Starting phenix.real_space_refine
on Thu Jun 12 12:37:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zho_60110/06_2025/8zho_60110.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.031
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 3069 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      43      5.16       5
     C    7231      2.51       5
     N    1900      2.21       5
     O    2249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11423
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 4932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4932
          Classifications: {'peptide': 622}
          Link IDs: {'PTRANS': 31, 'TRANS': 590}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1661
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1557
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 196}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1589
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1670
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.19, per 1000 atoms: 0.63
  Number of scatterers: 11423
  At special positions: 0
  Unit cell: (94.86, 119.04, 179.49, 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      43     16.00
     O    2249      8.00
     N    1900      7.00
     C    7231      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 151 " - pdb=" SG  CYS D 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 139 " - pdb=" SG  CYS E 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 145 " - pdb=" SG  CYS L 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 203 " 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
    NAG-ASN
      " NAG C 701 " - " ASN C 343 "
  Time building additional restraints: 3.18
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2758

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 35 sheets defined
      5.5% alpha, 40.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.33
  Creating SS restraints...
    Processing helix  chain 'C' and resid 294 through 304
      removed outlier: 3.875A  pdb=" N   LYS C 300 " --> pdb=" O   LEU C 296 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS C 301 " --> pdb=" O   SER C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 4.076A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 368
      removed outlier: 3.996A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
      removed outlier: 3.634A  pdb=" N   ARG C 408 " --> pdb=" O   GLY C 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 404 through 408'
    Processing helix  chain 'D' and resid 198 through 200
      No H-bonds generated for 'chain 'D' and resid 198 through 200'
    Processing helix  chain 'E' and resid 81 through 85
      removed outlier: 4.168A  pdb=" N   GLU E  85 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 126 through 133
      removed outlier: 3.515A  pdb=" N   GLU E 129 " --> pdb=" O   SER E 126 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLN E 131 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA E 132 " --> pdb=" O   GLU E 129 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN E 133 " --> pdb=" O   LEU E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 186 through 191
      removed outlier: 4.018A  pdb=" N   LYS E 191 " --> pdb=" O   PRO E 187 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 86
      removed outlier: 3.581A  pdb=" N   ASP L  85 " --> pdb=" O   LYS L  82 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 132 through 138
    Processing helix  chain 'L' and resid 192 through 199
      removed outlier: 3.569A  pdb=" N   LYS L 197 " --> pdb=" O   PRO L 193 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   HIS L 199 " --> pdb=" O   GLN L 195 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.862A  pdb=" N   THR H  92 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 134 through 138
      removed outlier: 3.729A  pdb=" N   THR H 138 " --> pdb=" O   SER H 135 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 196
      No H-bonds generated for 'chain 'H' and resid 194 through 196'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 48 through 54
      removed outlier: 4.120A  pdb=" N   HIS C  49 " --> pdb=" O   LEU C 277 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU C 277 " --> pdb=" O   HIS C  49 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ASP C  53 " --> pdb=" O   ARG C 273 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67
      removed outlier: 3.546A  pdb=" N   THR C  63 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ALA C 264 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR C  95 " --> pdb=" O   ALA C 264 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL C  90 " --> pdb=" O   PHE C 194 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLU C 191 " --> pdb=" O   LYS C 206 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS C 206 " --> pdb=" O   GLU C 191 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS C 195 " --> pdb=" O   LYS C 202 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS C 202 " --> pdb=" O   LYS C 195 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE C 203 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85
      removed outlier: 3.882A  pdb=" N   GLY C 103 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   PHE C 168 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 160
