Starting phenix.real_space_refine
on Thu Jul 31 03:06:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uwf_26831/07_2025/7uwf_26831.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.274
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      94      5.16       5
     C    8394      2.51       5
     N    2306      2.21       5
     O    2380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13174
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2725
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 17, 'TRANS': 343}
          Unresolved chain links: 3
          Chain breaks: 1
          Unresolved chain link angles: 9
          Unresolved chain link dihedrals: 12
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "C"
      Number of atoms: 3862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 519, 3862
          Classifications: {'peptide': 519}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 32, 'TRANS': 486}
          Unresolved chain links: 1
          Chain breaks: 5
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "B"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2725
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 17, 'TRANS': 343}
          Unresolved chain links: 3
          Chain breaks: 1
          Unresolved chain link angles: 9
          Unresolved chain link dihedrals: 12
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 49
    Chain: "D"
      Number of atoms: 3862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 519, 3862
          Classifications: {'peptide': 519}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 32, 'TRANS': 486}
          Unresolved chain links: 1
          Chain breaks: 5
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 8.30, per 1000 atoms: 0.63
  Number of scatterers: 13174
  At special positions: 0
  Unit cell: (93.984, 108.768, 107.712, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      94     16.00
     O    2380      8.00
     N    2306      7.00
     C    8394      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.57
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3256

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 16 sheets defined
      52.4% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 322 through 327
      removed outlier: 3.521A  pdb=" N   LEU A 326 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
    Processing helix  chain 'C' and resid 31 through 42
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 65 through 77
    Processing helix  chain 'C' and resid 86 through 101
      removed outlier: 3.605A  pdb=" N   SER C 101 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 119
    Processing helix  chain 'C' and resid 120 through 140
      removed outlier: 3.506A  pdb=" N   GLN C 125 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   VAL C 129 " --> pdb=" O   GLN C 125 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   SER C 130 " --> pdb=" O   GLN C 126 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN C 140 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 163
    Processing helix  chain 'C' and resid 165 through 186
      removed outlier: 3.606A  pdb=" N   ARG C 170 " --> pdb=" O   PRO C 166 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP C 171 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      Proline residue:  C 178  - end of helix
    Processing helix  chain 'C' and resid 188 through 190
      No H-bonds generated for 'chain 'C' and resid 188 through 190'
    Processing helix  chain 'C' and resid 191 through 206
    Processing helix  chain 'C' and resid 207 through 212
      removed outlier: 4.268A  pdb=" N   SER C 212 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 226
      removed outlier: 3.930A  pdb=" N   SER C 223 " --> pdb=" O   SER C 219 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ARG C 224 " --> pdb=" O   PHE C 220 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP C 226 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 241
    Processing helix  chain 'C' and resid 242 through 246
    Processing helix  chain 'C' and resid 249 through 279
      removed outlier: 5.338A  pdb=" N   LYS C 255 " --> pdb=" O   SER C 251 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   HIS C 256 " --> pdb=" O   GLN C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 306 through 327
    Processing helix  chain 'C' and resid 337 through 350
      removed outlier: 3.579A  pdb=" N   ILE C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 388
      Proline residue:  C 370  - end of helix
    Processing helix  chain 'C' and resid 389 through 393
      removed outlier: 4.335A  pdb=" N   ARG C 393 " --> pdb=" O   ARG C 390 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 409
      Proline residue:  C 403  - end of helix
    Processing helix  chain 'C' and resid 424 through 443
    Processing helix  chain 'C' and resid 444 through 446
      No H-bonds generated for 'chain 'C' and resid 444 through 446'
    Processing helix  chain 'C' and resid 451 through 467
      removed outlier: 4.229A  pdb=" N   GLY C 455 " --> pdb=" O   GLY C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 518 through 537
    Processing helix  chain 'C' and resid 541 through 561
      Proline residue:  C 554  - end of helix
      removed outlier: 4.065A  pdb=" N   GLN C 560 " --> pdb=" O   VAL C 556 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN C 561 " --> pdb=" O   MET C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 568 through 571
    Processing helix  chain 'C' and resid 572 through 589
    Processing helix  chain 'C' and resid 597 through 609
    Processing helix  chain 'C' and resid 613 through 632
    Processing helix  chain 'B' and resid 150 through 155
    Processing helix  chain 'B' and resid 322 through 327
      removed outlier: 3.522A  pdb=" N   LEU B 326 " --> pdb=" O   PRO B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 427
    Processing helix  chain 'D' and resid 31 through 42
    Processing helix  chain 'D' and resid 43 through 45
      No H-bonds generated for 'chain 'D' and resid 43 through 45'
    Processing helix  chain 'D' and resid 65 through 77
    Processing helix  chain 'D' and resid 86 through 101
      removed outlier: 3.605A  pdb=" N   SER D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 119
    Processing helix  chain 'D' and resid 120 through 140
      removed outlier: 3.507A  pdb=" N   GLN D 125 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   VAL D 129 " --> pdb=" O   GLN D 125 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER D 130 " --> pdb=" O   GLN D 126 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN D 140 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 163
