Starting phenix.real_space_refine
on Thu Jun 12 06:26:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bp7_44763/06_2025/9bp7_44763.cif"
  }
  resolution = 3.6
  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=   0.010 sd=   0.105
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      93      5.16       5
     C    8966      2.51       5
     N    2196      2.21       5
     O    2476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13731
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2760
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 343, 2751
          Classifications: {'peptide': 343}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 16, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 29
      Conformer: "B"
        Number of residues, atoms: 343, 2751
          Classifications: {'peptide': 343}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 16, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 29
          bond proxies already assigned to first conformer: 2812
    Chain: "B"
      Number of atoms: 2734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2734
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 16, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "C"
      Number of atoms: 2728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2728
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 16, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "D"
      Number of atoms: 2765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2765
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 16, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 2659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2659
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 18, 'TRANS': 317}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      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
    Chain: "C"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      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
    Chain: "E"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {'NAG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Modifications used: {'COO': 1}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLU A 192 " occ=0.79
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 192 " occ=0.21
  Time building chain proxies: 9.24, per 1000 atoms: 0.67
  Number of scatterers: 13731
  At special positions: 0
  Unit cell: (89.64, 92.13, 137.78, 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      93     16.00
     O    2476      8.00
     N    2196      7.00
     C    8966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 138 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 198 " - pdb=" SG  CYS B 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 138 " - pdb=" SG  CYS C 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 198 " - pdb=" SG  CYS C 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 198 " - pdb=" SG  CYS D 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 161 " - pdb=" SG  CYS E 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 221 " - pdb=" SG  CYS E 233 " 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 A 501 " - " ASN A  38 "
      " NAG B 501 " - " ASN B  38 "
      " NAG C 501 " - " ASN C  38 "
      " NAG D 501 " - " ASN D  38 "
      " NAG E 501 " - " ASN E 220 "
  Time building additional restraints: 3.36
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3286

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 14 sheets defined
      39.8% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 19
    Processing helix  chain 'A' and resid 71 through 74
      removed outlier: 3.717A  pdb=" N   ALA A  74 " --> pdb=" O   PRO A  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 74'
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 4.010A  pdb=" N   ASP A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A  93 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 220 through 241
      removed outlier: 4.547A  pdb=" N   ILE A 229 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      Proline residue:  A 230  - end of helix
      removed outlier: 3.903A  pdb=" N   SER A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 244
      No H-bonds generated for 'chain 'A' and resid 242 through 244'
    Processing helix  chain 'A' and resid 248 through 272
      removed outlier: 3.598A  pdb=" N   VAL A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 309
    Processing helix  chain 'A' and resid 388 through 420
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'B' and resid 10 through 19
    Processing helix  chain 'B' and resid 20 through 23
      removed outlier: 3.700A  pdb=" N   GLY B  23 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 20 through 23'
    Processing helix  chain 'B' and resid 71 through 74
      removed outlier: 4.059A  pdb=" N   ALA B  74 " --> pdb=" O   PRO B  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 71 through 74'
    Processing helix  chain 'B' and resid 86 through 93
      removed outlier: 3.778A  pdb=" N   ASP B  91 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ILE B  93 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 239
      removed outlier: 3.726A  pdb=" N   ILE B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE B 229 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
      Proline residue:  B 230  - end of helix
      removed outlier: 3.815A  pdb=" N   TRP B 239 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 244
      removed outlier: 4.164A  pdb=" N   TRP B 243 " --> pdb=" O   TRP B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 273
      removed outlier: 3.606A  pdb=" N   ILE B 257 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   THR B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   THR B 259 " --> pdb=" O   LEU B 255 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 309
    Processing helix  chain 'B' and resid 387 through 420
      Proline residue:  B 404  - end of helix
    Processing helix  chain 'C' and resid 9 through 19
    Processing helix  chain 'C' and resid 71 through 74
      removed outlier: 3.690A  pdb=" N   ALA C  74 " --> pdb=" O   PRO C  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 71 through 74'
    Processing helix  chain 'C' and resid 86 through 93
      removed outlier: 3.805A  pdb=" N   ASP C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE C  93 " --> pdb=" O   LEU C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 147
    Processing helix  chain 'C' and resid 220 through 243
      removed outlier: 4.035A  pdb=" N   ILE C 225 " --> pdb=" O   GLY C 221 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ILE C 229 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      Proline residue:  C 230  - end of helix
      removed outlier: 3.782A  pdb=" N   SER C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE C 242 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TRP C 243 " --> pdb=" O   TRP C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 267
      removed outlier: 3.898A  pdb=" N   ARG C 252 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 309
