Starting phenix.real_space_refine
on Fri Jun 13 08:10:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dpt_27642/06_2025/8dpt_27642.cif"
  }
  resolution = 4.0
  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=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1420 atoms to isotropic.
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      46      5.16       5
     C    8608      2.51       5
     N    2330      2.21       5
     O    2566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13550
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3169
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 375}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 1262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1262
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150}
    Chain: "C"
      Number of atoms: 2249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2249
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 33, 'TRANS': 260}
    Chain: "I"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    F, H, D, E, L
  Time building chain proxies: 10.23, per 1000 atoms: 0.75
  Number of scatterers: 13550
  At special positions: 0
  Unit cell: (148.03, 184.71, 137.55, 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      46     16.00
     O    2566      8.00
     N    2330      7.00
     C    8608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 150 " - pdb=" SG  CYS A 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C  25 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  98 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 148 " - pdb=" SG  CYS C 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 112 " - pdb=" SG  CYS D 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 150 " - pdb=" SG  CYS D 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   4 " - pdb=" SG  CYS F  25 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  26 " - pdb=" SG  CYS F  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  98 " - pdb=" SG  CYS F 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 148 " - pdb=" SG  CYS F 158 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG L   1 " - " NAG L   2 "
      " NAG L   2 " - " BMA L   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A  21 "
      " NAG A 602 " - " ASN A 135 "
      " NAG D 601 " - " ASN D  21 "
      " NAG D 602 " - " ASN D 135 "
      " NAG G   1 " - " ASN A  61 "
      " NAG H   1 " - " ASN D  61 "
      " NAG I   1 " - " ASN C 172 "
      " NAG L   1 " - " ASN F 172 "
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3212

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 34 sheets defined
      19.5% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 37
    Processing helix  chain 'A' and resid 39 through 41
      No H-bonds generated for 'chain 'A' and resid 39 through 41'
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 193 through 196
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.712A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
    Processing helix  chain 'B' and resid 15 through 43
    Processing helix  chain 'B' and resid 68 through 94
      removed outlier: 3.539A  pdb=" N   VAL B  72 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 102
      removed outlier: 4.371A  pdb=" N   THR B 100 " --> pdb=" O   SER B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 126
      removed outlier: 3.577A  pdb=" N   ARG B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 176
      removed outlier: 3.864A  pdb=" N   LEU B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASP B 165 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 67
    Processing helix  chain 'C' and resid 190 through 194
    Processing helix  chain 'D' and resid 29 through 37
    Processing helix  chain 'D' and resid 39 through 41
      No H-bonds generated for 'chain 'D' and resid 39 through 41'
    Processing helix  chain 'D' and resid 53 through 55
      No H-bonds generated for 'chain 'D' and resid 53 through 55'
    Processing helix  chain 'D' and resid 193 through 196
    Processing helix  chain 'D' and resid 225 through 230
    Processing helix  chain 'D' and resid 251 through 256
      removed outlier: 3.712A  pdb=" N   ALA D 256 " --> pdb=" O   GLU D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 338
    Processing helix  chain 'E' and resid 15 through 43
    Processing helix  chain 'E' and resid 68 through 94
      removed outlier: 3.538A  pdb=" N   VAL E  72 " --> pdb=" O   GLN E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 102
      removed outlier: 4.371A  pdb=" N   THR E 100 " --> pdb=" O   SER E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 126
      removed outlier: 3.577A  pdb=" N   ARG E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 145 through 176
      removed outlier: 3.864A  pdb=" N   LEU E 162 " --> pdb=" O   GLY E 158 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASP E 165 " --> pdb=" O   HIS E 161 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 63 through 67
    Processing helix  chain 'F' and resid 190 through 194
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10
      removed outlier: 6.622A  pdb=" N   ALA A  64 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51
      removed outlier: 3.626A  pdb=" N   LYS A  46 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE A  83 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ASN A  92 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 161
      removed outlier: 4.437A  pdb=" N   ASP A 125 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   ASN A 109 " --> pdb=" O   ASP A 125 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   LYS A 199 " --> pdb=" O   CYS A 112 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VAL A 114 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 146
      removed outlier: 3.765A  pdb=" N   GLU A 173 " --> pdb=" O   GLU A 141 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 150 through 151
      removed outlier: 3.765A  pdb=" N   GLU A 173 " --> pdb=" O   GLU A 141 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 204 through 209