    Processing helix  chain 'D' and resid 165 through 186
      removed outlier: 3.606A  pdb=" N   ARG D 170 " --> pdb=" O   PRO D 166 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP D 171 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
    Processing helix  chain 'D' and resid 188 through 190
      No H-bonds generated for 'chain 'D' and resid 188 through 190'
    Processing helix  chain 'D' and resid 191 through 206
    Processing helix  chain 'D' and resid 207 through 212
      removed outlier: 4.269A  pdb=" N   SER D 212 " --> pdb=" O   ALA D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 226
      removed outlier: 3.931A  pdb=" N   SER D 223 " --> pdb=" O   SER D 219 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ARG D 224 " --> pdb=" O   PHE D 220 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ASP D 226 " --> pdb=" O   LEU D 222 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 229 through 241
    Processing helix  chain 'D' and resid 242 through 246
    Processing helix  chain 'D' and resid 249 through 279
      removed outlier: 5.337A  pdb=" N   LYS D 255 " --> pdb=" O   SER D 251 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   HIS D 256 " --> pdb=" O   GLN D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 327
    Processing helix  chain 'D' and resid 337 through 350
      removed outlier: 3.580A  pdb=" N   ILE D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 388
      Proline residue:  D 370  - end of helix
    Processing helix  chain 'D' and resid 389 through 393
      removed outlier: 4.335A  pdb=" N   ARG D 393 " --> pdb=" O   ARG D 390 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 409
      Proline residue:  D 403  - end of helix
    Processing helix  chain 'D' and resid 424 through 443
    Processing helix  chain 'D' and resid 444 through 446
      No H-bonds generated for 'chain 'D' and resid 444 through 446'
    Processing helix  chain 'D' and resid 451 through 467
      removed outlier: 4.229A  pdb=" N   GLY D 455 " --> pdb=" O   GLY D 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 518 through 537
    Processing helix  chain 'D' and resid 541 through 561
      Proline residue:  D 554  - end of helix
      removed outlier: 4.065A  pdb=" N   GLN D 560 " --> pdb=" O   VAL D 556 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN D 561 " --> pdb=" O   MET D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 568 through 571
    Processing helix  chain 'D' and resid 572 through 589
    Processing helix  chain 'D' and resid 597 through 609
    Processing helix  chain 'D' and resid 613 through 632
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34
      removed outlier: 6.952A  pdb=" N   ASN A  30 " --> pdb=" O   GLU A  24 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLU A  24 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 47
      removed outlier: 5.844A  pdb=" N   ALA A  55 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 9.306A  pdb=" N   ARG A  42 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 10.017A  pdb=" N   LEU A  53 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 9.926A  pdb=" N   LEU A  44 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
      removed outlier: 11.292A  pdb=" N   TYR A  51 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   TYR A  61 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88
      removed outlier: 3.609A  pdb=" N   VAL A 115 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   GLU A 107 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU A 113 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 129
    Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 180
      removed outlier: 3.557A  pdb=" N   ASP A 177 " --> pdb=" O   SER A 192 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 197 " --> pdb=" O   SER A 193 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLU A 202 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   LEU A 208 " --> pdb=" O   GLU A 202 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 223
    Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277
      removed outlier: 3.909A  pdb=" N   THR A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   VAL A 293 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   THR A 306 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LEU A 295 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN A 302 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 398
    Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 34
      removed outlier: 6.951A  pdb=" N   ASN B  30 " --> pdb=" O   GLU B  24 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLU B  24 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 47
      removed outlier: 5.844A  pdb=" N   ALA B  55 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 9.306A  pdb=" N   ARG B  42 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 10.019A  pdb=" N   LEU B  53 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 9.925A  pdb=" N   LEU B  44 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 11.293A  pdb=" N   TYR B  51 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   TYR B  61 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88
      removed outlier: 3.611A  pdb=" N   VAL B 115 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   GLU B 107 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU B 113 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 124 through 129
    Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 180
      removed outlier: 3.556A  pdb=" N   ASP B 177 " --> pdb=" O   SER B 192 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR B 197 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLU B 202 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   LEU B 208 " --> pdb=" O   GLU B 202 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 223
    Processing sheet with id=AB6, first strand: chain 'B' and resid 272 through 277
      removed outlier: 3.909A  pdb=" N   THR B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL B 293 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   THR B 306 " --> pdb=" O   VAL B 293 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU B 295 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN B 302 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 398

    782 hydrogen bonds defined for protein.