    Processing helix  chain 'C' and resid 388 through 420
      Proline residue:  C 404  - end of helix
    Processing helix  chain 'D' and resid 9 through 19
    Processing helix  chain 'D' and resid 71 through 74
      removed outlier: 3.948A  pdb=" N   ALA D  74 " --> pdb=" O   PRO D  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 71 through 74'
    Processing helix  chain 'D' and resid 86 through 92
      removed outlier: 3.758A  pdb=" N   ASP D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 147
    Processing helix  chain 'D' and resid 220 through 239
      removed outlier: 3.593A  pdb=" N   ILE D 225 " --> pdb=" O   GLY D 221 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE D 229 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      Proline residue:  D 230  - end of helix
      removed outlier: 3.713A  pdb=" N   TRP D 239 " --> pdb=" O   VAL D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 244
      removed outlier: 4.148A  pdb=" N   TRP D 243 " --> pdb=" O   TRP D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.514A  pdb=" N   ALA D 272 " --> pdb=" O   SER D 268 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 281 through 309
    Processing helix  chain 'D' and resid 388 through 420
      Proline residue:  D 404  - end of helix
    Processing helix  chain 'E' and resid 32 through 39
    Processing helix  chain 'E' and resid 109 through 116
      removed outlier: 3.847A  pdb=" N   LYS E 114 " --> pdb=" O   THR E 111 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU E 116 " --> pdb=" O   TYR E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 170
    Processing helix  chain 'E' and resid 245 through 264
      removed outlier: 4.075A  pdb=" N   MET E 249 " --> pdb=" O   GLY E 245 " (cutoff:3.500A)
      Proline residue:  E 254  - end of helix
    Processing helix  chain 'E' and resid 265 through 268
    Processing helix  chain 'E' and resid 269 through 273
    Processing helix  chain 'E' and resid 275 through 295
      removed outlier: 3.836A  pdb=" N   LEU E 279 " --> pdb=" O   ALA E 275 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA E 295 " --> pdb=" O   CYS E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 305 through 332
    Processing helix  chain 'E' and resid 446 through 474
      Proline residue:  E 460  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 52
      removed outlier: 6.576A  pdb=" N   ASN A  38 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ASN A  69 " --> pdb=" O   ASN A  38 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE A  44 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ASN A  61 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   PHE A  48 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG A  59 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   SER A  50 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ASP A  57 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 57 through 69
    current: chain 'A' and resid 125 through 137
    Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 149 through 157
    current: chain 'A' and resid 209 through 218
    Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 41
    Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 47
      removed outlier: 3.778A  pdb=" N   PHE B  44 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASN B  61 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 57 through 69
    current: chain 'B' and resid 125 through 137
    Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 149 through 157
    current: chain 'B' and resid 209 through 218
    Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 52
      removed outlier: 6.346A  pdb=" N   ASN C  38 " --> pdb=" O   ASN C  69 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN C  69 " --> pdb=" O   ASN C  38 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE C  44 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ASN C  61 " --> pdb=" O   ASN C  46 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   PHE C  48 " --> pdb=" O   ARG C  59 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ARG C  59 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   SER C  50 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ASP C  57 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 57 through 69
    current: chain 'C' and resid 125 through 137
    Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 100
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 149 through 157
    current: chain 'C' and resid 209 through 218
    Processing sheet with id=AA8, first strand: chain 'D' and resid 37 through 52
      removed outlier: 6.557A  pdb=" N   ASN D  38 " --> pdb=" O   ASN D  69 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   ASN D  69 " --> pdb=" O   ASN D  38 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE D  44 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASN D  61 " --> pdb=" O   ASN D  46 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE D  48 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ARG D  59 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   SER D  50 " --> pdb=" O   ASP D  57 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ASP D  57 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 57 through 69
    current: chain 'D' and resid 125 through 137
    Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 157
      removed outlier: 4.660A  pdb=" N   HIS D 215 " --> pdb=" O   GLU D 192 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   GLU D 192 " --> pdb=" O   HIS D 215 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   GLU D 217 " --> pdb=" O   LYS D 190 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   LYS D 190 " --> pdb=" O   GLU D 217 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 201 through 202
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 73
      removed outlier: 6.456A  pdb=" N   ASP E  59 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ASN E  90 " --> pdb=" O   ASP E  59 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE E  65 " --> pdb=" O   PHE E  84 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASN E  82 " --> pdb=" O   ASN E  67 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   PHE E  69 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   ARG E  80 " --> pdb=" O   PHE E  69 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   SER E  71 " --> pdb=" O   ASP E  78 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP E  78 " --> pdb=" O   SER E  71 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 78 through 90
    current: chain 'E' and resid 148 through 156
    Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 123
      removed outlier: 3.581A  pdb=" N   GLY E 219 " --> pdb=" O   GLU E 235 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 172 through 173
      removed outlier: 3.668A  pdb=" N   ARG E 241 " --> pdb=" O   ASP E 210 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASP E 210 " --> pdb=" O   ARG E 241 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 224 through 225

    512 hydrogen bonds defined for protein.