      removed outlier: 5.514A  pdb=" N   ASN A 205 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   THR A 223 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 249
      removed outlier: 3.680A  pdb=" N   ARG A 278 " --> pdb=" O   ASN A 236 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN A 238 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ARG A 276 " --> pdb=" O   GLN A 238 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ARG A 240 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 274 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 316
      removed outlier: 3.664A  pdb=" N   VAL A 325 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A 367 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 327 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 360
      removed outlier: 3.822A  pdb=" N   ASP A 343 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ALA A 376 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LEU A 392 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 378 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 16
      removed outlier: 3.761A  pdb=" N   GLN C  14 " --> pdb=" O   THR C  84 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN C  86 " --> pdb=" O   GLN C  14 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU C  79 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   THR C  74 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY C  81 " --> pdb=" O   CYS C  72 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 25
    Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 99
      removed outlier: 3.798A  pdb=" N   CYS C 108 " --> pdb=" O   CYS C 158 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 128
      removed outlier: 3.625A  pdb=" N   ARG C 121 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 128
      removed outlier: 3.625A  pdb=" N   ARG C 121 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 206
      removed outlier: 6.305A  pdb=" N   GLY C 201 " --> pdb=" O   THR C 219 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   THR C 219 " --> pdb=" O   GLY C 201 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 247 through 249
    Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10
      removed outlier: 6.623A  pdb=" N   ALA D  64 " --> pdb=" O   ILE D  60 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 17
    Processing sheet with id=AC2, first strand: chain 'D' and resid 50 through 51
      removed outlier: 3.627A  pdb=" N   LYS D  46 " --> pdb=" O   THR D  80 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE D  83 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ASN D  92 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 161
      removed outlier: 4.437A  pdb=" N   ASP D 125 " --> pdb=" O   ASN D 109 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   ASN D 109 " --> pdb=" O   ASP D 125 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   LYS D 199 " --> pdb=" O   CYS D 112 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VAL D 114 " --> pdb=" O   LYS D 199 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 146
      removed outlier: 3.765A  pdb=" N   GLU D 173 " --> pdb=" O   GLU D 141 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 150 through 151
      removed outlier: 3.765A  pdb=" N   GLU D 173 " --> pdb=" O   GLU D 141 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE D 192 " --> pdb=" O   ILE D 172 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 209
      removed outlier: 5.514A  pdb=" N   ASN D 205 " --> pdb=" O   THR D 223 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   THR D 223 " --> pdb=" O   ASN D 205 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 248 through 249
      removed outlier: 3.679A  pdb=" N   ARG D 278 " --> pdb=" O   ASN D 236 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN D 238 " --> pdb=" O   ARG D 276 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG D 276 " --> pdb=" O   GLN D 238 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG D 240 " --> pdb=" O   VAL D 274 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL D 274 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 310 through 316
      removed outlier: 3.664A  pdb=" N   VAL D 325 " --> pdb=" O   VAL D 367 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL D 367 " --> pdb=" O   VAL D 325 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU D 327 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 356 through 360
      removed outlier: 3.822A  pdb=" N   ASP D 343 " --> pdb=" O   ARG D 381 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ALA D 376 " --> pdb=" O   LEU D 392 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU D 392 " --> pdb=" O   ALA D 376 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU D 378 " --> pdb=" O   ALA D 390 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 14 through 16
      removed outlier: 3.760A  pdb=" N   GLN F  14 " --> pdb=" O   THR F  84 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLN F  86 " --> pdb=" O   GLN F  14 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   LEU F  79 " --> pdb=" O   THR F  74 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   THR F  74 " --> pdb=" O   LEU F  79 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY F  81 " --> pdb=" O   CYS F  72 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'F' and resid 22 through 25
    Processing sheet with id=AD3, first strand: chain 'F' and resid 95 through 99
      removed outlier: 3.797A  pdb=" N   CYS F 108 " --> pdb=" O   CYS F 158 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'F' and resid 121 through 128
      removed outlier: 3.624A  pdb=" N   ARG F 121 " --> pdb=" O   VAL F 176 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'F' and resid 121 through 128
      removed outlier: 3.624A  pdb=" N   ARG F 121 " --> pdb=" O   VAL F 176 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'F' and resid 200 through 206
      removed outlier: 6.305A  pdb=" N   GLY F 201 " --> pdb=" O   THR F 219 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   THR F 219 " --> pdb=" O   GLY F 201 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'F' and resid 247 through 249

    548 hydrogen bonds defined for protein.