    2256 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: 4.38

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4330
        1.34 -     1.46: 2720
        1.46 -     1.58: 6254
        1.58 -     1.69: 0
        1.69 -     1.81: 126
  Bond restraints: 13430
  Sorted by residual:
  bond pdb=" SD  MET D  70 "
       pdb=" CE  MET D  70 "
    ideal  model  delta    sigma   weight residual
    1.791  1.756  0.035 2.50e-02 1.60e+03 1.99e+00
  bond pdb=" SD  MET C  70 "
       pdb=" CE  MET C  70 "
    ideal  model  delta    sigma   weight residual
    1.791  1.757  0.034 2.50e-02 1.60e+03 1.89e+00
  bond pdb=" CB  VAL A 283 "
       pdb=" CG1 VAL A 283 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.23e+00
  bond pdb=" CB  VAL B 283 "
       pdb=" CG1 VAL B 283 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" CG  LEU B 412 "
       pdb=" CD1 LEU B 412 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  ... (remaining 13425 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 17639
        1.49 -     2.97: 486
        2.97 -     4.46: 95
        4.46 -     5.94: 28
        5.94 -     7.43: 4
  Bond angle restraints: 18252
  Sorted by residual:
  angle pdb=" C   LEU A 412 "
        pdb=" N   ARG A 413 "
        pdb=" CA  ARG A 413 "
      ideal   model   delta    sigma   weight residual
     121.14  116.41    4.73 1.75e+00 3.27e-01 7.30e+00
  angle pdb=" C   LEU B 412 "
        pdb=" N   ARG B 413 "
        pdb=" CA  ARG B 413 "
      ideal   model   delta    sigma   weight residual
     121.14  116.42    4.72 1.75e+00 3.27e-01 7.29e+00
  angle pdb=" C   LEU C 534 "
        pdb=" N   MET C 535 "
        pdb=" CA  MET C 535 "
      ideal   model   delta    sigma   weight residual
     121.92  117.87    4.05 1.73e+00 3.34e-01 5.47e+00
  angle pdb=" C   LEU D 534 "
        pdb=" N   MET D 535 "
        pdb=" CA  MET D 535 "
      ideal   model   delta    sigma   weight residual
     121.92  117.90    4.02 1.73e+00 3.34e-01 5.41e+00
  angle pdb=" N   ARG B 413 "
        pdb=" CA  ARG B 413 "
        pdb=" CB  ARG B 413 "
      ideal   model   delta    sigma   weight residual
     110.40  114.03   -3.63 1.63e+00 3.76e-01 4.97e+00
  ... (remaining 18247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 7446
       16.24 -    32.47: 522
       32.47 -    48.71: 88
       48.71 -    64.94: 18
       64.94 -    81.18: 14
  Dihedral angle restraints: 8088
    sinusoidal: 3070
      harmonic: 5018
  Sorted by residual:
  dihedral pdb=" CA  TRP A  65 "
           pdb=" C   TRP A  65 "
           pdb=" N   GLU A  66 "
           pdb=" CA  GLU A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.37   15.63     0      5.00e+00 4.00e-02 9.77e+00
  dihedral pdb=" CA  TRP B  65 "
           pdb=" C   TRP B  65 "
           pdb=" N   GLU B  66 "
           pdb=" CA  GLU B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.40   15.60     0      5.00e+00 4.00e-02 9.74e+00
  dihedral pdb=" CA  SER D 519 "
           pdb=" C   SER D 519 "
           pdb=" N   ASP D 520 "
           pdb=" CA  ASP D 520 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.46  -15.54     0      5.00e+00 4.00e-02 9.65e+00
  ... (remaining 8085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1617
       0.041 -    0.082: 389
       0.082 -    0.122: 154
       0.122 -    0.163: 19
       0.163 -    0.204: 3
  Chirality restraints: 2182
  Sorted by residual:
  chirality pdb=" CG  LEU D  37 "
            pdb=" CB  LEU D  37 "
            pdb=" CD1 LEU D  37 "
            pdb=" CD2 LEU D  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CG  LEU C  37 "
            pdb=" CB  LEU C  37 "
            pdb=" CD1 LEU C  37 "
            pdb=" CD2 LEU C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.94e-01
  chirality pdb=" CA  ARG B 413 "
            pdb=" N   ARG B 413 "
            pdb=" C   ARG B 413 "
            pdb=" CB  ARG B 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 2179 not shown)

  Planarity restraints: 2310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 165 "   -0.042 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO D 166 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D 166 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 166 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 165 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO C 166 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO C 166 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 166 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 173 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.89e+00
        pdb=" C   SER D 173 "    0.034 2.00e-02 2.50e+03
        pdb=" O   SER D 173 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET D 174 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2307 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 160
        2.68 -     3.24: 12733
        3.24 -     3.79: 21540
        3.79 -     4.35: 29247
        4.35 -     4.90: 48540
  Nonbonded interactions: 112220
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 432 "
            pdb=" OD2 ASP D 465 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR C 432 "
            pdb=" OD2 ASP C 465 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   LEU D 115 "
            pdb=" OG  SER D 119 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   LEU C 115 "
            pdb=" OG  SER C 119 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   LEU D  38 "
            pdb=" OG  SER D  42 "
     model   vdw
     2.277 3.040
  ... (remaining 112215 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             0.690