    1449 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: 3.77

  Time building geometry restraints manager: 3.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3473
        1.33 -     1.45: 3019
        1.45 -     1.58: 7441
        1.58 -     1.70: 0
        1.70 -     1.82: 150
  Bond restraints: 14083
  Sorted by residual:
  bond pdb=" N   PRO A 250 "
       pdb=" CD  PRO A 250 "
    ideal  model  delta    sigma   weight residual
    1.473  1.513 -0.040 1.40e-02 5.10e+03 8.26e+00
  bond pdb=" N   LEU E 140 "
       pdb=" CA  LEU E 140 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.21e-02 6.83e+03 7.26e+00
  bond pdb=" N   ILE E 139 "
       pdb=" CA  ILE E 139 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.27e+00
  bond pdb=" N   MET C 246 "
       pdb=" CA  MET C 246 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.07e+00
  bond pdb=" N   ARG B 252 "
       pdb=" CA  ARG B 252 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.86e+00
  ... (remaining 14078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 18787
        1.46 -     2.93: 256
        2.93 -     4.39: 82
        4.39 -     5.86: 28
        5.86 -     7.32: 2
  Bond angle restraints: 19155
  Sorted by residual:
  angle pdb=" CA  ILE E 139 "
        pdb=" C   ILE E 139 "
        pdb=" O   ILE E 139 "
      ideal   model   delta    sigma   weight residual
     120.43  117.16    3.27 1.09e+00 8.42e-01 9.00e+00
  angle pdb=" C   LYS D 419 "
        pdb=" N   ILE D 420 "
        pdb=" CA  ILE D 420 "
      ideal   model   delta    sigma   weight residual
     122.97  120.05    2.92 9.80e-01 1.04e+00 8.89e+00
  angle pdb=" C   VAL C 111 "
        pdb=" N   THR C 112 "
        pdb=" CA  THR C 112 "
      ideal   model   delta    sigma   weight residual
     121.54  126.58   -5.04 1.91e+00 2.74e-01 6.97e+00
  angle pdb=" C   VAL D 111 "
        pdb=" N   THR D 112 "
        pdb=" CA  THR D 112 "
      ideal   model   delta    sigma   weight residual
     121.54  126.54   -5.00 1.91e+00 2.74e-01 6.85e+00
  angle pdb=" C   VAL B 111 "
        pdb=" N   THR B 112 "
        pdb=" CA  THR B 112 "
      ideal   model   delta    sigma   weight residual
     121.54  126.30   -4.76 1.91e+00 2.74e-01 6.20e+00
  ... (remaining 19150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 7886
       17.26 -    34.53: 436
       34.53 -    51.79: 98
       51.79 -    69.05: 8
       69.05 -    86.32: 3
  Dihedral angle restraints: 8431
    sinusoidal: 3375
      harmonic: 5056
  Sorted by residual:
  dihedral pdb=" CB  CYS E 221 "
           pdb=" SG  CYS E 221 "
           pdb=" SG  CYS E 233 "
           pdb=" CB  CYS E 233 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.25   72.25     1      1.00e+01 1.00e-02 6.67e+01
  dihedral pdb=" CA  ILE D 420 "
           pdb=" C   ILE D 420 "
           pdb=" N   LEU D 421 "
           pdb=" CA  LEU D 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.28  -16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  MET C 227 "
           pdb=" C   MET C 227 "
           pdb=" N   TYR C 228 "
           pdb=" CA  TYR C 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.52  -16.48     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 8428 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1863
       0.056 -    0.112: 293
       0.112 -    0.168: 23
       0.168 -    0.224: 4
       0.224 -    0.280: 2
  Chirality restraints: 2185
  Sorted by residual:
  chirality pdb=" C1  NAG E 501 "
            pdb=" ND2 ASN E 220 "
            pdb=" C2  NAG E 501 "
            pdb=" O5  NAG E 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ILE E 139 "
            pdb=" N   ILE E 139 "
            pdb=" C   ILE E 139 "
            pdb=" CB  ILE E 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" C2  NAG B 501 "
            pdb=" C1  NAG B 501 "
            pdb=" C3  NAG B 501 "
            pdb=" N2  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.29   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 2182 not shown)

  Planarity restraints: 2400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 249 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.04e+00
        pdb=" N   PRO A 250 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 250 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 250 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 224 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   LEU B 224 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU B 224 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 225 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 224 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.72e+00