    1410 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: 4.33

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4370
        1.35 -     1.47: 3344
        1.47 -     1.59: 6148
        1.59 -     1.71: 0
        1.71 -     1.83: 56
  Bond restraints: 13918
  Sorted by residual:
  bond pdb=" C1  NAG I   1 "
       pdb=" O5  NAG I   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.33e+00
  bond pdb=" C1  NAG L   1 "
       pdb=" O5  NAG L   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.27e+00
  bond pdb=" CA  ASP F 151 "
       pdb=" C   ASP F 151 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.26e-02 6.30e+03 3.67e+00
  bond pdb=" CA  ASP C 151 "
       pdb=" C   ASP C 151 "
    ideal  model  delta    sigma   weight residual
    1.524  1.546 -0.023 1.26e-02 6.30e+03 3.20e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.92e+00
  ... (remaining 13913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.90: 18721
        3.90 -     7.80: 279
        7.80 -    11.70: 30
       11.70 -    15.60: 6
       15.60 -    19.50: 4
  Bond angle restraints: 19040
  Sorted by residual:
  angle pdb=" CG  ARG B  85 "
        pdb=" CD  ARG B  85 "
        pdb=" NE  ARG B  85 "
      ideal   model   delta    sigma   weight residual
     112.00  131.50  -19.50 2.20e+00 2.07e-01 7.86e+01
  angle pdb=" CG  ARG E  85 "
        pdb=" CD  ARG E  85 "
        pdb=" NE  ARG E  85 "
      ideal   model   delta    sigma   weight residual
     112.00  131.46  -19.46 2.20e+00 2.07e-01 7.82e+01
  angle pdb=" CD  ARG E  85 "
        pdb=" NE  ARG E  85 "
        pdb=" CZ  ARG E  85 "
      ideal   model   delta    sigma   weight residual
     124.40  132.31   -7.91 1.40e+00 5.10e-01 3.19e+01
  angle pdb=" CD  ARG B  85 "
        pdb=" NE  ARG B  85 "
        pdb=" CZ  ARG B  85 "
      ideal   model   delta    sigma   weight residual
     124.40  132.25   -7.85 1.40e+00 5.10e-01 3.14e+01
  angle pdb=" CB  ARG E  85 "
        pdb=" CG  ARG E  85 "
        pdb=" CD  ARG E  85 "
      ideal   model   delta    sigma   weight residual
     111.30  123.84  -12.54 2.30e+00 1.89e-01 2.97e+01
  ... (remaining 19035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.66: 8026
       21.66 -    43.32: 426
       43.32 -    64.98: 66
       64.98 -    86.64: 32
       86.64 -   108.30: 8
  Dihedral angle restraints: 8558
    sinusoidal: 3580
      harmonic: 4978
  Sorted by residual:
  dihedral pdb=" C   ASP F 151 "
           pdb=" N   ASP F 151 "
           pdb=" CA  ASP F 151 "
           pdb=" CB  ASP F 151 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.12   14.52     0      2.50e+00 1.60e-01 3.38e+01
  dihedral pdb=" C   ASP C 151 "
           pdb=" N   ASP C 151 "
           pdb=" CA  ASP C 151 "
           pdb=" CB  ASP C 151 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.12   14.52     0      2.50e+00 1.60e-01 3.38e+01
  dihedral pdb=" CG  ARG B  85 "
           pdb=" CD  ARG B  85 "
           pdb=" NE  ARG B  85 "
           pdb=" CZ  ARG B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00   -9.21  -80.79     2      1.50e+01 4.44e-03 2.08e+01
  ... (remaining 8555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1895
       0.088 -    0.175: 262
       0.175 -    0.263: 19
       0.263 -    0.351: 4
       0.351 -    0.438: 2
  Chirality restraints: 2182
  Sorted by residual:
  chirality pdb=" CA  ASP C 151 "
            pdb=" N   ASP C 151 "
            pdb=" C   ASP C 151 "
            pdb=" CB  ASP C 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.80e+00
  chirality pdb=" CA  ASP F 151 "
            pdb=" N   ASP F 151 "
            pdb=" C   ASP F 151 "
            pdb=" CB  ASP F 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.79e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A  61 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 2179 not shown)

  Planarity restraints: 2440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  69 "    0.060 5.00e-02 4.00e+02   8.97e-02 1.29e+01
        pdb=" N   PRO B  70 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B  70 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B  70 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  69 "   -0.060 5.00e-02 4.00e+02   8.95e-02 1.28e+01
        pdb=" N   PRO E  70 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO E  70 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO E  70 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  85 "    0.129 9.50e-02 1.11e+02   6.27e-02 9.55e+00
        pdb=" NE  ARG E  85 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  85 "   -0.049 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  85 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  85 "    0.020 2.00e-02 2.50e+03
  ... (remaining 2437 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 254
        2.65 -     3.22: 12538
        3.22 -     3.78: 20119
        3.78 -     4.34: 26435
        4.34 -     4.90: 42637
  Nonbonded interactions: 101983
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 261 "
            pdb=" OG  SER F 247 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" OG  SER A 261 "
            pdb=" OG  SER C 247 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" NE2 GLN B  38 "
            pdb=" OE1 GLU B 104 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" NE2 GLN E  38 "
            pdb=" OE1 GLU E 104 "
     model   vdw
     2.136 3.120
  nonbonded pdb=" OG1 THR A 347 "
            pdb=" OG1 THR A 377 "
     model   vdw
     2.150 3.040
  ... (remaining 101978 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.160
  Process input model:                     34.540
  Find NCS groups from input model:        0.420
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13948  Z= 0.203
  Angle     :  1.211  19.503  19114  Z= 0.630
  Chirality :  0.059   0.438   2182
  Planarity :  0.007   0.090   2432