  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:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     32.520
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13430  Z= 0.154
  Angle     :  0.617   7.430  18252  Z= 0.310
  Chirality :  0.043   0.204   2182
  Planarity :  0.005   0.064   2310
  Dihedral  : 12.055  81.179   4832
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.21), residues: 1708
  helix:  2.14 (0.18), residues: 816
  sheet:  0.32 (0.30), residues: 278
  loop : -0.27 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 201 
 HIS   0.005   0.001   HIS D 373 
 PHE   0.026   0.002   PHE D 619 
 TYR   0.017   0.002   TYR D 240 
 ARG   0.012   0.001   ARG C 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13799 (  782)
  hydrogen bonds       : angle       5.69216 ( 2256)
  covalent geometry    : bond        0.00353 (13430)
  covalent geometry    : angle       0.61711 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.397 
Fit side-chains
REVERT: C  520 ASP cc_start: 0.6601 (t0) cc_final: 0.6285 (t0)
REVERT: C  535 MET cc_start: 0.8255 (mmm) cc_final: 0.7904 (mmm)
REVERT: B  310 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7984 (mptt)
REVERT: B  325 MET cc_start: 0.8491 (mtt) cc_final: 0.8254 (mtt)
REVERT: D   70 MET cc_start: 0.7211 (mmm) cc_final: 0.6946 (tpt)
REVERT: D  240 TYR cc_start: 0.8259 (t80) cc_final: 0.8058 (t80)
REVERT: D  308 LEU cc_start: 0.8375 (mt) cc_final: 0.8164 (tp)
REVERT: D  535 MET cc_start: 0.8216 (mmm) cc_final: 0.7901 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 1.5425
  time to fit residues: 406.3010
Evaluate side-chains
  197 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 146 optimal weight:    0.9990
   chunk 131 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0060
   chunk 70 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 158 optimal weight:    0.7980
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
D 560 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.163059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.133440 restraints weight = 13405.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.31
r_work: 0.3264 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13430  Z= 0.131
  Angle     :  0.573   9.281  18252  Z= 0.291
  Chirality :  0.041   0.175   2182
  Planarity :  0.005   0.048   2310
  Dihedral  :  4.088  15.472   1856
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  7.91 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.21), residues: 1708
  helix:  2.70 (0.18), residues: 818
  sheet:  0.61 (0.31), residues: 278
  loop : -0.40 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 201 
 HIS   0.004   0.001   HIS A 120 
 PHE   0.018   0.002   PHE B 136 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.007   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04393 (  782)
  hydrogen bonds       : angle       4.60413 ( 2256)
  covalent geometry    : bond        0.00292 (13430)
  covalent geometry    : angle       0.57299 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 1.498 
Fit side-chains
REVERT: A  305 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7911 (ttm170)
REVERT: A  413 ARG cc_start: 0.6038 (mpp-170) cc_final: 0.5189 (mtm-85)
REVERT: C  170 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7030 (ptp90)
REVERT: C  188 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6367 (mtm-85)
REVERT: C  197 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7654 (mt-10)
REVERT: C  310 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7283 (tp40)
REVERT: C  593 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7183 (ptt-90)
REVERT: B   72 GLN cc_start: 0.5808 (tp40) cc_final: 0.5263 (tp40)
REVERT: B  263 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8288 (mmtp)
REVERT: B  282 SER cc_start: 0.8813 (p) cc_final: 0.8563 (p)
REVERT: B  305 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7424 (ttp80)
REVERT: B  310 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8087 (mptt)
REVERT: D  132 LEU cc_start: 0.8368 (tp) cc_final: 0.8077 (tt)
REVERT: D  197 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7731 (mt-10)
REVERT: D  262 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7919 (mp10)
REVERT: D  465 ASP cc_start: 0.8168 (m-30) cc_final: 0.7948 (m-30)
REVERT: D  577 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7983 (ttp80)
  outliers start: 28
  outliers final: 6
  residues processed: 228
  average time/residue: 1.6090
  time to fit residues: 393.3965
Evaluate side-chains
  225 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  172 ILE
Chi-restraints excluded: chain C residue  197 GLU
Chi-restraints excluded: chain C residue  310 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  305 ARG
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  310 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 152 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 120 optimal weight:    0.0020
   chunk 54 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
C 193 GLN
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
D 560 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.163191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.133291 restraints weight = 13611.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.37
r_work: 0.3245 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13430  Z= 0.121
  Angle     :  0.547   7.919  18252  Z= 0.275
  Chirality :  0.041   0.186   2182
  Planarity :  0.005   0.042   2310
  Dihedral  :  3.987  14.844   1856
