Starting phenix.real_space_refine
on Sat Aug 23 21:33:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dpt_27642/08_2025/8dpt_27642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dpt_27642/08_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_27642/08_2025/8dpt_27642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dpt_27642/08_2025/8dpt_27642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dpt_27642/08_2025/8dpt_27642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dpt_27642/08_2025/8dpt_27642.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    D, E, F, L, H
  Time building chain proxies: 4.04, per 1000 atoms: 0.30
  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: 1.22
  Conformation dependent library (CDL) restraints added in 636.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.48
  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: 2.89

  Time building geometry restraints manager: 1.61 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

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:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.210
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.150
-------------------------------------------------------------------------------
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 : 17.05
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.047   0.001   ARG B  85 
 TYR   0.020   0.003   TYR A 344 
 PHE   0.039   0.003   PHE D  36 
 TRP   0.047   0.003   TRP D 142 
 HIS   0.012   0.001   HIS E  86 

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

*********************** 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  : 0.372 
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: 0.1151
  time to fit residues: 30.1203
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  : 0.405 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
B  38 GLN
D  92 ASN
D 115 ASN
F 229 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.219398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.208188 restraints weight = 17407.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.193128 restraints weight = 31568.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.189083 restraints weight = 24525.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.189077 restraints weight = 23802.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.189388 restraints weight = 20672.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  13948  Z= 0.178
  Angle     :  0.820   9.327  19114  Z= 0.402
  Chirality :  0.048   0.297   2182
  Planarity :  0.006   0.056   2432
  Dihedral  :  8.844  67.989   2160
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.88 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.58 %
    Favored  : 91.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.20), residues: 1702
  helix:  1.91 (0.30), residues: 252
  sheet:  0.29 (0.19), residues: 546
  loop : -0.37 (0.21), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  85 
 TYR   0.022   0.002   TYR C 103 
 PHE   0.019   0.002   PHE F 230 
 TRP   0.016   0.002   TRP A 124 
 HIS   0.007   0.001   HIS E 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (13918)
  covalent geometry    : angle       0.81068 (19040)
  SS BOND              : bond        0.00759 (   16)
  SS BOND              : angle       2.04144 (   32)
  hydrogen bonds       : bond        0.05168 (  520)
  hydrogen bonds       : angle       6.04183 ( 1410)
  link_BETA1-4         : bond        0.00847 (    6)
  link_BETA1-4         : angle       2.88817 (   18)
  link_NAG-ASN         : bond        0.00457 (    8)
  link_NAG-ASN         : angle       1.67093 (   24)

*********************** 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
  161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.4733 (mmt) cc_final: 0.4405 (mmt)
REVERT: C  182 SER cc_start: 0.7312 (p) cc_final: 0.7059 (p)
REVERT: F  182 SER cc_start: 0.7225 (p) cc_final: 0.6985 (p)
REVERT: F  288 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6572 (mm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 156
  average time/residue: 0.0799
  time to fit residues: 19.5363
Evaluate side-chains
  123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain C residue  151 ASP
Chi-restraints excluded: chain C residue  183 THR
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 149 optimal weight:    2.9990
   chunk 164 optimal weight:    0.0980
   chunk 151 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 165 optimal weight:    0.8980
   chunk 143 optimal weight:    0.0050
   chunk 17 optimal weight:    0.7980
   chunk 147 optimal weight:    0.9990
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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**
C  14 GLN
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  14 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.217447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.191454 restraints weight = 17670.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.187818 restraints weight = 20770.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.188579 restraints weight = 20899.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.188583 restraints weight = 17148.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.188794 restraints weight = 15743.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  13948  Z= 0.141
  Angle     :  0.730  15.917  19114  Z= 0.353
  Chirality :  0.047   0.305   2182
  Planarity :  0.005   0.058   2432
  Dihedral  :  7.250  57.289   2156
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.06 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.38 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.20), residues: 1702
  helix:  1.62 (0.31), residues: 262
  sheet:  0.38 (0.20), residues: 556
  loop : -0.16 (0.22), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  85 
 TYR   0.015   0.002   TYR A 344 
 PHE   0.019   0.001   PHE D  50 
 TRP   0.013   0.002   TRP C 282 
 HIS   0.011   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13918)
  covalent geometry    : angle       0.71964 (19040)
  SS BOND              : bond        0.00182 (   16)
  SS BOND              : angle       1.89071 (   32)
  hydrogen bonds       : bond        0.04433 (  520)
  hydrogen bonds       : angle       5.52922 ( 1410)
  link_BETA1-4         : bond        0.00569 (    6)
  link_BETA1-4         : angle       2.89040 (   18)
  link_NAG-ASN         : bond        0.00384 (    8)
  link_NAG-ASN         : angle       1.59858 (   24)