  Dihedral  : 14.568 108.305   5298
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.52 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.39 %
    Favored  : 97.20 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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: -0.83 (0.19), residues: 1702
  helix:  1.25 (0.29), residues: 250
  sheet: -0.06 (0.20), residues: 558
  loop : -1.42 (0.19), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP D 142 
 HIS   0.012   0.001   HIS E  86 
 PHE   0.039   0.003   PHE D  36 
 TYR   0.020   0.003   TYR A 344 
 ARG   0.047   0.001   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00927 (    8)
  link_NAG-ASN         : angle       3.18960 (   24)
  link_BETA1-4         : bond        0.00723 (    6)
  link_BETA1-4         : angle       3.51647 (   18)
  hydrogen bonds       : bond        0.25308 (  520)
  hydrogen bonds       : angle       8.79719 ( 1410)
  SS BOND              : bond        0.00269 (   16)
  SS BOND              : angle       2.64312 (   32)
  covalent geometry    : bond        0.00445 (13918)
  covalent geometry    : angle       1.19847 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 178
  time to evaluate  : 1.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 THR cc_start: 0.7698 (m) cc_final: 0.7137 (t)
REVERT: A  220 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7004 (mp)
REVERT: B  109 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7859 (tm-30)
REVERT: C  157 ARG cc_start: 0.7161 (ptm-80) cc_final: 0.6855 (ttp-170)
REVERT: C  282 TRP cc_start: 0.7501 (m100) cc_final: 0.6368 (m100)
REVERT: D   35 TYR cc_start: 0.7123 (t80) cc_final: 0.6696 (t80)
REVERT: D   57 TYR cc_start: 0.6498 (m-80) cc_final: 0.6284 (m-80)
REVERT: D  220 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6846 (mp)
REVERT: F  157 ARG cc_start: 0.7134 (ptm-80) cc_final: 0.6855 (ttp-170)
REVERT: F  202 LEU cc_start: 0.6647 (tp) cc_final: 0.6293 (tp)
REVERT: F  282 TRP cc_start: 0.7522 (m100) cc_final: 0.6403 (m100)
  outliers start: 6
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2766
  time to fit residues: 73.3870
Evaluate side-chains
  120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain D residue  220 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 127 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0060
   chunk 68 optimal weight:    9.9990
   chunk 131 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   chunk 80 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 152 optimal weight:    0.8980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
D 115 ASN
F 229 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.230162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.203177 restraints weight = 179609.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.205759 restraints weight = 109463.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.204061 restraints weight = 91243.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  13948  Z= 0.165
  Angle     :  0.809   9.464  19114  Z= 0.396
  Chirality :  0.048   0.295   2182
  Planarity :  0.006   0.057   2432
  Dihedral  :  8.966  70.291   2160
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.65 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.29 (0.20), residues: 1702
  helix:  1.99 (0.30), residues: 252
  sheet:  0.35 (0.20), residues: 546
  loop : -0.38 (0.21), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 147 
 HIS   0.006   0.001   HIS E 161 
 PHE   0.016   0.002   PHE F 230 
 TYR   0.023   0.002   TYR C 103 
 ARG   0.008   0.001   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00443 (    8)
  link_NAG-ASN         : angle       1.68798 (   24)
  link_BETA1-4         : bond        0.00659 (    6)
  link_BETA1-4         : angle       2.82483 (   18)
  hydrogen bonds       : bond        0.05253 (  520)
  hydrogen bonds       : angle       6.11645 ( 1410)
  SS BOND              : bond        0.00782 (   16)
  SS BOND              : angle       1.64428 (   32)
  covalent geometry    : bond        0.00369 (13918)
  covalent geometry    : angle       0.80095 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  288 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6684 (mm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 156
  average time/residue: 0.2347
  time to fit residues: 55.7504
Evaluate side-chains
  116 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain F residue  151 ASP
Chi-restraints excluded: chain F residue  230 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 152 optimal weight:    8.9990
   chunk 165 optimal weight:    0.5980
   chunk 136 optimal weight:    0.5980
   chunk 151 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0010
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
C  14 GLN
F  14 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.214567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.203012 restraints weight = 17466.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.189453 restraints weight = 34710.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.184882 restraints weight = 27491.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  13948  Z= 0.162
  Angle     :  0.731  15.774  19114  Z= 0.356
  Chirality :  0.047   0.301   2182
  Planarity :  0.005   0.060   2432
  Dihedral  :  7.041  57.524   2156
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.17 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.11 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.26 (0.20), residues: 1702
  helix:  1.28 (0.31), residues: 276
  sheet:  0.29 (0.20), residues: 566
  loop : -0.18 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 282 
 HIS   0.012   0.001   HIS C 229 
 PHE   0.018   0.002   PHE D  50 
 TYR   0.016   0.002   TYR A 344 
 ARG   0.010   0.001   ARG F 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00348 (    8)
