+02
  angle pdb=" F2  ALF A 402 "
        pdb="AL   ALF A 402 "
        pdb=" F4  ALF A 402 "
      ideal   model   delta    sigma   weight residual
     110.21   89.46   20.75 3.00e+00 1.11e-01 4.78e+01
  angle pdb=" F1  ALF A 402 "
        pdb="AL   ALF A 402 "
        pdb=" F3  ALF A 402 "
      ideal   model   delta    sigma   weight residual
     109.69   88.95   20.74 3.00e+00 1.11e-01 4.78e+01
  angle pdb=" F1  ALF A 402 "
        pdb="AL   ALF A 402 "
        pdb=" F4  ALF A 402 "
      ideal   model   delta    sigma   weight residual
     109.02   90.34   18.68 3.00e+00 1.11e-01 3.88e+01
  ... (remaining 11839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4760
       17.74 -    35.48: 443
       35.48 -    53.21: 88
       53.21 -    70.95: 13
       70.95 -    88.69: 9
  Dihedral angle restraints: 5313
    sinusoidal: 2166
      harmonic: 3147
  Sorted by residual:
  dihedral pdb=" CA  PHE B 783 "
           pdb=" C   PHE B 783 "
           pdb=" N   PRO B 784 "
           pdb=" CA  PRO B 784 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  LEU A 161 "
           pdb=" C   LEU A 161 "
           pdb=" N   ASN A 162 "
           pdb=" CA  ASN A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" C5' GDP A 401 "
           pdb=" O5' GDP A 401 "
           pdb=" PA  GDP A 401 "
           pdb=" O3A GDP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.98 -108.30  -71.72     1      2.00e+01 2.50e-03 1.65e+01
  ... (remaining 5310 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 911
       0.049 -    0.099: 318
       0.099 -    0.148: 81
       0.148 -    0.197: 8
       0.197 -    0.247: 1
  Chirality restraints: 1319
  Sorted by residual:
  chirality pdb=" CA  LYS B 238 "
            pdb=" N   LYS B 238 "
            pdb=" C   LYS B 238 "
            pdb=" CB  LYS B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CB  VAL B 621 "
            pdb=" CA  VAL B 621 "
            pdb=" CG1 VAL B 621 "
            pdb=" CG2 VAL B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CB  VAL B 584 "
            pdb=" CA  VAL B 584 "
            pdb=" CG1 VAL B 584 "
            pdb=" CG2 VAL B 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.29e-01
  ... (remaining 1316 not shown)

  Planarity restraints: 1533
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 369 "    0.045 5.00e-02 4.00e+02   6.76e-02 7.31e+00
        pdb=" N   PRO B 370 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 370 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 370 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  46 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.48e+00
        pdb=" N   PRO B  47 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B  47 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  47 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 451 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO B 452 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 452 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 452 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1530 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.42: 36
        2.42 -     2.96: 3799
        2.96 -     3.51: 9265
        3.51 -     4.05: 14774
        4.05 -     4.60: 21748
  Nonbonded interactions: 49622
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  53 "
            pdb="MG    MG A 403 "
     model   vdw
     1.875 2.050
  nonbonded pdb=" O1B GDP A 401 "
            pdb="MG    MG A 403 "
     model   vdw
     2.022 2.050
  nonbonded pdb=" OG1 THR A 186 "
            pdb="MG    MG A 403 "
     model   vdw
     2.087 2.050
  nonbonded pdb=" OH  TYR A 261 "
            pdb=" O   TYR B 855 "
     model   vdw
     2.206 2.800
  nonbonded pdb=" OE1 GLN A 209 "
            pdb=" H1  HOH A 501 "
     model   vdw
     2.236 2.450
  ... (remaining 49617 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:             3.620
  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:             0.070
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
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      :  0.008   0.096   8732  Z= 0.339
  Angle     :  1.274  70.825  11843  Z= 0.565
  Chirality :  0.052   0.247   1319
  Planarity :  0.006   0.068   1533
  Dihedral  : 14.447  88.691   3271
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.45 (0.17), residues: 1059
  helix: -4.91 (0.07), residues: 402
  sheet: -2.74 (0.39), residues: 138
  loop : -2.66 (0.20), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 760 
 TYR   0.015   0.002   TYR B 746 