*********************** 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
  160 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7527 (tt)
REVERT: B   89 TRP cc_start: 0.8616 (t60) cc_final: 0.8312 (t60)
REVERT: B  116 LEU cc_start: 0.8143 (tt) cc_final: 0.7899 (tp)
REVERT: C   95 VAL cc_start: 0.8190 (t) cc_final: 0.7941 (m)
  outliers start: 19
  outliers final: 11
  residues processed: 155
  average time/residue: 0.0886
  time to fit residues: 21.1227
Evaluate side-chains
  129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 CYS
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   35 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  183 THR
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue  160 CYS
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 110 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 149 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 117 optimal weight:   30.0000
   chunk 108 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 126 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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  38 GLN
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.211684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.198792 restraints weight = 17723.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.184725 restraints weight = 42379.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.180745 restraints weight = 32964.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.181967 restraints weight = 32299.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.181892 restraints weight = 23531.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13948  Z= 0.159
  Angle     :  0.703  13.855  19114  Z= 0.342
  Chirality :  0.047   0.311   2182
  Planarity :  0.005   0.060   2432
  Dihedral  :  6.300  57.779   2156
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.66 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.20), residues: 1702
  helix:  1.43 (0.31), residues: 264
  sheet:  0.29 (0.20), residues: 560
  loop :  0.00 (0.22), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 121 
 TYR   0.016   0.002   TYR A 344 
 PHE   0.012   0.002   PHE D  50 
 TRP   0.015   0.002   TRP F 166 
 HIS   0.017   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (13918)
  covalent geometry    : angle       0.69032 (19040)
  SS BOND              : bond        0.00694 (   16)
  SS BOND              : angle       2.32637 (   32)
  hydrogen bonds       : bond        0.03933 (  520)
  hydrogen bonds       : angle       5.19870 ( 1410)
  link_BETA1-4         : bond        0.00453 (    6)
  link_BETA1-4         : angle       2.78024 (   18)
  link_NAG-ASN         : bond        0.00333 (    8)
  link_NAG-ASN         : angle       1.69319 (   24)