  link_NAG-ASN         : angle       1.64544 (   24)
  link_BETA1-4         : bond        0.00608 (    6)
  link_BETA1-4         : angle       2.91695 (   18)
  hydrogen bonds       : bond        0.04386 (  520)
  hydrogen bonds       : angle       5.47243 ( 1410)
  SS BOND              : bond        0.00759 (   16)
  SS BOND              : angle       2.00028 (   32)
  covalent geometry    : bond        0.00370 (13918)
  covalent geometry    : angle       0.71988 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 TYR cc_start: 0.5923 (p90) cc_final: 0.5642 (p90)
REVERT: B   89 TRP cc_start: 0.8658 (t60) cc_final: 0.8380 (t60)
REVERT: C   95 VAL cc_start: 0.8342 (t) cc_final: 0.8056 (m)
REVERT: D  280 MET cc_start: 0.6810 (ttt) cc_final: 0.6576 (ttt)
  outliers start: 26
  outliers final: 15
  residues processed: 151
  average time/residue: 0.2448
  time to fit residues: 57.3243
Evaluate side-chains
  125 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain F residue  151 ASP
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  230 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 114 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 147 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 36 optimal weight:   20.0000
   chunk 25 optimal weight:    1.9990
   chunk 140 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
D  82 ASN
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  38 GLN
** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.207052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.198696 restraints weight = 17691.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.194002 restraints weight = 26122.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.191548 restraints weight = 40419.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13948  Z= 0.192
  Angle     :  0.741  13.252  19114  Z= 0.362
  Chirality :  0.048   0.321   2182
  Planarity :  0.005   0.062   2432
  Dihedral  :  6.384  57.989   2156
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.32 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.31 (0.20), residues: 1702
  helix:  1.26 (0.32), residues: 252
  sheet:  0.19 (0.20), residues: 548
  loop :  0.03 (0.22), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F 166 
 HIS   0.020   0.002   HIS F 229 
 PHE   0.024   0.002   PHE C 230 
 TYR   0.014   0.002   TYR A 344 
 ARG   0.005   0.001   ARG B 117 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00298 (    8)
  link_NAG-ASN         : angle       1.77314 (   24)
  link_BETA1-4         : bond        0.00438 (    6)
  link_BETA1-4         : angle       2.82082 (   18)
  hydrogen bonds       : bond        0.04164 (  520)
  hydrogen bonds       : angle       5.26926 ( 1410)
  SS BOND              : bond        0.00782 (   16)
  SS BOND              : angle       2.14428 (   32)
  covalent geometry    : bond        0.00447 (13918)
  covalent geometry    : angle       0.72956 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.7962 (mp10) cc_final: 0.7676 (mt0)
REVERT: C  182 SER cc_start: 0.7193 (p) cc_final: 0.6964 (p)
REVERT: D   17 GLN cc_start: 0.8049 (mp10) cc_final: 0.7785 (mt0)
REVERT: D  280 MET cc_start: 0.7109 (ttt) cc_final: 0.6871 (ttt)
REVERT: F  182 SER cc_start: 0.7081 (p) cc_final: 0.6876 (p)
  outliers start: 31
  outliers final: 19
  residues processed: 143
  average time/residue: 0.2220
  time to fit residues: 51.8161
Evaluate side-chains
  124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 2.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue  151 ASP
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 166 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 146 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 157 optimal weight:    0.0370
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 161 HIS ** 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 = 0.4489 r_free = 0.4489 target = 0.209463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.197199 restraints weight = 17517.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.183452 restraints weight = 38254.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178115 restraints weight = 33269.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13948  Z= 0.129
  Angle     :  0.679  15.861  19114  Z= 0.331
  Chirality :  0.045   0.312   2182
  Planarity :  0.005   0.062   2432
  Dihedral  :  6.111  57.143   2156
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.80 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.52 (0.21), residues: 1702
  helix:  1.74 (0.32), residues: 240
  sheet:  0.33 (0.20), residues: 538
  loop :  0.07 (0.22), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 166 
 HIS   0.012   0.001   HIS C 229 
 PHE   0.023   0.002   PHE C 230 
 TYR   0.022   0.001   TYR F 103 
 ARG   0.003   0.000   ARG F 274 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    8)
  link_NAG-ASN         : angle       1.68764 (   24)
  link_BETA1-4         : bond        0.00467 (    6)
  link_BETA1-4         : angle       2.60045 (   18)
  hydrogen bonds       : bond        0.03667 (  520)
  hydrogen bonds       : angle       5.02755 ( 1410)
  SS BOND              : bond        0.00988 (   16)
  SS BOND              : angle       2.27004 (   32)
  covalent geometry    : bond        0.00290 (13918)
  covalent geometry    : angle       0.66658 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.8040 (mp10) cc_final: 0.7792 (mt0)
REVERT: C  164 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7929 (tp30)
REVERT: C  182 SER cc_start: 0.7162 (p) cc_final: 0.6959 (p)
REVERT: C  257 VAL cc_start: 0.6018 (OUTLIER) cc_final: 0.5729 (m)
REVERT: D   17 GLN cc_start: 0.8081 (mp10) cc_final: 0.7830 (mt0)
REVERT: D  287 TYR cc_start: 0.5201 (m-10) cc_final: 0.4795 (m-10)
REVERT: E   59 MET cc_start: 0.7928 (mtm) cc_final: 0.7651 (mtm)