 PHE   0.025   0.002   PHE B 712 
 TRP   0.010   0.002   TRP A 263 
 HIS   0.005   0.001   HIS B 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00794 ( 8732)
  covalent geometry    : angle       1.27373 (11843)
  hydrogen bonds       : bond        0.32672 (  243)
  hydrogen bonds       : angle      10.27151 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASN cc_start: 0.8364 (m-40) cc_final: 0.8160 (m-40)
REVERT: A  214 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7511 (ttm-80)
REVERT: B  159 LYS cc_start: 0.9060 (tttt) cc_final: 0.8803 (ttpt)
REVERT: B  252 GLN cc_start: 0.8234 (mp10) cc_final: 0.7728 (mp10)
REVERT: B  626 MET cc_start: 0.7755 (tpp) cc_final: 0.7358 (mmm)
REVERT: B  861 ASN cc_start: 0.8597 (t0) cc_final: 0.8334 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1173
  time to fit residues: 24.5804
Evaluate side-chains
  102 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
A 109 HIS
A 142 GLN
A 237 GLN
A 244 ASN
B 254 GLN
B 284 GLN
B 332 HIS
B 415 HIS
B 770 ASN
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 865 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.097444 restraints weight = 12487.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 3.00
r_work: 0.3012 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8732  Z= 0.132
  Angle     :  0.501   6.560  11843  Z= 0.261
  Chirality :  0.041   0.132   1319
  Planarity :  0.004   0.029   1533
  Dihedral  :  5.233  66.544   1179
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.93 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.84 (0.21), residues: 1059
  helix: -3.20 (0.18), residues: 382
  sheet: -2.27 (0.40), residues: 147
  loop : -2.01 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.014   0.001   TYR B 746 
 PHE   0.020   0.001   PHE A 339 
 TRP   0.007   0.001   TRP A 136 
 HIS   0.008   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8732)
  covalent geometry    : angle       0.50099 (11843)
  hydrogen bonds       : bond        0.04454 (  243)
  hydrogen bonds       : angle       5.24361 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8578 (tttt) cc_final: 0.8014 (tptp)
REVERT: A  214 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7617 (ttm-80)
REVERT: A  256 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.8324 (ttm-80)
REVERT: A  284 MET cc_start: 0.8503 (mmm) cc_final: 0.8264 (mmm)
REVERT: B  129 LYS cc_start: 0.8176 (tttp) cc_final: 0.7970 (ttmm)
REVERT: B  159 LYS cc_start: 0.8953 (tttt) cc_final: 0.8624 (ttpt)
REVERT: B  252 GLN cc_start: 0.8037 (mp10) cc_final: 0.7288 (mp10)
REVERT: B  330 SER cc_start: 0.8806 (p) cc_final: 0.8425 (p)
REVERT: B  411 SER cc_start: 0.9317 (m) cc_final: 0.8949 (t)
REVERT: B  458 ASP cc_start: 0.9091 (m-30) cc_final: 0.8741 (m-30)
REVERT: B  626 MET cc_start: 0.8318 (tpp) cc_final: 0.7951 (mmm)
  outliers start: 9
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1010
  time to fit residues: 16.5813
Evaluate side-chains
  114 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  624 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 90 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
A 244 ASN
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3473 r_free = 0.3473 target = 0.123145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.095027 restraints weight = 12641.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.98
r_work: 0.2976 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8732  Z= 0.201
  Angle     :  0.522   6.510  11843  Z= 0.266
  Chirality :  0.042   0.132   1319
  Planarity :  0.003   0.029   1533
  Dihedral  :  4.989  66.306   1179
  Min Nonbonded Distance : 1.777

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.41 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.22), residues: 1059
  helix: -2.18 (0.23), residues: 385
  sheet: -2.15 (0.40), residues: 146
  loop : -1.93 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 695 
 TYR   0.016   0.001   TYR B 746 
 PHE   0.017   0.001   PHE A 339 
 TRP   0.007   0.001   TRP A 136 
 HIS   0.019   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8732)
  covalent geometry    : angle       0.52168 (11843)
  hydrogen bonds       : bond        0.03857 (  243)
  hydrogen bonds       : angle       4.81635 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  133 LYS cc_start: 0.8563 (tttt) cc_final: 0.8009 (tptp)
REVERT: A  214 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7381 (ptm160)
REVERT: A  256 ARG cc_start: 0.8841 (tpt-90) cc_final: 0.8358 (ttm-80)
REVERT: A  284 MET cc_start: 0.8506 (mmm) cc_final: 0.8089 (mmm)