        pdb=" C   LEU A 224 "    0.023 2.00e-02 2.50e+03
        pdb=" O   LEU A 224 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 225 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2397 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 66
        2.52 -     3.11: 10177
        3.11 -     3.71: 20475
        3.71 -     4.30: 27423
        4.30 -     4.90: 47435
  Nonbonded interactions: 105576
  Sorted by model distance:
  nonbonded pdb=" O   PRO E 278 "
            pdb=" CD2 PHE E 282 "
     model   vdw
     1.924 3.340
  nonbonded pdb=" CD1 LEU A 255 "
            pdb=" CD1 ILE E 281 "
     model   vdw
     1.983 3.880
  nonbonded pdb=" CE  MET C 246 "
            pdb=" CG1 VAL C 304 "
     model   vdw
     2.083 3.880
  nonbonded pdb=" O   ALA A 254 "
            pdb=" OG1 THR A 258 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG1 THR A 112 "
            pdb=" O   LEU E 121 "
     model   vdw
     2.154 3.040
  ... (remaining 105571 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 9 through 191 or resid 193 through 310 or resid 386 throug \ 
h 395 or (resid 396 through 401 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'B' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 78 through 191 or resid 193 through 310 or res \ 
id 386 through 387 or (resid 388 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 389 through 392 or (resid 393 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 394 through 421 or (resid 422 and (name N or  \ 
name CA or name C or name O or name CB ))))
  selection = (chain 'C' and (resid 9 through 76 or (resid 77 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 78 through 191 or resid 193 through 387 or (re \ 
sid 388 and (name N or name CA or name C or name O or name CB )) or resid 389 th \ 
rough 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 394 through 396 or (resid 397 through 401 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 402 through 422))
  selection = (chain 'D' and (resid 9 through 191 or resid 193 through 387 or (resid 388 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 389 through 392 or  \ 
(resid 393 and (name N or name CA or name C or name O or name CB )) or resid 394 \ 
 through 396 or (resid 397 through 401 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 402 through 421 or (resid 422 and (name N or name CA or \ 
 name C or name O or name CB ))))
}

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=0.21 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:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     33.330
  Find NCS groups from input model:        0.670
  Set up NCS constraints:                  0.060
  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:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0500
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   0.040  14098  Z= 0.132
  Angle     :  0.540   7.402  19190  Z= 0.277
  Chirality :  0.042   0.280   2185
  Planarity :  0.003   0.050   2395
  Dihedral  : 10.982  86.319   5115
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.39 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  :  7.04 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.22), residues: 1686
  helix:  2.50 (0.22), residues: 571
  sheet: -0.68 (0.27), residues: 386
  loop : -1.23 (0.23), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 415 
 HIS   0.002   0.001   HIS C 109 
 PHE   0.010   0.001   PHE C  48 
 TYR   0.013   0.001   TYR C 414 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00447 (    5)
  link_NAG-ASN         : angle       3.67425 (   15)
  hydrogen bonds       : bond        0.14316 (  512)
  hydrogen bonds       : angle       6.30867 ( 1449)
  SS BOND              : bond        0.00152 (   10)
  SS BOND              : angle       0.54946 (   20)
  covalent geometry    : bond        0.00263 (14083)
  covalent geometry    : angle       0.52986 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 198
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 TYR cc_start: 0.2246 (t80) cc_final: 0.2024 (t80)
REVERT: B  264 THR cc_start: 0.4766 (m) cc_final: 0.4468 (m)
REVERT: C  198 CYS cc_start: 0.2218 (OUTLIER) cc_final: 0.0029 (t)
REVERT: C  219 GLN cc_start: 0.2146 (OUTLIER) cc_final: 0.1596 (pt0)
REVERT: C  287 MET cc_start: 0.3960 (mmt) cc_final: 0.2123 (ptt)
REVERT: D  287 MET cc_start: 0.2700 (mmt) cc_final: 0.1958 (ptt)
REVERT: E   76 THR cc_start: 0.4715 (OUTLIER) cc_final: 0.4502 (m)
  outliers start: 53
  outliers final: 16
  residues processed: 248