REVERT: F  164 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7903 (tp30)
REVERT: F  257 VAL cc_start: 0.5798 (OUTLIER) cc_final: 0.5500 (m)
  outliers start: 35
  outliers final: 16
  residues processed: 156
  average time/residue: 0.1878
  time to fit residues: 47.8480
Evaluate side-chains
  132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  204 VAL
Chi-restraints excluded: chain F residue  236 LEU
Chi-restraints excluded: chain F residue  257 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 167 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 114 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 132 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 HIS
C  73 GLN
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 115 ASN
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 154 HIS
F  73 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.200533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.184230 restraints weight = 17667.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.172438 restraints weight = 38876.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.170300 restraints weight = 31231.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  13948  Z= 0.218
  Angle     :  0.764  16.310  19114  Z= 0.373
  Chirality :  0.048   0.397   2182
  Planarity :  0.006   0.063   2432
  Dihedral  :  6.289  58.719   2156
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.55 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.02 (0.21), residues: 1702
  helix:  0.93 (0.31), residues: 252
  sheet:  0.04 (0.21), residues: 548
  loop : -0.17 (0.22), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 166 
 HIS   0.014   0.002   HIS C 229 
 PHE   0.044   0.002   PHE F 230 
 TYR   0.050   0.002   TYR C 103 
 ARG   0.009   0.001   ARG D 121 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00310 (    8)
  link_NAG-ASN         : angle       1.96038 (   24)
  link_BETA1-4         : bond        0.00458 (    6)
  link_BETA1-4         : angle       2.73675 (   18)
  hydrogen bonds       : bond        0.04131 (  520)
  hydrogen bonds       : angle       5.18016 ( 1410)
  SS BOND              : bond        0.00930 (   16)
  SS BOND              : angle       2.48529 (   32)
  covalent geometry    : bond        0.00513 (13918)
  covalent geometry    : angle       0.75027 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 116
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 MET cc_start: 0.7050 (ttt) cc_final: 0.6850 (ttt)
REVERT: C  164 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7959 (tp30)
REVERT: C  182 SER cc_start: 0.7513 (p) cc_final: 0.7282 (p)
REVERT: C  230 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7190 (p90)
REVERT: C  282 TRP cc_start: 0.7966 (m100) cc_final: 0.7641 (m100)
REVERT: D  280 MET cc_start: 0.6415 (ttt) cc_final: 0.5847 (ttt)
REVERT: E   38 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8362 (tt0)
REVERT: F  164 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7893 (tp30)
REVERT: F  230 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7473 (p90)
  outliers start: 50
  outliers final: 28
  residues processed: 159
  average time/residue: 0.2186
  time to fit residues: 56.6439
Evaluate side-chains
  131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  230 PHE
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   38 GLN
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue  161 HIS
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  204 VAL
Chi-restraints excluded: chain F residue  230 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 164 optimal weight:    0.8980
   chunk 139 optimal weight:    6.9990
   chunk 77 optimal weight:    0.4980
   chunk 93 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   chunk 82 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0980
   chunk 141 optimal weight:   30.0000
   chunk 140 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 HIS ** 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 = 0.4540 r_free = 0.4540 target = 0.214757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.185105 restraints weight = 181773.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.187044 restraints weight = 110980.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185622 restraints weight = 94147.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13948  Z= 0.130
  Angle     :  0.689  17.243  19114  Z= 0.334
  Chirality :  0.045   0.314   2182
  Planarity :  0.005   0.061   2432
  Dihedral  :  6.024  57.351   2156
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.12 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.31 (0.21), residues: 1702
  helix:  1.66 (0.33), residues: 240
  sheet:  0.08 (0.21), residues: 554
  loop : -0.01 (0.23), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 222 
 HIS   0.016   0.001   HIS C 229 
 PHE   0.018   0.001   PHE F 230 
 TYR   0.023   0.001   TYR C 103 
 ARG   0.002   0.000   ARG B 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00297 (    8)
  link_NAG-ASN         : angle       1.77162 (   24)
  link_BETA1-4         : bond        0.00459 (    6)
  link_BETA1-4         : angle       2.53634 (   18)
  hydrogen bonds       : bond        0.03519 (  520)
  hydrogen bonds       : angle       4.98121 ( 1410)
  SS BOND              : bond        0.00725 (   16)
  SS BOND              : angle       2.55233 (   32)
  covalent geometry    : bond        0.00295 (13918)
  covalent geometry    : angle       0.67517 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 2.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 MET cc_start: 0.7182 (ttt) cc_final: 0.6942 (ttt)
REVERT: A  291 TRP cc_start: 0.8043 (m100) cc_final: 0.7692 (m100)
REVERT: B   49 HIS cc_start: 0.7764 (p-80) cc_final: 0.7528 (p-80)
REVERT: C  164 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7900 (tp30)
REVERT: C  182 SER cc_start: 0.7363 (p) cc_final: 0.7138 (t)