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.17 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.21), residues: 1708
  helix:  2.87 (0.18), residues: 820
  sheet:  0.76 (0.31), residues: 278
  loop : -0.41 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 201 
 HIS   0.004   0.001   HIS B 120 
 PHE   0.017   0.002   PHE B 136 
 TYR   0.015   0.001   TYR B  61 
 ARG   0.005   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  782)
  hydrogen bonds       : angle       4.44599 ( 2256)
  covalent geometry    : bond        0.00272 (13430)
  covalent geometry    : angle       0.54653 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 1.566 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.5661 (tp40) cc_final: 0.5187 (tp40)
REVERT: C  170 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6412 (ptp90)
REVERT: C  174 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6307 (mpp)
REVERT: C  188 ARG cc_start: 0.6970 (mtm-85) cc_final: 0.6480 (mtm-85)
REVERT: C  197 GLU cc_start: 0.7881 (mp0) cc_final: 0.7640 (mt-10)
REVERT: C  310 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7194 (tp40)
REVERT: C  465 ASP cc_start: 0.8170 (m-30) cc_final: 0.7963 (m-30)
REVERT: C  593 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7081 (ptt-90)
REVERT: B   69 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7830 (tpp80)
REVERT: B   72 GLN cc_start: 0.5757 (tp40) cc_final: 0.5423 (tp40)
REVERT: B  263 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8262 (mmtp)
REVERT: B  282 SER cc_start: 0.8868 (p) cc_final: 0.8642 (p)
REVERT: B  310 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8077 (mptt)
REVERT: D  132 LEU cc_start: 0.8329 (tp) cc_final: 0.8054 (tt)
REVERT: D  197 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7683 (mt-10)
REVERT: D  262 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7880 (mp10)
REVERT: D  577 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8002 (ttp80)
REVERT: D  593 ARG cc_start: 0.7502 (ptp90) cc_final: 0.7138 (ptt90)
  outliers start: 26
  outliers final: 6
  residues processed: 227
  average time/residue: 1.6232
  time to fit residues: 394.9024
Evaluate side-chains
  222 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  310 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 160 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 165 optimal weight:    0.7980
   chunk 125 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 GLN
C 373 HIS
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
D 560 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.162361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.132748 restraints weight = 13360.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.25
r_work: 0.3258 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13430  Z= 0.129
  Angle     :  0.556   8.107  18252  Z= 0.278
  Chirality :  0.041   0.182   2182
  Planarity :  0.005   0.049   2310
  Dihedral  :  4.021  15.908   1856
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.21 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.21), residues: 1708
  helix:  2.91 (0.18), residues: 820
  sheet:  0.80 (0.31), residues: 278
  loop : -0.43 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 201 
 HIS   0.004   0.001   HIS B 120 
 PHE   0.018   0.002   PHE B 136 
 TYR   0.016   0.001   TYR B  61 
 ARG   0.006   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (  782)
  hydrogen bonds       : angle       4.40790 ( 2256)
  covalent geometry    : bond        0.00296 (13430)
  covalent geometry    : angle       0.55550 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 1.397 
Fit side-chains
REVERT: A   72 GLN cc_start: 0.5687 (tp40) cc_final: 0.5278 (tp40)
REVERT: C   70 MET cc_start: 0.6990 (mmm) cc_final: 0.6779 (mmm)
REVERT: C  170 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6989 (ptp90)
REVERT: C  174 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6574 (mmt)
REVERT: C  188 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6481 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7944 (mp10)
REVERT: C  593 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7148 (ptt-90)
REVERT: B   72 GLN cc_start: 0.5888 (tp40) cc_final: 0.5435 (tp40)
REVERT: B  263 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8267 (mmtt)
REVERT: B  282 SER cc_start: 0.8859 (p) cc_final: 0.8632 (p)
REVERT: B  295 LEU cc_start: 0.9161 (mm) cc_final: 0.8803 (mm)
REVERT: B  310 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8058 (mptt)
REVERT: D  132 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8078 (tt)
REVERT: D  197 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7679 (mt-10)
REVERT: D  238 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7814 (mt-10)
REVERT: D  262 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7912 (mp10)
REVERT: D  577 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8015 (ttp80)
  outliers start: 28
  outliers final: 6
  residues processed: 220
  average time/residue: 2.1842
  time to fit residues: 515.0756
Evaluate side-chains
  215 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 201
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 164 optimal weight:    3.9990
   chunk 155 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 GLN
C 310 GLN
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
D 234 GLN
D 373 HIS
D 560 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.159788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.129813 restraints weight = 13490.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.26