*********************** 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
  161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 TRP cc_start: 0.8756 (t60) cc_final: 0.8439 (t60)
REVERT: B  116 LEU cc_start: 0.8321 (tt) cc_final: 0.8069 (tp)
REVERT: D   17 GLN cc_start: 0.8040 (mp10) cc_final: 0.7752 (mt0)
REVERT: D  280 MET cc_start: 0.6515 (ttt) cc_final: 0.6202 (ttt)
  outliers start: 30
  outliers final: 20
  residues processed: 153
  average time/residue: 0.0777
  time to fit residues: 19.0980
Evaluate side-chains
  133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
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   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  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 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 165 optimal weight:    0.3980
   chunk 66 optimal weight:    0.0770
   chunk 65 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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  38 GLN
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 338 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.211579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.199274 restraints weight = 17559.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.186349 restraints weight = 33818.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.181800 restraints weight = 26604.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.181995 restraints weight = 26714.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.182151 restraints weight = 23371.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13948  Z= 0.131
  Angle     :  0.675  16.492  19114  Z= 0.328
  Chirality :  0.045   0.308   2182
  Planarity :  0.005   0.060   2432
  Dihedral  :  6.048  57.182   2156
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.00 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.20), residues: 1702
  helix:  1.46 (0.32), residues: 264
  sheet:  0.36 (0.20), residues: 542
  loop :  0.02 (0.22), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 118 
 TYR   0.020   0.001   TYR F 103 
 PHE   0.022   0.002   PHE F 230 
 TRP   0.014   0.001   TRP F 166 
 HIS   0.012   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13918)
  covalent geometry    : angle       0.66265 (19040)
  SS BOND              : bond        0.00758 (   16)
  SS BOND              : angle       2.22455 (   32)
  hydrogen bonds       : bond        0.03650 (  520)
  hydrogen bonds       : angle       5.00321 ( 1410)
  link_BETA1-4         : bond        0.00470 (    6)
  link_BETA1-4         : angle       2.56800 (   18)
  link_NAG-ASN         : bond        0.00322 (    8)
  link_NAG-ASN         : angle       1.65844 (   24)

*********************** 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
  170 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 133
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.8004 (mp10) cc_final: 0.7729 (mt0)
REVERT: B  116 LEU cc_start: 0.8368 (tt) cc_final: 0.8087 (tp)
REVERT: C  164 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7760 (tp30)
REVERT: D   17 GLN cc_start: 0.8038 (mp10) cc_final: 0.7756 (mt0)
REVERT: D  222 TRP cc_start: 0.8405 (p90) cc_final: 0.8123 (p90)
REVERT: D  280 MET cc_start: 0.6427 (ttt) cc_final: 0.6219 (ttt)
REVERT: F  164 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7849 (tp30)
  outliers start: 37
  outliers final: 16
  residues processed: 163
  average time/residue: 0.0726
  time to fit residues: 19.2262
Evaluate side-chains
  134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue  160 CYS
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  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   47 THR
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain E residue   18 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 166 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 151 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 115 optimal weight:    0.0870
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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  38 GLN
B 161 HIS
** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 161 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.209822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.196900 restraints weight = 17491.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.184649 restraints weight = 36239.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.179943 restraints weight = 28290.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.180697 restraints weight = 24003.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.180011 restraints weight = 20810.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13948  Z= 0.137
  Angle     :  0.676  15.982  19114  Z= 0.329
  Chirality :  0.045   0.314   2182
  Planarity :  0.005   0.062   2432
  Dihedral  :  5.935  57.344   2156
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.96 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.21), residues: 1702
  helix:  1.59 (0.32), residues: 252
  sheet:  0.41 (0.21), residues: 524
  loop :  0.09 (0.22), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 121 
 TYR   0.017   0.001   TYR A 344 
 PHE   0.017   0.002   PHE C 230 
 TRP   0.016   0.001   TRP C 166 
 HIS   0.011   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13918)
  covalent geometry    : angle       0.66261 (19040)
  SS BOND              : bond        0.00778 (   16)
  SS BOND              : angle       2.39137 (   32)
  hydrogen bonds       : bond        0.03551 (  520)
  hydrogen bonds       : angle       4.89906 ( 1410)
  link_BETA1-4         : bond        0.00485 (    6)
  link_BETA1-4         : angle       2.51145 (   18)
  link_NAG-ASN         : bond        0.00303 (    8)
  link_NAG-ASN         : angle       1.70874 (   24)