REVERT: C  257 VAL cc_start: 0.5614 (OUTLIER) cc_final: 0.5268 (m)
REVERT: D  280 MET cc_start: 0.6754 (ttt) cc_final: 0.6385 (ttt)
REVERT: D  291 TRP cc_start: 0.8053 (m100) cc_final: 0.7672 (m100)
REVERT: F  164 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8019 (tp30)
REVERT: F  257 VAL cc_start: 0.5803 (OUTLIER) cc_final: 0.5428 (m)
  outliers start: 36
  outliers final: 22
  residues processed: 152
  average time/residue: 0.2269
  time to fit residues: 57.1053
Evaluate side-chains
  134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue  151 ASP
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  257 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 150 optimal weight:    1.9990
   chunk 157 optimal weight:    0.0870
   chunk 54 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** C 229 HIS ** 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 = 0.4545 r_free = 0.4545 target = 0.214824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.185092 restraints weight = 181842.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.188273 restraints weight = 111492.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.186146 restraints weight = 93969.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13948  Z= 0.138
  Angle     :  0.704  17.941  19114  Z= 0.340
  Chirality :  0.046   0.316   2182
  Planarity :  0.005   0.072   2432
  Dihedral  :  5.938  57.540   2156
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.28 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.28 (0.21), residues: 1702
  helix:  1.37 (0.32), residues: 252
  sheet:  0.16 (0.22), residues: 540
  loop : -0.03 (0.23), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 222 
 HIS   0.015   0.001   HIS C 229 
 PHE   0.023   0.002   PHE C 230 
 TYR   0.041   0.001   TYR C 103 
 ARG   0.003   0.000   ARG E 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00271 (    8)
  link_NAG-ASN         : angle       1.78912 (   24)
  link_BETA1-4         : bond        0.00460 (    6)
  link_BETA1-4         : angle       2.53968 (   18)
  hydrogen bonds       : bond        0.03507 (  520)
  hydrogen bonds       : angle       4.95864 ( 1410)
  SS BOND              : bond        0.00653 (   16)
  SS BOND              : angle       2.81573 (   32)
  covalent geometry    : bond        0.00318 (13918)
  covalent geometry    : angle       0.68840 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 121
  time to evaluate  : 2.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.6281 (tmm) cc_final: 0.5937 (tmm)
REVERT: A  280 MET cc_start: 0.6923 (ttt) cc_final: 0.6649 (ttt)
REVERT: B   49 HIS cc_start: 0.7872 (p-80) cc_final: 0.7658 (p-80)
REVERT: C  164 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7987 (tp30)
REVERT: C  257 VAL cc_start: 0.5880 (OUTLIER) cc_final: 0.5494 (m)
REVERT: D   33 MET cc_start: 0.6259 (tmm) cc_final: 0.5885 (tmm)
REVERT: D  280 MET cc_start: 0.6907 (ttt) cc_final: 0.6596 (ttt)
REVERT: D  291 TRP cc_start: 0.8039 (m100) cc_final: 0.7708 (m100)
REVERT: E   41 ASP cc_start: 0.8130 (t0) cc_final: 0.7928 (t0)
REVERT: F  164 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8130 (tp30)
REVERT: F  257 VAL cc_start: 0.5795 (OUTLIER) cc_final: 0.5378 (m)
  outliers start: 35
  outliers final: 27
  residues processed: 150
  average time/residue: 0.2527
  time to fit residues: 63.3652
Evaluate side-chains
  142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  230 PHE
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue  161 HIS
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  204 VAL
Chi-restraints excluded: chain F residue  257 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 163 optimal weight:    0.0870
   chunk 145 optimal weight:    0.9980
   chunk 155 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.7558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.214121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.184215 restraints weight = 182514.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.186734 restraints weight = 109943.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.185637 restraints weight = 96765.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13948  Z= 0.139
  Angle     :  0.708  19.035  19114  Z= 0.342
  Chirality :  0.046   0.313   2182
  Planarity :  0.005   0.060   2432
  Dihedral  :  5.911  57.610   2156
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.62 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.31 (0.21), residues: 1702
  helix:  1.42 (0.32), residues: 252
  sheet:  0.18 (0.22), residues: 544
  loop : -0.02 (0.23), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 166 
 HIS   0.014   0.001   HIS C 229 
 PHE   0.021   0.002   PHE E  43 
 TYR   0.031   0.001   TYR C 103 
 ARG   0.008   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    8)
  link_NAG-ASN         : angle       1.78904 (   24)
  link_BETA1-4         : bond        0.00459 (    6)
  link_BETA1-4         : angle       2.51442 (   18)
  hydrogen bonds       : bond        0.03445 (  520)
  hydrogen bonds       : angle       4.94190 ( 1410)
  SS BOND              : bond        0.00547 (   16)
  SS BOND              : angle       2.90004 (   32)
  covalent geometry    : bond        0.00324 (13918)
  covalent geometry    : angle       0.69239 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 1.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 TRP cc_start: 0.8024 (m100) cc_final: 0.7698 (m100)
REVERT: C  164 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8315 (tp30)
REVERT: C  257 VAL cc_start: 0.5724 (OUTLIER) cc_final: 0.5466 (m)
REVERT: D  280 MET cc_start: 0.6913 (ttt) cc_final: 0.6680 (ttt)
REVERT: D  291 TRP cc_start: 0.8060 (m100) cc_final: 0.7739 (m100)
REVERT: E   41 ASP cc_start: 0.8199 (t0) cc_final: 0.7979 (t0)
REVERT: F  164 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8324 (tp30)