r_work: 0.3224 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13430  Z= 0.162
  Angle     :  0.599   8.660  18252  Z= 0.298
  Chirality :  0.042   0.192   2182
  Planarity :  0.005   0.043   2310
  Dihedral  :  4.173  16.361   1856
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.52 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.21), residues: 1708
  helix:  2.80 (0.18), residues: 820
  sheet:  0.67 (0.31), residues: 278
  loop : -0.46 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 201 
 HIS   0.005   0.001   HIS C 373 
 PHE   0.020   0.002   PHE B 136 
 TYR   0.016   0.002   TYR B  61 
 ARG   0.007   0.000   ARG B  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  782)
  hydrogen bonds       : angle       4.55145 ( 2256)
  covalent geometry    : bond        0.00380 (13430)
  covalent geometry    : angle       0.59926 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 213
  time to evaluate  : 1.459 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (ptt)
REVERT: A   72 GLN cc_start: 0.5792 (tp40) cc_final: 0.5356 (tp40)
REVERT: C  188 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.6500 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7971 (mp10)
REVERT: C  593 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7004 (ptt-90)
REVERT: B   72 GLN cc_start: 0.5737 (tp40) cc_final: 0.5246 (tp40)
REVERT: B  295 LEU cc_start: 0.9243 (mm) cc_final: 0.8946 (mm)
REVERT: D  197 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7753 (mt-10)
REVERT: D  262 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7950 (mp10)
REVERT: D  560 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7059 (mm110)
REVERT: D  577 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8022 (ttp80)
  outliers start: 36
  outliers final: 8
  residues processed: 224
  average time/residue: 1.4943
  time to fit residues: 361.2559
Evaluate side-chains
  222 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 208
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 140 optimal weight:    0.9980
   chunk 147 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 138 optimal weight:    0.7980
   chunk 119 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.160907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.131003 restraints weight = 13637.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.35
r_work: 0.3221 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13430  Z= 0.130
  Angle     :  0.563   8.197  18252  Z= 0.282
  Chirality :  0.041   0.184   2182
  Planarity :  0.005   0.043   2310
  Dihedral  :  4.092  16.052   1856
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.63 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.21), residues: 1708
  helix:  2.84 (0.18), residues: 820
  sheet:  0.73 (0.31), residues: 278
  loop : -0.44 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 201 
 HIS   0.004   0.001   HIS B 120 
 PHE   0.018   0.002   PHE B 136 
 TYR   0.016   0.002   TYR B  61 
 ARG   0.006   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  782)
  hydrogen bonds       : angle       4.43545 ( 2256)
  covalent geometry    : bond        0.00299 (13430)
  covalent geometry    : angle       0.56280 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 1.581 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8436 (ptt)
REVERT: A   72 GLN cc_start: 0.5832 (tp40) cc_final: 0.5413 (tp40)
REVERT: C  170 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6421 (ptp90)
REVERT: C  174 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6375 (mpp)
REVERT: C  188 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6471 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8025 (mp10)
REVERT: C  593 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7037 (ptt-90)
REVERT: D  197 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7768 (mt-10)
REVERT: D  262 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (mp10)
REVERT: D  577 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8061 (ttp80)
REVERT: D  593 ARG cc_start: 0.7489 (ptp90) cc_final: 0.7183 (ptt90)
  outliers start: 28
  outliers final: 7
  residues processed: 214
  average time/residue: 1.8694
  time to fit residues: 429.4840
Evaluate side-chains
  211 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 159 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 153 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 139 optimal weight:    7.9990
   chunk 122 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  65 HIS
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  65 HIS
D 164 GLN
D 560 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.158618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.128735 restraints weight = 13394.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.33
r_work: 0.3203 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13430  Z= 0.190
  Angle     :  0.637   9.290  18252  Z= 0.316
  Chirality :  0.044   0.239   2182
  Planarity :  0.005   0.044   2310
  Dihedral  :  4.315  17.396   1856
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.42 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.21), residues: 1708
  helix:  2.60 (0.18), residues: 820
  sheet:  0.65 (0.31), residues: 280
  loop : -0.47 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 201 
 HIS   0.006   0.001   HIS C 373 
 PHE   0.020   0.003   PHE B 136 
 TYR   0.015   0.002   TYR B  61 
 ARG   0.007   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  782)
  hydrogen bonds       : angle       4.60001 ( 2256)
  covalent geometry    : bond        0.00450 (13430)