      removed outlier: 5.472A  pdb=" N   GLU C 154 " --> pdb=" O   TYR C 144 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   TYR C 144 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG C 158 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   TYR C 160 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
      removed outlier: 10.744A  pdb=" N   ASP C 138 " --> pdb=" O   TYR C 160 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   LEU C 244 " --> pdb=" O   PRO C 139 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   ARG C 246 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL C 143 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 313
      removed outlier: 3.840A  pdb=" N   GLY C 311 " --> pdb=" O   THR C 599 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   THR C 599 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR C 313 " --> pdb=" O   VAL C 597 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328
      removed outlier: 3.701A  pdb=" N   GLY C 550 " --> pdb=" O   VAL C 539 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.549A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.991A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'C' and resid 466 through 467
      removed outlier: 3.862A  pdb=" N   ARG C 466 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLY D 104 " --> pdb=" O   ARG C 466 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667
      removed outlier: 6.452A  pdb=" N   ILE C 670 " --> pdb=" O   ILE C 666 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   ALA D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.607A  pdb=" N   TRP D  36 " --> pdb=" O   GLY D  49 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE D  57 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12
      removed outlier: 4.168A  pdb=" N   LEU D 113 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 131 through 135
      removed outlier: 5.802A  pdb=" N   LYS D 154 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   LEU D 189 " --> pdb=" O   LYS D 154 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TYR D 156 " --> pdb=" O   TYR D 187 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TYR D 187 " --> pdb=" O   TYR D 156 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 131 through 135
    Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 165
      removed outlier: 4.543A  pdb=" N   TYR D 205 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   CYS D 207 " --> pdb=" O   LYS D 220 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LYS D 220 " --> pdb=" O   CYS D 207 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL D 209 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL D 218 " --> pdb=" O   VAL D 209 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 10
      removed outlier: 6.514A  pdb=" N   TRP E  37 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 9 through 10
    Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 23
    Processing sheet with id=AC4, first strand: chain 'E' and resid 119 through 123
      removed outlier: 4.113A  pdb=" N   PHE E 123 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   VAL E 138 " --> pdb=" O   PHE E 123 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ASP E 143 " --> pdb=" O   TYR E 177 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   TYR E 177 " --> pdb=" O   ASP E 143 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'E' and resid 159 through 160
      removed outlier: 4.588A  pdb=" N   TRP E 153 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS E 154 " --> pdb=" O   SER E 197 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   TYR E 196 " --> pdb=" O   VAL E 211 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL E 211 " --> pdb=" O   TYR E 196 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   CYS E 198 " --> pdb=" O   LYS E 209 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LYS E 209 " --> pdb=" O   CYS E 198 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL E 200 " --> pdb=" O   VAL E 207 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL E 207 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 11
      removed outlier: 7.493A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'L' and resid 125 through 129
      removed outlier: 5.459A  pdb=" N   TYR L 183 " --> pdb=" O   ASP L 149 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129
      removed outlier: 5.459A  pdb=" N   TYR L 183 " --> pdb=" O   ASP L 149 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'L' and resid 165 through 166
      removed outlier: 4.162A  pdb=" N   TRP L 159 " --> pdb=" O   VAL L 166 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.843A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD3
    Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 61
      removed outlier: 5.093A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY H  51 " --> pdb=" O   TRP H  38 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'H' and resid 59 through 61
      removed outlier: 5.093A  pdb=" N   TRP H  49 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ARG H  40 " --> pdb=" O   TRP H  49 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY H  51 " --> pdb=" O   TRP H  38 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'H' and resid 127 through 131
      removed outlier: 3.964A  pdb=" N   GLY H 146 " --> pdb=" O   LEU H 131 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP H 151 " --> pdb=" O   TYR H 183 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TYR H 183 " --> pdb=" O   ASP H 151 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'H' and resid 127 through 131