  average time/residue: 0.2331
  time to fit residues: 87.6164
Evaluate side-chains
  162 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  219 GLN
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  251 VAL
Chi-restraints excluded: chain E residue  277 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 142 optimal weight:    7.9990
   chunk 128 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 68 optimal weight:    0.6980
   chunk 132 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0770
   chunk 80 optimal weight:    4.9990
   chunk 98 optimal weight:   20.0000
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
C 219 GLN
E 200 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.192510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160185 restraints weight = 36723.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.167419 restraints weight = 15059.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.170280 restraints weight = 7612.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0895
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14098  Z= 0.139
  Angle     :  0.650   9.916  19190  Z= 0.320
  Chirality :  0.044   0.246   2185
  Planarity :  0.004   0.045   2395
  Dihedral  :  6.238  73.269   1972
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.57 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.80 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.21), residues: 1686
  helix:  2.39 (0.22), residues: 555
  sheet: -0.54 (0.27), residues: 404
  loop : -1.15 (0.22), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 263 
 HIS   0.006   0.001   HIS A 215 
 PHE   0.013   0.001   PHE E 131 
 TYR   0.014   0.001   TYR A 279 
 ARG   0.005   0.000   ARG D 252 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01215 (    5)
  link_NAG-ASN         : angle       4.27983 (   15)
  hydrogen bonds       : bond        0.03978 (  512)
  hydrogen bonds       : angle       5.25579 ( 1449)
  SS BOND              : bond        0.00348 (   10)
  SS BOND              : angle       1.37779 (   20)
  covalent geometry    : bond        0.00287 (14083)
  covalent geometry    : angle       0.63792 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.4905 (mp) cc_final: 0.4381 (mm)
REVERT: A  163 MET cc_start: -0.0536 (mtt) cc_final: -0.1599 (tpt)
REVERT: A  220 MET cc_start: 0.1921 (tpp) cc_final: 0.1636 (tpt)
REVERT: B  198 CYS cc_start: -0.0342 (OUTLIER) cc_final: -0.2273 (m)
REVERT: C  235 VAL cc_start: 0.6146 (OUTLIER) cc_final: 0.5853 (p)
REVERT: C  287 MET cc_start: 0.4073 (mmt) cc_final: 0.2010 (ptt)
REVERT: D  111 VAL cc_start: 0.2534 (OUTLIER) cc_final: 0.1785 (m)
REVERT: D  163 MET cc_start: 0.3861 (mmt) cc_final: 0.2140 (ppp)
REVERT: D  287 MET cc_start: 0.3165 (mmt) cc_final: 0.2031 (ptt)
REVERT: E  212 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4742 (ptpp)
  outliers start: 33
  outliers final: 19
  residues processed: 175
  average time/residue: 0.2389
  time to fit residues: 63.1624
Evaluate side-chains
  150 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  219 GLN
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  307 VAL
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  251 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Chi-restraints excluded: chain E residue  311 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 127 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 137 optimal weight:    0.9980
   chunk 157 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 134 optimal weight:    0.0870
   chunk 105 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 138 optimal weight:    4.9990
   chunk 159 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.198723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.167387 restraints weight = 43264.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.175098 restraints weight = 16119.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.178736 restraints weight = 7522.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4006 r_free = 0.4006    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4006 r_free = 0.4006    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1297
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  14098  Z= 0.138
  Angle     :  0.639   9.173  19190  Z= 0.312
  Chirality :  0.044   0.226   2185
  Planarity :  0.004   0.039   2395
  Dihedral  :  6.074  67.740   1959
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.15 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.13 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.21), residues: 1686
  helix:  2.16 (0.22), residues: 557