*********************** 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
  165 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLN cc_start: 0.8036 (mp10) cc_final: 0.7833 (mt0)
REVERT: B  116 LEU cc_start: 0.8411 (tt) cc_final: 0.8110 (tp)
REVERT: C  164 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7948 (tp30)
REVERT: D   17 GLN cc_start: 0.8051 (mp10) cc_final: 0.7831 (mt0)
REVERT: D  280 MET cc_start: 0.6336 (ttt) cc_final: 0.5958 (ttt)
REVERT: D  291 TRP cc_start: 0.8017 (m100) cc_final: 0.7759 (m100)
REVERT: F  164 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7871 (tp30)
  outliers start: 38
  outliers final: 26
  residues processed: 158
  average time/residue: 0.0738
  time to fit residues: 18.9089
Evaluate side-chains
  142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  232 ILE
Chi-restraints excluded: chain A residue  348 LEU
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  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  207 VAL
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   67 VAL
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   18 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 139 optimal weight:    9.9990
   chunk 16 optimal weight:    0.3980
   chunk 15 optimal weight:    0.7980
   chunk 160 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 152 optimal weight:    0.0370
   chunk 38 optimal weight:   30.0000
   chunk 49 optimal weight:    0.7980
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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  38 GLN
C  73 GLN
C 229 HIS
** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  73 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.210356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.198155 restraints weight = 17496.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.185965 restraints weight = 36386.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.183063 restraints weight = 27728.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.182311 restraints weight = 24832.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.182272 restraints weight = 24927.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13948  Z= 0.125
  Angle     :  0.673  15.734  19114  Z= 0.327
  Chirality :  0.044   0.309   2182
  Planarity :  0.005   0.061   2432
  Dihedral  :  5.824  57.258   2156
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.12 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.21), residues: 1702
  helix:  1.65 (0.32), residues: 252
  sheet:  0.39 (0.21), residues: 552
  loop :  0.05 (0.23), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.022   0.001   TYR C 103 
 PHE   0.017   0.001   PHE C 230 
 TRP   0.022   0.001   TRP A 222 
 HIS   0.009   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (13918)
  covalent geometry    : angle       0.65853 (19040)
  SS BOND              : bond        0.00766 (   16)
  SS BOND              : angle       2.65902 (   32)
  hydrogen bonds       : bond        0.03420 (  520)
  hydrogen bonds       : angle       4.81018 ( 1410)
  link_BETA1-4         : bond        0.00470 (    6)
  link_BETA1-4         : angle       2.47022 (   18)
  link_NAG-ASN         : bond        0.00299 (    8)
  link_NAG-ASN         : angle       1.68605 (   24)

*********************** 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
  161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 HIS cc_start: 0.7622 (p-80) cc_final: 0.7276 (p-80)
REVERT: B  116 LEU cc_start: 0.8443 (tt) cc_final: 0.8105 (tp)
REVERT: C  164 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7903 (tp30)
REVERT: D  232 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8579 (mm)
REVERT: D  279 CYS cc_start: 0.6989 (p) cc_final: 0.6745 (p)
REVERT: D  280 MET cc_start: 0.6438 (ttt) cc_final: 0.6036 (ttt)
REVERT: F  164 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7874 (tp30)
  outliers start: 32
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0677
  time to fit residues: 17.2792
Evaluate side-chains
  138 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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  348 LEU
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  164 GLU
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  207 VAL
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   86 PHE
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   18 LEU
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  151 ASP
Chi-restraints excluded: chain F residue  164 GLU
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0970
   chunk 66 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  38 GLN
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.219006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.189889 restraints weight = 180440.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.193263 restraints weight = 110675.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.192404 restraints weight = 99066.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.190923 restraints weight = 98889.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.190884 restraints weight = 100019.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13948  Z= 0.136
  Angle     :  0.685  17.880  19114  Z= 0.333
  Chirality :  0.045   0.310   2182
  Planarity :  0.005   0.061   2432
  Dihedral  :  5.804  57.482   2156
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.33 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.21), residues: 1702
  helix:  1.62 (0.32), residues: 252
  sheet:  0.36 (0.22), residues: 540
  loop :  0.03 (0.22), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 235 
 TYR   0.024   0.001   TYR C 103 
 PHE   0.018   0.001   PHE C 230 
 TRP   0.018   0.001   TRP F 282 
 HIS   0.013   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13918)
  covalent geometry    : angle       0.66985 (19040)
  SS BOND              : bond        0.00835 (   16)
  SS BOND              : angle       2.83531 (   32)
  hydrogen bonds       : bond        0.03426 (  520)
  hydrogen bonds       : angle       4.80860 ( 1410)
  link_BETA1-4         : bond        0.00460 (    6)
  link_BETA1-4         : angle       2.47134 (   18)
  link_NAG-ASN         : bond        0.00278 (    8)
  link_NAG-ASN         : angle       1.71377 (   24)