      removed outlier: 3.964A  pdb=" N   GLY H 146 " --> pdb=" O   LEU H 131 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP H 151 " --> pdb=" O   TYR H 183 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TYR H 183 " --> pdb=" O   ASP H 151 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'H' and resid 158 through 161
      removed outlier: 4.221A  pdb=" N   TYR H 201 " --> pdb=" O   VAL H 218 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    987 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.20

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3635
        1.34 -     1.46: 2830
        1.46 -     1.58: 5195
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 11708
  Sorted by residual:
  bond pdb=" N   VAL C 382 "
       pdb=" CA  VAL C 382 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.21e-02 6.83e+03 7.99e+00
  bond pdb=" N   LYS C 378 "
       pdb=" CA  LYS C 378 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.21e-02 6.83e+03 7.21e+00
  bond pdb=" N   CYS C 379 "
       pdb=" CA  CYS C 379 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.033 1.27e-02 6.20e+03 6.90e+00
  bond pdb=" N   THR C 376 "
       pdb=" CA  THR C 376 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.19e-02 7.06e+03 6.14e+00
  bond pdb=" N   TYR C 380 "
       pdb=" CA  TYR C 380 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.029 1.17e-02 7.31e+03 6.04e+00
  ... (remaining 11703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 15798
        2.35 -     4.70: 148
        4.70 -     7.05: 9
        7.05 -     9.40: 4
        9.40 -    11.75: 1
  Bond angle restraints: 15960
  Sorted by residual:
  angle pdb=" CB  MET C 153 "
        pdb=" CG  MET C 153 "
        pdb=" SD  MET C 153 "
      ideal   model   delta    sigma   weight residual
     112.70  124.45  -11.75 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" N   LYS C 386 "
        pdb=" CA  LYS C 386 "
        pdb=" C   LYS C 386 "
      ideal   model   delta    sigma   weight residual
     114.64  108.81    5.83 1.52e+00 4.33e-01 1.47e+01
  angle pdb=" C   ASN L   1 "
        pdb=" CA  ASN L   1 "
        pdb=" CB  ASN L   1 "
      ideal   model   delta    sigma   weight residual
     110.10  116.65   -6.55 1.90e+00 2.77e-01 1.19e+01
  angle pdb=" CA  GLU L 194 "
        pdb=" CB  GLU L 194 "
        pdb=" CG  GLU L 194 "
      ideal   model   delta    sigma   weight residual
     114.10  120.99   -6.89 2.00e+00 2.50e-01 1.19e+01
  angle pdb=" N   ASP L 162 "
        pdb=" CA  ASP L 162 "
        pdb=" C   ASP L 162 "
      ideal   model   delta    sigma   weight residual
     111.36  107.92    3.44 1.09e+00 8.42e-01 9.97e+00
  ... (remaining 15955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6175
       17.91 -    35.82: 598
       35.82 -    53.74: 156
       53.74 -    71.65: 21
       71.65 -    89.56: 14
  Dihedral angle restraints: 6964
    sinusoidal: 2642
      harmonic: 4322
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.44  -89.56     1      1.00e+01 1.00e-02 9.53e+01
  dihedral pdb=" CB  CYS C 538 "
           pdb=" SG  CYS C 538 "
           pdb=" SG  CYS C 590 "
           pdb=" CB  CYS C 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.29   57.29     1      1.00e+01 1.00e-02 4.41e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  97 "
           pdb=" CB  CYS H  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.59   38.41     1      1.00e+01 1.00e-02 2.08e+01
  ... (remaining 6961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1162
       0.034 -    0.068: 397
       0.068 -    0.103: 143
       0.103 -    0.137: 92
       0.137 -    0.171: 3
  Chirality restraints: 1797
  Sorted by residual:
  chirality pdb=" CG  LEU C 118 "
            pdb=" CB  LEU C 118 "
            pdb=" CD1 LEU C 118 "
            pdb=" CD2 LEU C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CA  LEU C 387 "
            pdb=" N   LEU C 387 "
            pdb=" C   LEU C 387 "
            pdb=" CB  LEU C 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CA  VAL C 382 "
            pdb=" N   VAL C 382 "
            pdb=" C   VAL C 382 "
            pdb=" CB  VAL C 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 1794 not shown)

  Planarity restraints: 2052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 155 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO H 156 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO H 156 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H 156 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  59 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.67e+00
        pdb=" N   PRO L  60 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO L  60 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L  60 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 208 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO H 209 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO H 209 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 209 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2049 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2789
        2.80 -     3.32: 9237
        3.32 -     3.85: 18795
        3.85 -     4.37: 20341
        4.37 -     4.90: 36500
  Nonbonded interactions: 87662
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  17 "
            pdb=" OE2 GLU D  82 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" ND2 ASN L  53 "