  sheet: -0.48 (0.27), residues: 392
  loop : -1.14 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP D 239 
 HIS   0.004   0.001   HIS A 423 
 PHE   0.028   0.001   PHE C 214 
 TYR   0.013   0.001   TYR A 279 
 ARG   0.009   0.001   ARG C 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01001 (    5)
  link_NAG-ASN         : angle       4.30213 (   15)
  hydrogen bonds       : bond        0.03544 (  512)
  hydrogen bonds       : angle       4.94525 ( 1449)
  SS BOND              : bond        0.00271 (   10)
  SS BOND              : angle       1.61617 (   20)
  covalent geometry    : bond        0.00286 (14083)
  covalent geometry    : angle       0.62619 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 154
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.5327 (mp) cc_final: 0.4765 (mm)
REVERT: A  220 MET cc_start: 0.1759 (tpp) cc_final: 0.1532 (tpt)
REVERT: B  198 CYS cc_start: 0.0360 (OUTLIER) cc_final: -0.2369 (m)
REVERT: C   56 MET cc_start: 0.1451 (mmm) cc_final: 0.1056 (mmt)
REVERT: D   56 MET cc_start: -0.1787 (mmt) cc_final: -0.2866 (ptp)
REVERT: D  111 VAL cc_start: 0.2811 (OUTLIER) cc_final: 0.1968 (m)
REVERT: D  287 MET cc_start: 0.3380 (mmt) cc_final: 0.1940 (ptt)
  outliers start: 40
  outliers final: 23
  residues processed: 189
  average time/residue: 0.2342
  time to fit residues: 67.0948
Evaluate side-chains
  161 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  219 GLN
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  234 ILE
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  211 ILE
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  251 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 138 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0980
   chunk 122 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.1980
   chunk 52 optimal weight:    4.9990
   chunk 130 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 ASN
C 109 HIS
D 109 HIS
D 266 GLN
E 138 ASN
E 178 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.212132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.183737 restraints weight = 38368.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.190036 restraints weight = 15758.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.193915 restraints weight = 8354.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4165 r_free = 0.4165    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4165 r_free = 0.4165    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2398
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  14098  Z= 0.201
  Angle     :  0.787  15.210  19190  Z= 0.393
  Chirality :  0.048   0.264   2185
  Planarity :  0.006   0.121   2395
  Dihedral  :  6.552  68.678   1959
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.98 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.67 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.21), residues: 1686
  helix:  1.48 (0.22), residues: 571
  sheet: -0.89 (0.26), residues: 401
  loop : -1.10 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP D 239 
 HIS   0.027   0.003   HIS B 215 
 PHE   0.032   0.002   PHE A 295 
 TYR   0.068   0.002   TYR D 301 
 ARG   0.007   0.001   ARG B 391 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00750 (    5)
  link_NAG-ASN         : angle       3.52665 (   15)
  hydrogen bonds       : bond        0.03895 (  512)
  hydrogen bonds       : angle       4.97530 ( 1449)
  SS BOND              : bond        0.00335 (   10)
  SS BOND              : angle       1.46080 (   20)
  covalent geometry    : bond        0.00415 (14083)
  covalent geometry    : angle       0.78006 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 186
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ILE cc_start: 0.6340 (mp) cc_final: 0.6000 (mp)
REVERT: A  154 MET cc_start: 0.2392 (tpp) cc_final: -0.1343 (mtt)
REVERT: A  163 MET cc_start: -0.1324 (mtt) cc_final: -0.1697 (tpt)
REVERT: A  227 MET cc_start: 0.3481 (tpp) cc_final: 0.3114 (tpp)
REVERT: B  216 LEU cc_start: 0.3252 (pt) cc_final: 0.2987 (pp)
REVERT: C  144 ASN cc_start: 0.3723 (OUTLIER) cc_final: 0.2735 (p0)
REVERT: D  111 VAL cc_start: 0.3616 (OUTLIER) cc_final: 0.2579 (m)
REVERT: D  227 MET cc_start: 0.4836 (mtt) cc_final: 0.4619 (mtt)
REVERT: E   89 TRP cc_start: 0.2937 (p90) cc_final: 0.2428 (p90)
  outliers start: 46
  outliers final: 22
  residues processed: 224
  average time/residue: 0.2126
  time to fit residues: 74.6456
Evaluate side-chains
  179 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  198 CYS
Chi-restraints excluded: chain D residue  207 PHE