*********************** 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
  158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8584 (mm)
REVERT: B   49 HIS cc_start: 0.7719 (p-80) cc_final: 0.7415 (p-80)
REVERT: B  116 LEU cc_start: 0.8544 (tt) cc_final: 0.8189 (tp)
REVERT: C  164 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7963 (tp30)
REVERT: C  282 TRP cc_start: 0.6845 (m-10) cc_final: 0.6337 (m-10)
REVERT: D   33 MET cc_start: 0.6199 (tmm) cc_final: 0.5851 (tmm)
REVERT: D  232 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8573 (mm)
REVERT: D  279 CYS cc_start: 0.7122 (p) cc_final: 0.6903 (p)
REVERT: D  280 MET cc_start: 0.6724 (ttt) cc_final: 0.6364 (ttt)
REVERT: F  164 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7841 (tp30)
  outliers start: 37
  outliers final: 27
  residues processed: 152
  average time/residue: 0.0746
  time to fit residues: 17.9650
Evaluate side-chains
  146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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  232 ILE
Chi-restraints excluded: chain A residue  348 LEU
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  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 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   86 PHE
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   18 LEU
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 137 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 156 optimal weight:    0.7980
   chunk 145 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.209745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.196444 restraints weight = 17515.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.182676 restraints weight = 37565.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.179235 restraints weight = 28656.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.179614 restraints weight = 27412.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.177996 restraints weight = 26950.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.4024

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     :  0.697  18.543  19114  Z= 0.337
  Chirality :  0.045   0.312   2182
  Planarity :  0.005   0.070   2432
  Dihedral  :  5.803  57.559   2156
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.42 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.21), residues: 1702
  helix:  1.59 (0.32), residues: 252
  sheet:  0.36 (0.22), residues: 530
  loop : -0.00 (0.22), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.027   0.001   TYR F 103 
 PHE   0.027   0.002   PHE F 230 
 TRP   0.024   0.002   TRP D 222 
 HIS   0.014   0.001   HIS F 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13918)
  covalent geometry    : angle       0.68084 (19040)
  SS BOND              : bond        0.00530 (   16)
  SS BOND              : angle       2.92222 (   32)
  hydrogen bonds       : bond        0.03436 (  520)
  hydrogen bonds       : angle       4.82706 ( 1410)
  link_BETA1-4         : bond        0.00480 (    6)
  link_BETA1-4         : angle       2.45779 (   18)
  link_NAG-ASN         : bond        0.00273 (    8)
  link_NAG-ASN         : angle       1.75047 (   24)

*********************** 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: 32
    poor density    : 120
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.5970 (tmm) cc_final: 0.5624 (tmm)
REVERT: B  116 LEU cc_start: 0.8459 (tt) cc_final: 0.8111 (tp)
REVERT: C  164 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7988 (tp30)
REVERT: D  232 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (mm)
REVERT: D  280 MET cc_start: 0.6677 (ttt) cc_final: 0.6292 (ttt)
REVERT: D  291 TRP cc_start: 0.7976 (m100) cc_final: 0.7691 (m100)
REVERT: F  164 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7587 (mm-30)
  outliers start: 32
  outliers final: 27
  residues processed: 147
  average time/residue: 0.0670
  time to fit residues: 16.3819
Evaluate side-chains
  141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  348 LEU
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  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 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   86 PHE
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain E residue   18 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 142 optimal weight:    9.9990
   chunk 129 optimal weight:    1.9990
   chunk 86 optimal weight:    0.2980
   chunk 113 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.216883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.187797 restraints weight = 181065.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.191700 restraints weight = 111162.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.189568 restraints weight = 94596.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.188816 restraints weight = 102227.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.188697 restraints weight = 98129.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13948  Z= 0.142
  Angle     :  0.700  18.076  19114  Z= 0.339
  Chirality :  0.045   0.310   2182
  Planarity :  0.005   0.065   2432
  Dihedral  :  5.806  57.651   2156
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.35 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.21), residues: 1702
  helix:  1.55 (0.32), residues: 252
  sheet:  0.29 (0.22), residues: 540
  loop :  0.01 (0.23), residues: 910