  covalent geometry    : angle       0.63746 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 1.607 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8433 (ptt)
REVERT: A   72 GLN cc_start: 0.5528 (tp40) cc_final: 0.5129 (tp40)
REVERT: C  170 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6331 (ptp90)
REVERT: C  174 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6462 (mpp)
REVERT: C  188 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.6456 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8008 (mp10)
REVERT: C  593 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7028 (ptt-90)
REVERT: B  238 SER cc_start: 0.8631 (p) cc_final: 0.8279 (m)
REVERT: D  197 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7739 (mt-10)
REVERT: D  262 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7935 (mp10)
REVERT: D  577 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7991 (ttp80)
  outliers start: 35
  outliers final: 12
  residues processed: 223
  average time/residue: 1.7380
  time to fit residues: 416.8894
Evaluate side-chains
  219 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue  170 ARG
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  199 MET
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  310 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  553 LEU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 160 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 153 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 167 optimal weight:    0.0570
   chunk 146 optimal weight:    6.9990
   overall best weight:    1.9504

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.157734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.127780 restraints weight = 13477.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.33
r_work: 0.3188 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13430  Z= 0.209
  Angle     :  0.674  10.345  18252  Z= 0.332
  Chirality :  0.045   0.245   2182
  Planarity :  0.005   0.047   2310
  Dihedral  :  4.470  18.290   1856
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.05 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.20), residues: 1708
  helix:  2.45 (0.18), residues: 820
  sheet:  0.53 (0.31), residues: 282
  loop : -0.48 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 201 
 HIS   0.006   0.001   HIS C 373 
 PHE   0.022   0.003   PHE A 136 
 TYR   0.015   0.002   TYR B  61 
 ARG   0.007   0.001   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04809 (  782)
  hydrogen bonds       : angle       4.73187 ( 2256)
  covalent geometry    : bond        0.00496 (13430)
  covalent geometry    : angle       0.67380 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 202
  time to evaluate  : 1.381 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (ptt)
REVERT: C  174 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6487 (mpp)
REVERT: C  188 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6417 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8034 (mp10)
REVERT: C  593 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7071 (ptt-90)
REVERT: C  630 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8039 (mt)
REVERT: B  238 SER cc_start: 0.8663 (p) cc_final: 0.8283 (m)
REVERT: D   73 LEU cc_start: 0.8034 (tp) cc_final: 0.7766 (mt)
REVERT: D  197 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7722 (mt-10)
REVERT: D  262 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7984 (mp10)
REVERT: D  577 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8029 (ttp80)
REVERT: D  630 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (mt)
  outliers start: 34
  outliers final: 12
  residues processed: 218
  average time/residue: 1.5052
  time to fit residues: 353.1825
Evaluate side-chains
  221 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  199 MET
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  553 LEU
Chi-restraints excluded: chain D residue  577 ARG
Chi-restraints excluded: chain D residue  630 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 164 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 126 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 162 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 ASN
** B  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.160241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.130071 restraints weight = 13612.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.33
r_work: 0.3227 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13430  Z= 0.137
  Angle     :  0.597   9.115  18252  Z= 0.296
  Chirality :  0.042   0.230   2182
  Planarity :  0.005   0.043   2310
  Dihedral  :  4.239  16.414   1856
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.09 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.21), residues: 1708
  helix:  2.68 (0.18), residues: 820
  sheet:  0.67 (0.31), residues: 280
  loop : -0.45 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 201 
 HIS   0.004   0.001   HIS A 120 
 PHE   0.019   0.002   PHE A 136 
 TYR   0.009   0.002   TYR C 570 
 ARG   0.008   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04095 (  782)
  hydrogen bonds       : angle       4.53875 ( 2256)
  covalent geometry    : bond        0.00315 (13430)
  covalent geometry    : angle       0.59693 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 202
  time to evaluate  : 1.525 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8321 (ptt)
REVERT: C  174 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6423 (mpp)
REVERT: C  188 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6415 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7997 (mp10)