            pdb=" OE1 GLN L  54 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OG  SER E   2 "
            pdb=" N   VAL E   3 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   LEU C  54 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OD1 ASN C 360 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.329 3.040
  ... (remaining 87657 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.140
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
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      :  0.003   0.039  11726  Z= 0.150
  Angle     :  0.541  11.750  15997  Z= 0.294
  Chirality :  0.045   0.171   1797
  Planarity :  0.004   0.041   2051
  Dihedral  : 15.241  87.837   4155
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 19.66 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1482
  helix: -3.05 (0.44), residues: 57
  sheet:  1.44 (0.23), residues: 528
  loop : -0.83 (0.20), residues: 897

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 196 
 HIS   0.002   0.000   HIS E  36 
 PHE   0.011   0.001   PHE C 135 
 TYR   0.014   0.001   TYR C 369 
 ARG   0.005   0.000   ARG D  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    1)
  link_NAG-ASN         : angle       0.89967 (    3)
  hydrogen bonds       : bond        0.27084 (  343)
  hydrogen bonds       : angle       9.92582 (  987)
  SS BOND              : bond        0.00103 (   17)
  SS BOND              : angle       0.43315 (   34)
  covalent geometry    : bond        0.00257 (11708)
  covalent geometry    : angle       0.54081 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   62 VAL cc_start: 0.4868 (m) cc_final: 0.4512 (t)
REVERT: C  285 ILE cc_start: 0.6882 (mt) cc_final: 0.6303 (pt)
REVERT: C  390 LEU cc_start: 0.5893 (mt) cc_final: 0.5692 (mt)
REVERT: C  549 THR cc_start: 0.5794 (p) cc_final: 0.5555 (p)
REVERT: D   43 GLN cc_start: 0.7595 (mp10) cc_final: 0.7272 (mp10)
REVERT: E  153 TRP cc_start: 0.5107 (m100) cc_final: 0.4284 (m100)
REVERT: L   61 ASP cc_start: 0.7692 (t70) cc_final: 0.7002 (m-30)
REVERT: L   86 GLU cc_start: 0.7288 (tt0) cc_final: 0.6979 (mt-10)
REVERT: L  109 VAL cc_start: 0.7148 (t) cc_final: 0.6635 (t)
REVERT: H  154 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.7083 (Cg_exo)
REVERT: H  208 LYS cc_start: 0.7753 (mttt) cc_final: 0.7332 (ptpp)
  outliers start: 8
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2339
  time to fit residues: 39.8281
Evaluate side-chains
  62 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  380 TYR
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain H residue  211 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:   40.0000
   chunk 112 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 75 optimal weight:   20.0000
   chunk 59 optimal weight:   30.0000
   chunk 116 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
C  69 HIS
L   8 HIS
L  38 GLN
L  53 ASN
L  54 GLN
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.215245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.192642 restraints weight = 18995.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.189336 restraints weight = 30871.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.186986 restraints weight = 31809.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6074
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  11726  Z= 0.197
  Angle     :  0.593  11.634  15997  Z= 0.312
  Chirality :  0.046   0.187   1797
  Planarity :  0.004   0.043   2051
  Dihedral  :  4.786  58.825   1640
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.81 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.22), residues: 1482
  helix: -2.69 (0.54), residues: 58
  sheet:  1.34 (0.24), residues: 511
  loop : -0.68 (0.20), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  49 
 HIS   0.008   0.001   HIS L   8 
 PHE   0.024   0.002   PHE H  80 
 TYR   0.025   0.002   TYR C 369 
 ARG   0.005   0.001   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       1.27769 (    3)
  hydrogen bonds       : bond        0.03862 (  343)
  hydrogen bonds       : angle       6.33143 (  987)
  SS BOND              : bond        0.00535 (   17)
  SS BOND              : angle       1.09038 (   34)
  covalent geometry    : bond        0.00453 (11708)
  covalent geometry    : angle       0.59083 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 65
  time to evaluate  : 1.992 
Fit side-chains
   revert: symmetry clash
REVERT: C  153 MET cc_start: 0.1994 (tpp) cc_final: 0.1726 (tpt)
REVERT: L   61 ASP cc_start: 0.6534 (t70) cc_final: 0.6215 (t0)
REVERT: L  109 VAL cc_start: 0.7029 (t) cc_final: 0.6676 (t)
REVERT: H  114 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (t)
  outliers start: 40
  outliers final: 21
  residues processed: 101
  average time/residue: 0.2785
  time to fit residues: 46.0302
Evaluate side-chains
  68 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  380 TYR
Chi-restraints excluded: chain C residue  386 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  202 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 128 optimal weight:    0.6980
   chunk 12 optimal weight:   50.0000
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
C 544 ASN
** L   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 171 HIS
** H 207 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 = 0.4781 r_free = 0.4781 target = 0.212474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.190280 restraints weight = 18918.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.185364 restraints weight = 28558.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.183974 restraints weight = 33273.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6181
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  11726  Z= 0.194