Chi-restraints excluded: chain D residue  208 THR
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  157 ILE
Chi-restraints excluded: chain E residue  211 ILE
Chi-restraints excluded: chain E residue  251 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 132 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 ASN
B 115 ASN
B 144 ASN
C  61 ASN
C 177 GLN
C 219 GLN
D 266 GLN
E  32 ASN
E 136 GLN
E 138 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.228732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.200626 restraints weight = 40461.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.207451 restraints weight = 17428.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.211633 restraints weight = 9322.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3923
moved from start:          0.8878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.133  14098  Z= 0.280
  Angle     :  0.936  19.955  19190  Z= 0.473
  Chirality :  0.053   0.492   2185
  Planarity :  0.006   0.061   2395
  Dihedral  :  6.907  58.578   1955
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.05 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 15.48 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.20), residues: 1686
  helix:  1.17 (0.22), residues: 574
  sheet: -1.43 (0.24), residues: 414
  loop : -1.29 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP D 239 
 HIS   0.010   0.002   HIS B 215 
 PHE   0.047   0.003   PHE C  48 
 TYR   0.024   0.003   TYR D 301 
 ARG   0.019   0.001   ARG A  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00767 (    5)
  link_NAG-ASN         : angle       3.45779 (   15)
  hydrogen bonds       : bond        0.03979 (  512)
  hydrogen bonds       : angle       5.22180 ( 1449)
  SS BOND              : bond        0.01648 (   10)
  SS BOND              : angle       2.02532 (   20)
  covalent geometry    : bond        0.00635 (14083)
  covalent geometry    : angle       0.92982 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 223
  time to evaluate  : 1.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4820 (mpp) cc_final: 0.3250 (tmm)
REVERT: A   62 ILE cc_start: 0.3770 (pt) cc_final: 0.3536 (mt)
REVERT: A  273 SER cc_start: 0.7910 (t) cc_final: 0.7691 (p)
REVERT: B   18 MET cc_start: 0.3011 (tpp) cc_final: 0.2739 (tpp)
REVERT: B   90 LEU cc_start: 0.2971 (OUTLIER) cc_final: 0.2769 (tt)
REVERT: C  147 MET cc_start: 0.6356 (mpp) cc_final: 0.5867 (mpp)
REVERT: C  154 MET cc_start: 0.7696 (pmm) cc_final: 0.6822 (ptt)
REVERT: C  234 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6875 (tt)
REVERT: E   89 TRP cc_start: 0.4494 (p90) cc_final: 0.3132 (p90)
  outliers start: 65
  outliers final: 32
  residues processed: 269
  average time/residue: 0.2208
  time to fit residues: 90.6201
Evaluate side-chains
  215 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   58 TYR
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  126 VAL
Chi-restraints excluded: chain C residue  138 CYS
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  234 ILE
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  207 PHE
Chi-restraints excluded: chain D residue  234 ILE
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 143 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 137 optimal weight:    0.0070
   chunk 30 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5200

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
B 144 ASN
B 219 GLN
C 201 HIS
C 226 GLN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 215 HIS
E 178 GLN
E 194 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.222672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.194469 restraints weight = 39906.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.201069 restraints weight = 17465.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.205189 restraints weight = 9565.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4352 r_free = 0.4352    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4352 r_free = 0.4352    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4073
moved from start:          0.9379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.106  14098  Z= 0.131
  Angle     :  0.700  10.966  19190  Z= 0.342
  Chirality :  0.044   0.245   2185
  Planarity :  0.004   0.046   2395
  Dihedral  :  6.317  58.863   1953
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.68 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.90 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.21), residues: 1686
  helix:  1.57 (0.22), residues: 565
  sheet: -1.26 (0.26), residues: 383