REVERT: C  593 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7014 (ptt-90)
REVERT: C  630 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8003 (mt)
REVERT: D  197 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7686 (mt-10)
REVERT: D  262 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (mp10)
REVERT: D  436 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (tt0)
REVERT: D  577 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7989 (ttp80)
  outliers start: 22
  outliers final: 7
  residues processed: 213
  average time/residue: 1.7155
  time to fit residues: 393.0633
Evaluate side-chains
  212 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 1.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  436 GLU
Chi-restraints excluded: chain D residue  577 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 139 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 113 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  74 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.159232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.129401 restraints weight = 13363.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.25
r_work: 0.3204 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13430  Z= 0.167
  Angle     :  0.641  11.008  18252  Z= 0.317
  Chirality :  0.043   0.300   2182
  Planarity :  0.005   0.044   2310
  Dihedral  :  4.323  16.758   1856
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.30 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.21), residues: 1708
  helix:  2.60 (0.18), residues: 820
  sheet:  0.61 (0.31), residues: 280
  loop : -0.45 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 201 
 HIS   0.005   0.001   HIS C 373 
 PHE   0.023   0.002   PHE D 206 
 TYR   0.011   0.002   TYR C 240 
 ARG   0.008   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  782)
  hydrogen bonds       : angle       4.60587 ( 2256)
  covalent geometry    : bond        0.00394 (13430)
  covalent geometry    : angle       0.64122 (18252)

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

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

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3416 Ramachandran restraints generated.
    1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 1.874 
Fit side-chains
REVERT: A   17 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (ptt)
REVERT: C   70 MET cc_start: 0.6499 (mmm) cc_final: 0.6247 (tpt)
REVERT: C  174 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6405 (mpp)
REVERT: C  188 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6420 (mtm-85)
REVERT: C  262 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8027 (mp10)
REVERT: C  593 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7006 (ptt-90)
REVERT: C  630 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (mt)
REVERT: D   70 MET cc_start: 0.6683 (mmm) cc_final: 0.6451 (tpt)
REVERT: D  107 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7344 (mp0)
REVERT: D  197 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7703 (mt-10)
REVERT: D  262 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7976 (mp10)
REVERT: D  436 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (tt0)
REVERT: D  577 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7998 (ttp80)
REVERT: D  630 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8014 (mt)
  outliers start: 22
  outliers final: 8
  residues processed: 207
  average time/residue: 1.9274
  time to fit residues: 430.7999
Evaluate side-chains
  211 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  174 MET
Chi-restraints excluded: chain C residue  262 GLN
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  593 ARG
Chi-restraints excluded: chain C residue  630 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  197 GLU
Chi-restraints excluded: chain D residue  199 MET
Chi-restraints excluded: chain D residue  262 GLN
Chi-restraints excluded: chain D residue  311 LEU
Chi-restraints excluded: chain D residue  436 GLU
Chi-restraints excluded: chain D residue  577 ARG
Chi-restraints excluded: chain D residue  630 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9980
   chunk 148 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0770
   chunk 73 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.1740

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.159821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.129875 restraints weight = 13475.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.26
r_work: 0.3220 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13430  Z= 0.154
  Angle     :  0.623  10.718  18252  Z= 0.308
  Chirality :  0.042   0.194   2182
  Planarity :  0.005   0.044   2310
  Dihedral  :  4.290  16.754   1856
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.44 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.21), residues: 1708
  helix:  2.62 (0.18), residues: 820
  sheet:  0.64 (0.31), residues: 280
  loop : -0.45 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 201 
 HIS   0.004   0.001   HIS D 265 
 PHE   0.021   0.002   PHE D 206 
 TYR   0.010   0.002   TYR C 240 
 ARG   0.008   0.000   ARG C 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  782)
  hydrogen bonds       : angle       4.57093 ( 2256)
  covalent geometry    : bond        0.00361 (13430)
  covalent geometry    : angle       0.62296 (18252)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11032.82 seconds
wall clock time: 195 minutes 43.91 seconds (11743.91 seconds total)