  Angle     :  0.574   8.799  15997  Z= 0.303
  Chirality :  0.046   0.180   1797
  Planarity :  0.004   0.066   2051
  Dihedral  :  4.643  48.936   1635
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 20.12 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1482
  helix: -2.24 (0.61), residues: 58
  sheet:  1.24 (0.23), residues: 538
  loop : -0.76 (0.21), residues: 886

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 110 
 HIS   0.008   0.001   HIS C  49 
 PHE   0.018   0.001   PHE H  80 
 TYR   0.024   0.002   TYR C 369 
 ARG   0.006   0.001   ARG E  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       1.74990 (    3)
  hydrogen bonds       : bond        0.03585 (  343)
  hydrogen bonds       : angle       5.80170 (  987)
  SS BOND              : bond        0.00537 (   17)
  SS BOND              : angle       0.98795 (   34)
  covalent geometry    : bond        0.00449 (11708)
  covalent geometry    : angle       0.57239 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 56
  time to evaluate  : 1.285 
Fit side-chains
REVERT: E   29 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8108 (mt)
REVERT: E  106 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8258 (t)
REVERT: E  141 ILE cc_start: 0.2485 (tp) cc_final: 0.1978 (mp)
REVERT: L  155 VAL cc_start: -0.2091 (OUTLIER) cc_final: -0.2475 (m)
  outliers start: 54
  outliers final: 31
  residues processed: 104
  average time/residue: 0.1661
  time to fit residues: 29.3280
Evaluate side-chains
  76 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 42
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  380 TYR
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  673 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  195 VAL
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   29 ILE
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain L residue  147 ILE
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  202 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 142 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0040
   chunk 127 optimal weight:    2.9990
   chunk 144 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   8 HIS
H 204 ASN
** H 207 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 = 0.4773 r_free = 0.4773 target = 0.203948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.190543 restraints weight = 17913.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.187972 restraints weight = 39212.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.186974 restraints weight = 46493.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11726  Z= 0.180
  Angle     :  0.545   8.652  15997  Z= 0.285
  Chirality :  0.045   0.183   1797
  Planarity :  0.004   0.048   2051
  Dihedral  :  4.153  30.308   1631
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 20.75 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.22), residues: 1482
  helix: -2.13 (0.63), residues: 58
  sheet:  1.02 (0.23), residues: 554
  loop : -0.67 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 110 
 HIS   0.011   0.001   HIS C  49 
 PHE   0.015   0.001   PHE D  29 
 TYR   0.020   0.001   TYR C 369 
 ARG   0.003   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00035 (    1)
  link_NAG-ASN         : angle       1.77748 (    3)
  hydrogen bonds       : bond        0.02898 (  343)
  hydrogen bonds       : angle       5.51790 (  987)
  SS BOND              : bond        0.00415 (   17)
  SS BOND              : angle       1.15137 (   34)
  covalent geometry    : bond        0.00423 (11708)
  covalent geometry    : angle       0.54201 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 47
  time to evaluate  : 1.198 
Fit side-chains
REVERT: D  102 TYR cc_start: 0.8244 (p90) cc_final: 0.8017 (p90)
REVERT: E  141 ILE cc_start: 0.2384 (tp) cc_final: 0.1943 (mp)
  outliers start: 52
  outliers final: 35
  residues processed: 94
  average time/residue: 0.1630
  time to fit residues: 25.7075
Evaluate side-chains
  77 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 42
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain L residue  147 ILE
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 139 optimal weight:    7.9990
   chunk 69 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 141 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0970
   chunk 3 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0980
   chunk 137 optimal weight:    3.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   8 HIS
** H 207 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 = 0.4795 r_free = 0.4795 target = 0.214003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.191733 restraints weight = 18787.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.188591 restraints weight = 29305.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.187109 restraints weight = 30887.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  11726  Z= 0.100
  Angle     :  0.500   8.301  15997  Z= 0.258
  Chirality :  0.044   0.160   1797
  Planarity :  0.004   0.065   2051
  Dihedral  :  3.856  27.105   1629
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.76 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.22), residues: 1482
  helix: -1.82 (0.66), residues: 58