REVERT: B  129 LYS cc_start: 0.8192 (tttp) cc_final: 0.7968 (ttmm)
REVERT: B  159 LYS cc_start: 0.8945 (tttt) cc_final: 0.8662 (ttmt)
REVERT: B  214 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7333 (mt-10)
REVERT: B  252 GLN cc_start: 0.7967 (mp10) cc_final: 0.7230 (mp10)
REVERT: B  330 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (p)
REVERT: B  411 SER cc_start: 0.9372 (m) cc_final: 0.9011 (t)
REVERT: B  458 ASP cc_start: 0.9110 (m-30) cc_final: 0.8751 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1022
  time to fit residues: 16.9334
Evaluate side-chains
  120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  866 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0670
   chunk 101 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
B 114 ASN
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3495 r_free = 0.3495 target = 0.124924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.097023 restraints weight = 12665.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.99
r_work: 0.3007 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8732  Z= 0.103
  Angle     :  0.434   5.997  11843  Z= 0.220
  Chirality :  0.040   0.130   1319
  Planarity :  0.003   0.029   1533
  Dihedral  :  4.594  62.020   1179
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.82 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.23), residues: 1059
  helix: -1.47 (0.25), residues: 391
  sheet: -1.99 (0.40), residues: 146
  loop : -1.74 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.010   0.001   TYR B 746 
 PHE   0.015   0.001   PHE A 339 
 TRP   0.005   0.001   TRP A 136 
 HIS   0.014   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8732)
  covalent geometry    : angle       0.43431 (11843)
  hydrogen bonds       : bond        0.02992 (  243)
  hydrogen bonds       : angle       4.37887 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8507 (tttt) cc_final: 0.7958 (tptp)
REVERT: A  214 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7357 (ptm160)
REVERT: A  278 LEU cc_start: 0.9203 (mt) cc_final: 0.8951 (mp)
REVERT: A  284 MET cc_start: 0.8581 (mmm) cc_final: 0.8329 (mmm)
REVERT: B   32 ASP cc_start: 0.8269 (m-30) cc_final: 0.7979 (m-30)
REVERT: B  111 ASP cc_start: 0.6852 (p0) cc_final: 0.6287 (p0)
REVERT: B  129 LYS cc_start: 0.8054 (tttp) cc_final: 0.7834 (ttmm)
REVERT: B  159 LYS cc_start: 0.8934 (tttt) cc_final: 0.8616 (ttmt)
REVERT: B  252 GLN cc_start: 0.7975 (mp10) cc_final: 0.7231 (mp10)
REVERT: B  294 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (pt0)
REVERT: B  330 SER cc_start: 0.8757 (p) cc_final: 0.8398 (p)
REVERT: B  411 SER cc_start: 0.9279 (m) cc_final: 0.8920 (t)
REVERT: B  458 ASP cc_start: 0.9084 (m-30) cc_final: 0.8745 (m-30)
REVERT: B  626 MET cc_start: 0.8233 (tpp) cc_final: 0.7815 (mmm)
  outliers start: 14
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1025
  time to fit residues: 16.6182
Evaluate side-chains
  116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  451 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0370
   chunk 80 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.8066

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3448 r_free = 0.3448 target = 0.121109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.094584 restraints weight = 12627.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.89
r_work: 0.2966 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8732  Z= 0.217
  Angle     :  0.527   6.604  11843  Z= 0.267
  Chirality :  0.043   0.135   1319
  Planarity :  0.003   0.038   1533
  Dihedral  :  4.801  64.762   1179
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.01 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.24), residues: 1059
  helix: -1.21 (0.26), residues: 391
  sheet: -2.09 (0.39), residues: 146
  loop : -1.78 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 695 
 TYR   0.016   0.001   TYR B 746 
 PHE   0.016   0.001   PHE A 339 
 TRP   0.007   0.001   TRP A 136 
 HIS   0.017   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 8732)
  covalent geometry    : angle       0.52659 (11843)
  hydrogen bonds       : bond        0.03463 (  243)
  hydrogen bonds       : angle       4.60666 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8506 (tttt) cc_final: 0.7988 (tptp)
REVERT: A  214 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7450 (ptm160)
REVERT: A  278 LEU cc_start: 0.9268 (mt) cc_final: 0.9018 (mp)
REVERT: A  284 MET cc_start: 0.8579 (mmm) cc_final: 0.8290 (mmm)
REVERT: B   32 ASP cc_start: 0.8284 (m-30) cc_final: 0.8004 (m-30)