REVERT: F  257 VAL cc_start: 0.5615 (OUTLIER) cc_final: 0.5393 (m)
  outliers start: 36
  outliers final: 31
  residues processed: 146
  average time/residue: 0.2403
  time to fit residues: 57.8568
Evaluate side-chains
  148 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 2.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 PHE
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  230 PHE
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue  161 HIS
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue  151 ASP
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  204 VAL
Chi-restraints excluded: chain F residue  257 VAL
Chi-restraints excluded: chain F residue  281 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 145 optimal weight:    0.9990
   chunk 158 optimal weight:    0.7980
   chunk 143 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 157 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C 229 HIS ** 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 = 0.4431 r_free = 0.4431 target = 0.204184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.190835 restraints weight = 17892.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.175089 restraints weight = 42319.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.171403 restraints weight = 34771.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13948  Z= 0.155
  Angle     :  0.719  17.627  19114  Z= 0.348
  Chirality :  0.046   0.317   2182
  Planarity :  0.005   0.062   2432
  Dihedral  :  5.958  57.947   2156
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.10 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.24 (0.21), residues: 1702
  helix:  1.33 (0.32), residues: 252
  sheet:  0.13 (0.21), residues: 544
  loop : -0.06 (0.23), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP F 166 
 HIS   0.017   0.002   HIS C 229 
 PHE   0.020   0.002   PHE E  43 
 TYR   0.027   0.001   TYR C 103 
 ARG   0.004   0.000   ARG C 274 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00253 (    8)
  link_NAG-ASN         : angle       1.85146 (   24)
  link_BETA1-4         : bond        0.00449 (    6)
  link_BETA1-4         : angle       2.54075 (   18)
  hydrogen bonds       : bond        0.03558 (  520)
  hydrogen bonds       : angle       4.99885 ( 1410)
  SS BOND              : bond        0.00546 (   16)
  SS BOND              : angle       2.88291 (   32)
  covalent geometry    : bond        0.00365 (13918)
  covalent geometry    : angle       0.70363 (19040)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 1.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.5904 (tmm) cc_final: 0.5659 (tmm)
REVERT: C  164 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: C  257 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.5582 (m)
REVERT: D   33 MET cc_start: 0.6135 (tmm) cc_final: 0.5915 (tmm)
REVERT: D   35 TYR cc_start: 0.7454 (t80) cc_final: 0.6932 (t80)
REVERT: E   41 ASP cc_start: 0.8048 (t0) cc_final: 0.7810 (t0)
REVERT: F  164 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7703 (mm-30)
REVERT: F  257 VAL cc_start: 0.5506 (OUTLIER) cc_final: 0.5076 (m)
  outliers start: 36
  outliers final: 29
  residues processed: 142
  average time/residue: 0.2697
  time to fit residues: 63.6865
Evaluate side-chains
  137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  161 HIS
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain C residue  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  257 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain D residue    4 ASP
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue  161 HIS
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue   58 VAL
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Chi-restraints excluded: chain F residue  204 VAL
Chi-restraints excluded: chain F residue  257 VAL
Chi-restraints excluded: chain F residue  281 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 75 optimal weight:    0.0060
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0170
   chunk 150 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 139 optimal weight:   30.0000
   chunk 51 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
B 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.205033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.191931 restraints weight = 17896.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.182853 restraints weight = 35806.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.179241 restraints weight = 28525.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13948  Z= 0.121
  Angle     :  0.692  17.489  19114  Z= 0.335
  Chirality :  0.045   0.305   2182
  Planarity :  0.005   0.062   2432
  Dihedral  :  5.782  57.258   2156
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.17 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    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:  0.50 (0.21), residues: 1702
  helix:  1.92 (0.33), residues: 240
  sheet:  0.21 (0.21), residues: 548
  loop :  0.09 (0.23), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 166 
 HIS   0.013   0.001   HIS C 229 
 PHE   0.019   0.001   PHE E  43 
 TYR   0.022   0.001   TYR A 344 
 ARG   0.004   0.000   ARG C 235 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    8)
  link_NAG-ASN         : angle       1.76045 (   24)
  link_BETA1-4         : bond        0.00449 (    6)
  link_BETA1-4         : angle       2.46364 (   18)
  hydrogen bonds       : bond        0.03280 (  520)
  hydrogen bonds       : angle       4.85978 ( 1410)
  SS BOND              : bond        0.00633 (   16)
  SS BOND              : angle       2.85859 (   32)
  covalent geometry    : bond        0.00276 (13918)
  covalent geometry    : angle       0.67672 (19040)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4496.11 seconds
wall clock time: 82 minutes 53.55 seconds (4973.55 seconds total)