  sheet:  1.05 (0.23), residues: 553
  loop : -0.58 (0.21), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 110 
 HIS   0.009   0.001   HIS L   8 
 PHE   0.010   0.001   PHE D  29 
 TYR   0.013   0.001   TYR C 369 
 ARG   0.002   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00156 (    1)
  link_NAG-ASN         : angle       1.51549 (    3)
  hydrogen bonds       : bond        0.02630 (  343)
  hydrogen bonds       : angle       5.21628 (  987)
  SS BOND              : bond        0.00368 (   17)
  SS BOND              : angle       0.92498 (   34)
  covalent geometry    : bond        0.00230 (11708)
  covalent geometry    : angle       0.49803 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 43
  time to evaluate  : 1.250 
Fit side-chains
REVERT: E  141 ILE cc_start: 0.2385 (tp) cc_final: 0.1983 (mp)
REVERT: H  155 GLU cc_start: 0.4212 (OUTLIER) cc_final: 0.3998 (pp20)
  outliers start: 36
  outliers final: 27
  residues processed: 75
  average time/residue: 0.1738
  time to fit residues: 22.0472
Evaluate side-chains
  66 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 38
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue  147 ILE
Chi-restraints excluded: chain L residue  155 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  155 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 11 optimal weight:   30.0000
   chunk 22 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 105 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.202072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.186224 restraints weight = 17987.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.184501 restraints weight = 42025.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.183698 restraints weight = 38546.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6089
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  11726  Z= 0.235
  Angle     :  0.582   9.485  15997  Z= 0.305
  Chirality :  0.046   0.202   1797
  Planarity :  0.004   0.053   2051
  Dihedral  :  4.314  42.491   1629
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 20.67 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.22), residues: 1482
  helix: -1.81 (0.67), residues: 58
  sheet:  0.84 (0.22), residues: 561
  loop : -0.66 (0.21), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  38 
 HIS   0.007   0.001   HIS C  49 
 PHE   0.019   0.002   PHE H  80 
 TYR   0.027   0.002   TYR C 369 
 ARG   0.004   0.001   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.90508 (    3)
  hydrogen bonds       : bond        0.02926 (  343)
  hydrogen bonds       : angle       5.47150 (  987)
  SS BOND              : bond        0.00538 (   17)
  SS BOND              : angle       1.33267 (   34)
  covalent geometry    : bond        0.00553 (11708)
  covalent geometry    : angle       0.57913 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 47
  time to evaluate  : 1.303 
Fit side-chains
REVERT: C   49 HIS cc_start: 0.3584 (t-170) cc_final: 0.3310 (t-170)
REVERT: C  465 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7761 (tt0)
REVERT: E   29 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8380 (mt)
REVERT: E  141 ILE cc_start: 0.2366 (tp) cc_final: 0.1967 (mp)
REVERT: L   78 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6873 (mm)
  outliers start: 52
  outliers final: 38
  residues processed: 94
  average time/residue: 0.1841
  time to fit residues: 28.1487
Evaluate side-chains
  82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 41
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   28 ASN
Chi-restraints excluded: chain E residue   29 ILE
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   62 ARG
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  147 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   60 ASN
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 19 optimal weight:    0.0270
   chunk 21 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 103 optimal weight:   50.0000
   chunk 76 optimal weight:    0.0970
   chunk 71 optimal weight:    0.8980
   chunk 100 optimal weight:   50.0000
   chunk 127 optimal weight:    0.9990
   chunk 96 optimal weight:   50.0000
   chunk 16 optimal weight:   30.0000
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.205537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.192330 restraints weight = 18124.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.190921 restraints weight = 40625.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.189246 restraints weight = 41804.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5928
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11726  Z= 0.102
  Angle     :  0.516   9.086  15997  Z= 0.265
  Chirality :  0.044   0.156   1797
  Planarity :  0.004   0.072   2051
  Dihedral  :  4.029  35.439   1629
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 21.53 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.22), residues: 1482
  helix: -1.52 (0.70), residues: 58
  sheet:  0.94 (0.22), residues: 565
  loop : -0.57 (0.22), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 110 
 HIS   0.008   0.001   HIS C  49 
 PHE   0.010   0.001   PHE D  29 
 TYR   0.024   0.001   TYR H 183 
 ARG   0.003   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       1.49729 (    3)
  hydrogen bonds       : bond        0.02588 (  343)
  hydrogen bonds       : angle       5.16791 (  987)
  SS BOND              : bond        0.00519 (   17)
  SS BOND              : angle       1.08889 (   34)