REVERT: B  129 LYS cc_start: 0.8125 (tttp) cc_final: 0.7898 (ttmm)
REVERT: B  159 LYS cc_start: 0.8942 (tttt) cc_final: 0.8628 (ttmt)
REVERT: B  252 GLN cc_start: 0.8000 (mp10) cc_final: 0.7275 (mp10)
REVERT: B  294 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7524 (pm20)
REVERT: B  411 SER cc_start: 0.9420 (m) cc_final: 0.9056 (t)
REVERT: B  458 ASP cc_start: 0.9082 (m-30) cc_final: 0.8705 (m-30)
  outliers start: 18
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1018
  time to fit residues: 15.9839
Evaluate side-chains
  114 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  606 GLU
Chi-restraints excluded: chain B residue  733 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    0.0000
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.2980
   chunk 105 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0370
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6664

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3485 r_free = 0.3485 target = 0.124082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097471 restraints weight = 12485.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.89
r_work: 0.3008 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8732  Z= 0.098
  Angle     :  0.424   5.939  11843  Z= 0.215
  Chirality :  0.040   0.130   1319
  Planarity :  0.003   0.035   1533
  Dihedral  :  4.409  60.050   1179
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.44 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.25), residues: 1059
  helix: -0.73 (0.27), residues: 395
  sheet: -1.89 (0.40), residues: 146
  loop : -1.52 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.010   0.001   TYR A 295 
 PHE   0.016   0.001   PHE A 339 
 TRP   0.004   0.001   TRP A 263 
 HIS   0.017   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8732)
  covalent geometry    : angle       0.42354 (11843)
  hydrogen bonds       : bond        0.02707 (  243)
  hydrogen bonds       : angle       4.18109 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8490 (tttt) cc_final: 0.7988 (tptp)
REVERT: A  214 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7422 (ptm160)
REVERT: A  278 LEU cc_start: 0.9248 (mt) cc_final: 0.9002 (mp)
REVERT: B   32 ASP cc_start: 0.8233 (m-30) cc_final: 0.7951 (m-30)
REVERT: B  129 LYS cc_start: 0.8009 (tttp) cc_final: 0.7783 (ttmm)
REVERT: B  159 LYS cc_start: 0.8884 (tttt) cc_final: 0.8562 (ttpt)
REVERT: B  252 GLN cc_start: 0.7967 (mp10) cc_final: 0.7195 (mp10)
REVERT: B  294 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7433 (pm20)
REVERT: B  330 SER cc_start: 0.8728 (p) cc_final: 0.8332 (p)
REVERT: B  411 SER cc_start: 0.9314 (m) cc_final: 0.8946 (t)
REVERT: B  458 ASP cc_start: 0.9082 (m-30) cc_final: 0.8710 (m-30)
REVERT: B  626 MET cc_start: 0.8201 (tpp) cc_final: 0.7736 (mmm)
  outliers start: 15
  outliers final: 13
  residues processed: 112
  average time/residue: 0.0970
  time to fit residues: 15.2406
Evaluate side-chains
  117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  834 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3508 r_free = 0.3508 target = 0.126300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.098468 restraints weight = 12565.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.99
r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8732  Z= 0.076
  Angle     :  0.405   5.808  11843  Z= 0.203
  Chirality :  0.039   0.130   1319
  Planarity :  0.002   0.031   1533
  Dihedral  :  4.162  58.392   1179
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 20.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.33 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.25), residues: 1059
  helix: -0.27 (0.28), residues: 391
  sheet: -1.62 (0.41), residues: 146
  loop : -1.38 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.016   0.001   TYR B 157 
 PHE   0.016   0.001   PHE A 339 
 TRP   0.004   0.000   TRP A 263 
 HIS   0.011   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 ( 8732)
  covalent geometry    : angle       0.40529 (11843)
  hydrogen bonds       : bond        0.02428 (  243)
  hydrogen bonds       : angle       3.87997 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8412 (tttt) cc_final: 0.7903 (tptp)
REVERT: A  214 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7331 (ptm160)
REVERT: A  278 LEU cc_start: 0.9194 (mt) cc_final: 0.8937 (mp)
REVERT: B   32 ASP cc_start: 0.8205 (m-30) cc_final: 0.7925 (m-30)
REVERT: B  129 LYS cc_start: 0.7769 (tttp) cc_final: 0.7561 (ttmm)
REVERT: B  159 LYS cc_start: 0.8746 (tttt) cc_final: 0.8436 (ttpt)
REVERT: B  252 GLN cc_start: 0.7860 (mp10) cc_final: 0.7046 (mp10)