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 235 
 TYR   0.026   0.002   TYR C 103 
 PHE   0.024   0.002   PHE F 230 
 TRP   0.020   0.002   TRP F 166 
 HIS   0.013   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (13918)
  covalent geometry    : angle       0.68392 (19040)
  SS BOND              : bond        0.00446 (   16)
  SS BOND              : angle       2.95407 (   32)
  hydrogen bonds       : bond        0.03439 (  520)
  hydrogen bonds       : angle       4.86066 ( 1410)
  link_BETA1-4         : bond        0.00451 (    6)
  link_BETA1-4         : angle       2.46474 (   18)
  link_NAG-ASN         : bond        0.00264 (    8)
  link_NAG-ASN         : angle       1.78191 (   24)

********************** 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
  142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  116 LEU cc_start: 0.8499 (tt) cc_final: 0.8103 (tp)
REVERT: C  164 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8016 (tp30)
REVERT: D   33 MET cc_start: 0.6183 (tmm) cc_final: 0.5931 (tmm)
REVERT: D  232 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8619 (mm)
REVERT: D  291 TRP cc_start: 0.8015 (m100) cc_final: 0.7727 (m100)
REVERT: F  164 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7797 (mm-30)
  outliers start: 33
  outliers final: 27
  residues processed: 136
  average time/residue: 0.0728
  time to fit residues: 16.4412
Evaluate side-chains
  137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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   18 LEU
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   57 LEU
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 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   86 PHE
Chi-restraints excluded: chain D residue  160 CYS
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  232 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 131 optimal weight:    0.1980
   chunk 162 optimal weight:    0.5980
   chunk 150 optimal weight:    0.9980
   chunk 119 optimal weight:   10.0000
   chunk 158 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  38 GLN
** E  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.216960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.187863 restraints weight = 181991.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.190851 restraints weight = 112216.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.188838 restraints weight = 93872.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.188810 restraints weight = 104914.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.188853 restraints weight = 99646.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13948  Z= 0.134
  Angle     :  0.690  16.475  19114  Z= 0.334
  Chirality :  0.045   0.310   2182
  Planarity :  0.005   0.067   2432
  Dihedral  :  5.741  57.569   2156
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.21), residues: 1702
  helix:  1.61 (0.33), residues: 252
  sheet:  0.28 (0.22), residues: 544
  loop :  0.02 (0.23), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 274 
 TYR   0.038   0.001   TYR C 103 
 PHE   0.021   0.002   PHE C 230 
 TRP   0.018   0.002   TRP F 166 
 HIS   0.015   0.001   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (13918)
  covalent geometry    : angle       0.67467 (19040)
  SS BOND              : bond        0.00543 (   16)
  SS BOND              : angle       2.79204 (   32)
  hydrogen bonds       : bond        0.03370 (  520)
  hydrogen bonds       : angle       4.78154 ( 1410)
  link_BETA1-4         : bond        0.00477 (    6)
  link_BETA1-4         : angle       2.44585 (   18)
  link_NAG-ASN         : bond        0.00275 (    8)
  link_NAG-ASN         : angle       1.77845 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1806.03 seconds
wall clock time: 32 minutes 3.97 seconds (1923.97 seconds total)