  covalent geometry    : bond        0.00234 (11708)
  covalent geometry    : angle       0.51403 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 49
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
REVERT: E  141 ILE cc_start: 0.2521 (tp) cc_final: 0.2149 (mp)
  outliers start: 41
  outliers final: 34
  residues processed: 86
  average time/residue: 0.1704
  time to fit residues: 23.9800
Evaluate side-chains
  78 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 44
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  673 SER
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   28 ASN
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   84 ASP
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue  114 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 42 optimal weight:    0.0040
   chunk 129 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 6 optimal weight:   40.0000
   chunk 125 optimal weight:   40.0000
   chunk 33 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 58 optimal weight:   30.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    2.4000

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 166 ASN
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   8 HIS
** H 207 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 = 0.4755 r_free = 0.4755 target = 0.202226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.190243 restraints weight = 17879.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.187779 restraints weight = 36225.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.186277 restraints weight = 34797.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6022
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11726  Z= 0.219
  Angle     :  0.576  10.297  15997  Z= 0.300
  Chirality :  0.046   0.187   1797
  Planarity :  0.004   0.049   2051
  Dihedral  :  4.347  44.776   1629
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 21.29 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.22), residues: 1482
  helix: -1.58 (0.70), residues: 58
  sheet:  0.80 (0.22), residues: 564
  loop : -0.61 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 110 
 HIS   0.011   0.001   HIS C  49 
 PHE   0.017   0.002   PHE H  80 
 TYR   0.028   0.002   TYR H 183 
 ARG   0.003   0.001   ARG H  68 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       1.89517 (    3)
  hydrogen bonds       : bond        0.02820 (  343)
  hydrogen bonds       : angle       5.39566 (  987)
  SS BOND              : bond        0.00571 (   17)
  SS BOND              : angle       1.31460 (   34)
  covalent geometry    : bond        0.00517 (11708)
  covalent geometry    : angle       0.57259 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 41
  time to evaluate  : 1.286 
Fit side-chains
REVERT: E  141 ILE cc_start: 0.2502 (tp) cc_final: 0.2121 (mp)
REVERT: L    8 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.5114 (t-90)
  outliers start: 52
  outliers final: 41
  residues processed: 86
  average time/residue: 0.1613
  time to fit residues: 23.9480
Evaluate side-chains
  81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 39
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  673 SER
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   28 ASN
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain L residue    8 HIS
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 114 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 109 optimal weight:    0.6980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   8 HIS
H 207 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.204127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.189246 restraints weight = 17963.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.187742 restraints weight = 38936.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.187013 restraints weight = 38161.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6004
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11726  Z= 0.124
  Angle     :  0.544  11.410  15997  Z= 0.277
  Chirality :  0.045   0.165   1797
  Planarity :  0.004   0.076   2051
  Dihedral  :  4.208  42.658   1629
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.68 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.22), residues: 1482
  helix: -1.64 (0.68), residues: 64
  sheet:  0.91 (0.22), residues: 564
  loop : -0.62 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 110 
 HIS   0.018   0.001   HIS L   8 
 PHE   0.024   0.001   PHE H 173 
 TYR   0.027   0.001   TYR H 183 
 ARG   0.002   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00124 (    1)
  link_NAG-ASN         : angle       1.65903 (    3)
  hydrogen bonds       : bond        0.02598 (  343)
  hydrogen bonds       : angle       5.22131 (  987)
  SS BOND              : bond        0.00457 (   17)
  SS BOND              : angle       1.05247 (   34)
  covalent geometry    : bond        0.00291 (11708)
  covalent geometry    : angle       0.54205 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 43
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
REVERT: C  465 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7712 (tt0)
REVERT: E  141 ILE cc_start: 0.2499 (tp) cc_final: 0.2159 (mp)
REVERT: L    8 HIS cc_start: 0.5296 (OUTLIER) cc_final: 0.4819 (t-90)
  outliers start: 47
  outliers final: 38
  residues processed: 84
  average time/residue: 0.1702
  time to fit residues: 23.7050
Evaluate side-chains
  82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 42