REVERT: B  294 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7235 (pm20)
REVERT: B  330 SER cc_start: 0.8756 (p) cc_final: 0.8368 (p)
REVERT: B  411 SER cc_start: 0.9185 (m) cc_final: 0.8821 (t)
REVERT: B  458 ASP cc_start: 0.9067 (m-30) cc_final: 0.8659 (m-30)
REVERT: B  626 MET cc_start: 0.8089 (tpp) cc_final: 0.7595 (mmm)
  outliers start: 15
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0949
  time to fit residues: 15.8465
Evaluate side-chains
  119 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  808 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 59 optimal weight:    0.0170
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.1622

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3464 r_free = 0.3464 target = 0.122544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.096006 restraints weight = 12518.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.87
r_work: 0.2993 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8732  Z= 0.149
  Angle     :  0.452   5.963  11843  Z= 0.226
  Chirality :  0.041   0.131   1319
  Planarity :  0.003   0.031   1533
  Dihedral  :  4.288  59.730   1179
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.65 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.44 (0.26), residues: 1059
  helix: -0.11 (0.28), residues: 388
  sheet: -1.63 (0.41), residues: 146
  loop : -1.35 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 359 
 TYR   0.012   0.001   TYR B 746 
 PHE   0.014   0.001   PHE A 339 
 TRP   0.005   0.001   TRP A 263 
 HIS   0.019   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8732)
  covalent geometry    : angle       0.45152 (11843)
  hydrogen bonds       : bond        0.02756 (  243)
  hydrogen bonds       : angle       4.02519 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8526 (tttt) cc_final: 0.8006 (tptp)
REVERT: A  214 ARG cc_start: 0.8269 (ttm110) cc_final: 0.7478 (ptm160)
REVERT: A  278 LEU cc_start: 0.9246 (mt) cc_final: 0.9006 (mp)
REVERT: B   32 ASP cc_start: 0.8264 (m-30) cc_final: 0.7983 (m-30)
REVERT: B  129 LYS cc_start: 0.8021 (tttp) cc_final: 0.7790 (ttmm)
REVERT: B  159 LYS cc_start: 0.8864 (tttt) cc_final: 0.8571 (ttpt)
REVERT: B  252 GLN cc_start: 0.8007 (mp10) cc_final: 0.7206 (mp10)
REVERT: B  294 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7578 (pt0)
REVERT: B  330 SER cc_start: 0.8765 (p) cc_final: 0.8375 (p)
REVERT: B  411 SER cc_start: 0.9338 (m) cc_final: 0.8945 (t)
REVERT: B  458 ASP cc_start: 0.9069 (m-30) cc_final: 0.8721 (m-30)
REVERT: B  626 MET cc_start: 0.8192 (tpp) cc_final: 0.7749 (mmm)
  outliers start: 17
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0972
  time to fit residues: 15.0253
Evaluate side-chains
  115 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  834 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0000
   chunk 95 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3470 r_free = 0.3470 target = 0.122867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.095417 restraints weight = 12653.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.93
r_work: 0.2980 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8732  Z= 0.170
  Angle     :  0.474   6.063  11843  Z= 0.237
  Chirality :  0.041   0.132   1319
  Planarity :  0.003   0.032   1533
  Dihedral  :  4.416  60.628   1179
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 21.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.65 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.26), residues: 1059
  helix: -0.10 (0.28), residues: 388
  sheet: -1.68 (0.41), residues: 146
  loop : -1.34 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.015   0.001   TYR B 157 
 PHE   0.009   0.001   PHE B 712 
 TRP   0.005   0.001   TRP A 136 
 HIS   0.016   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8732)
  covalent geometry    : angle       0.47363 (11843)
  hydrogen bonds       : bond        0.02935 (  243)
  hydrogen bonds       : angle       4.12264 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8518 (tttt) cc_final: 0.8015 (tptp)
REVERT: A  214 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7483 (ptm160)
REVERT: A  278 LEU cc_start: 0.9256 (mt) cc_final: 0.9009 (mp)
REVERT: B   32 ASP cc_start: 0.8243 (m-30) cc_final: 0.7968 (m-30)
REVERT: B  129 LYS cc_start: 0.8020 (tttp) cc_final: 0.7800 (ttmm)
REVERT: B  159 LYS cc_start: 0.8861 (tttt) cc_final: 0.8573 (ttpt)
REVERT: B  252 GLN cc_start: 0.7991 (mp10) cc_final: 0.7185 (mp10)
REVERT: B  294 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7458 (pm20)