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  673 SER
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   28 ASN
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue    8 HIS
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  155 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 127 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:   30.0000
   chunk 11 optimal weight:   40.0000
   chunk 8 optimal weight:    3.9990
   chunk 141 optimal weight:    9.9990
   chunk 132 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.203616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.191884 restraints weight = 17797.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.189258 restraints weight = 36298.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.187643 restraints weight = 34749.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5981
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11726  Z= 0.147
  Angle     :  0.549  10.368  15997  Z= 0.279
  Chirality :  0.045   0.166   1797
  Planarity :  0.004   0.053   2051
  Dihedral  :  4.202  42.899   1629
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.53 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.22), residues: 1482
  helix: -1.62 (0.68), residues: 64
  sheet:  0.89 (0.22), residues: 564
  loop : -0.62 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 110 
 HIS   0.014   0.001   HIS L   8 
 PHE   0.018   0.001   PHE H 173 
 TYR   0.040   0.001   TYR D 156 
 ARG   0.002   0.000   ARG H 104 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       1.70548 (    3)
  hydrogen bonds       : bond        0.02605 (  343)
  hydrogen bonds       : angle       5.19898 (  987)
  SS BOND              : bond        0.00465 (   17)
  SS BOND              : angle       1.05845 (   34)
  covalent geometry    : bond        0.00346 (11708)
  covalent geometry    : angle       0.54650 (15960)

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

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

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2964 Ramachandran restraints generated.
    1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 42
  time to evaluate  : 1.352 
Fit side-chains
REVERT: C  424 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7699 (tptt)
REVERT: C  465 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7729 (tt0)
REVERT: E  106 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8240 (t)
REVERT: E  141 ILE cc_start: 0.2506 (tp) cc_final: 0.2145 (mp)
  outliers start: 48
  outliers final: 39
  residues processed: 87
  average time/residue: 0.1881
  time to fit residues: 26.7022
Evaluate side-chains
  81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 39
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   64 TRP
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  375 SER
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  424 LYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  465 GLU
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  549 THR
Chi-restraints excluded: chain C residue  610 VAL
Chi-restraints excluded: chain C residue  673 SER
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   28 ASN
Chi-restraints excluded: chain E residue   53 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   61 ASP
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   75 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   52 CYS
Chi-restraints excluded: chain H residue   54 TYR
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue   87 VAL
Chi-restraints excluded: chain H residue   92 THR
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  155 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0050
   chunk 123 optimal weight:    8.9990
   chunk 102 optimal weight:    0.0030
   chunk 6 optimal weight:   40.0000
   chunk 146 optimal weight:    7.9990
   chunk 11 optimal weight:   30.0000
   chunk 117 optimal weight:    7.9990
   overall best weight:    0.9406

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.204545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.192722 restraints weight = 17757.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.190327 restraints weight = 36071.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.188460 restraints weight = 32882.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5959
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11726  Z= 0.121
  Angle     :  0.540   9.918  15997  Z= 0.273
  Chirality :  0.044   0.161   1797
  Planarity :  0.004   0.072   2051
  Dihedral  :  4.112  39.833   1629
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.76 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.23), residues: 1482
  helix: -1.56 (0.69), residues: 64
  sheet:  0.92 (0.23), residues: 562
  loop : -0.57 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 110 
 HIS   0.012   0.001   HIS C  49 
 PHE   0.015   0.001   PHE H 173 
 TYR   0.034   0.001   TYR D 156 
 ARG   0.002   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       1.62076 (    3)
  hydrogen bonds       : bond        0.02501 (  343)
  hydrogen bonds       : angle       5.05497 (  987)
  SS BOND              : bond        0.00435 (   17)
  SS BOND              : angle       0.98873 (   34)
  covalent geometry    : bond        0.00285 (11708)
  covalent geometry    : angle       0.53823 (15960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3604.66 seconds
wall clock time: 64 minutes 49.65 seconds (3889.65 seconds total)