REVERT: B  330 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8384 (p)
REVERT: B  411 SER cc_start: 0.9365 (m) cc_final: 0.8976 (t)
REVERT: B  458 ASP cc_start: 0.9092 (m-30) cc_final: 0.8733 (m-30)
REVERT: B  626 MET cc_start: 0.8195 (tpp) cc_final: 0.7764 (mmm)
  outliers start: 19
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1010
  time to fit residues: 15.4802
Evaluate side-chains
  116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  834 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 94 optimal weight:    0.4980
   chunk 8 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3503 r_free = 0.3503 target = 0.125829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.098000 restraints weight = 12449.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.97
r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8732  Z= 0.086
  Angle     :  0.407   5.853  11843  Z= 0.204
  Chirality :  0.039   0.133   1319
  Planarity :  0.002   0.030   1533
  Dihedral  :  4.151  58.109   1179
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 20.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.65 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.26), residues: 1059
  helix:  0.15 (0.28), residues: 391
  sheet: -1.64 (0.40), residues: 152
  loop : -1.18 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.014   0.001   TYR B 157 
 PHE   0.015   0.001   PHE A 339 
 TRP   0.004   0.000   TRP A 263 
 HIS   0.018   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 8732)
  covalent geometry    : angle       0.40734 (11843)
  hydrogen bonds       : bond        0.02429 (  243)
  hydrogen bonds       : angle       3.83019 (  696)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LYS cc_start: 0.8486 (tttt) cc_final: 0.7984 (tptp)
REVERT: A  214 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7435 (ptm160)
REVERT: A  278 LEU cc_start: 0.9237 (mt) cc_final: 0.8998 (mp)
REVERT: B   32 ASP cc_start: 0.8198 (m-30) cc_final: 0.7923 (m-30)
REVERT: B  129 LYS cc_start: 0.7804 (tttp) cc_final: 0.7590 (ttmm)
REVERT: B  159 LYS cc_start: 0.8814 (tttt) cc_final: 0.8504 (ttpt)
REVERT: B  176 LEU cc_start: 0.8879 (mt) cc_final: 0.8595 (mp)
REVERT: B  252 GLN cc_start: 0.7873 (mp10) cc_final: 0.7069 (mp10)
REVERT: B  294 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7241 (pm20)
REVERT: B  330 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8362 (p)
REVERT: B  411 SER cc_start: 0.9281 (m) cc_final: 0.8886 (t)
REVERT: B  414 ASN cc_start: 0.8998 (t0) cc_final: 0.8689 (t0)
REVERT: B  458 ASP cc_start: 0.9075 (m-30) cc_final: 0.8699 (m-30)
REVERT: B  626 MET cc_start: 0.8070 (tpp) cc_final: 0.7614 (mmm)
  outliers start: 16
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1001
  time to fit residues: 16.0943
Evaluate side-chains
  118 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  144 CYS
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  583 GLU
Chi-restraints excluded: chain B residue  808 HIS
Chi-restraints excluded: chain B residue  834 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0170
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    0.2980
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8220

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
** B 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 861 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 = 0.3491 r_free = 0.3491 target = 0.124873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.097179 restraints weight = 12459.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.96
r_work: 0.3005 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8732  Z= 0.112
  Angle     :  0.423   5.859  11843  Z= 0.211
  Chirality :  0.040   0.130   1319
  Planarity :  0.003   0.029   1533
  Dihedral  :  4.147  58.489   1179
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 21.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.87 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.26), residues: 1059
  helix:  0.30 (0.28), residues: 390
  sheet: -1.55 (0.40), residues: 152
  loop : -1.11 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 223 
 TYR   0.010   0.001   TYR B 157 
 PHE   0.006   0.001   PHE B 615 
 TRP   0.005   0.001   TRP A 263 
 HIS   0.014   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8732)
  covalent geometry    : angle       0.42319 (11843)
  hydrogen bonds       : bond        0.02505 (  243)
  hydrogen bonds       : angle       3.82516 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2010.40 seconds
wall clock time: 35 minutes 17.77 seconds (2117.77 seconds total)