  loop : -1.27 (0.22), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.001   TRP D 239 
 HIS   0.010   0.001   HIS A 423 
 PHE   0.028   0.001   PHE E 246 
 TYR   0.017   0.001   TYR A 414 
 ARG   0.006   0.000   ARG A 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    5)
  link_NAG-ASN         : angle       3.32668 (   15)
  hydrogen bonds       : bond        0.03139 (  512)
  hydrogen bonds       : angle       4.80066 ( 1449)
  SS BOND              : bond        0.00559 (   10)
  SS BOND              : angle       3.24822 (   20)
  covalent geometry    : bond        0.00297 (14083)
  covalent geometry    : angle       0.68642 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4736 (mpp) cc_final: 0.3130 (tmm)
REVERT: A   69 ASN cc_start: 0.5800 (p0) cc_final: 0.5596 (p0)
REVERT: A  163 MET cc_start: -0.0550 (mtt) cc_final: -0.2094 (tpt)
REVERT: B   90 LEU cc_start: 0.3220 (pp) cc_final: 0.2971 (tt)
REVERT: C  147 MET cc_start: 0.6563 (mpp) cc_final: 0.6161 (mpp)
REVERT: C  154 MET cc_start: 0.7648 (pmm) cc_final: 0.6960 (ptt)
REVERT: D   70 ASP cc_start: 0.2755 (OUTLIER) cc_final: -0.0408 (m-30)
REVERT: D  198 CYS cc_start: 0.3984 (m) cc_final: 0.3762 (m)
REVERT: D  281 LYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5487 (ptpt)
REVERT: E   89 TRP cc_start: 0.4761 (p90) cc_final: 0.4115 (p90)
REVERT: E  212 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.4455 (ttpp)
  outliers start: 47
  outliers final: 29
  residues processed: 236
  average time/residue: 0.2034
  time to fit residues: 75.0835
Evaluate side-chains
  213 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 181
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  138 CYS
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain C residue  280 VAL
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  207 PHE
Chi-restraints excluded: chain D residue  234 ILE
Chi-restraints excluded: chain D residue  281 LYS
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  194 GLN
Chi-restraints excluded: chain E residue  211 ILE
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 156 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 105 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0870
   chunk 98 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 135 optimal weight:    0.5980
   chunk 125 optimal weight:    5.9990
   chunk 129 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 ASN
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.233181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.201276 restraints weight = 42329.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.208195 restraints weight = 18394.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.212537 restraints weight = 10016.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4352 r_free = 0.4352    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4352 r_free = 0.4352    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4408
moved from start:          1.0188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  14098  Z= 0.152
  Angle     :  0.696  14.968  19190  Z= 0.340
  Chirality :  0.044   0.294   2185
  Planarity :  0.004   0.047   2395
  Dihedral  :  6.204  59.226   1953
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.52 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.63 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.21), residues: 1686
  helix:  1.70 (0.22), residues: 565
  sheet: -1.24 (0.25), residues: 396
  loop : -1.27 (0.22), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP D 239 
 HIS   0.008   0.001   HIS A 423 
 PHE   0.028   0.001   PHE A 295 
 TYR   0.032   0.002   TYR A  75 
 ARG   0.005   0.000   ARG A 271 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00659 (    5)
  link_NAG-ASN         : angle       3.78446 (   15)
  hydrogen bonds       : bond        0.03052 (  512)
  hydrogen bonds       : angle       4.68615 ( 1449)
  SS BOND              : bond        0.00392 (   10)
  SS BOND              : angle       2.01892 (   20)
  covalent geometry    : bond        0.00313 (14083)
  covalent geometry    : angle       0.68582 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4671 (mpp) cc_final: 0.3158 (tmm)
REVERT: A   51 ILE cc_start: 0.7386 (mp) cc_final: 0.7093 (mt)
REVERT: A   89 MET cc_start: 0.4250 (mtt) cc_final: 0.3594 (mtp)
REVERT: A  163 MET cc_start: -0.0350 (mtt) cc_final: -0.2152 (tpt)
REVERT: D   70 ASP cc_start: 0.3295 (OUTLIER) cc_final: 0.0292 (m-30)
REVERT: D  227 MET cc_start: 0.5323 (mtt) cc_final: 0.4942 (mtm)
REVERT: E   89 TRP cc_start: 0.4795 (p90) cc_final: 0.4191 (p90)
REVERT: E  177 MET cc_start: 0.0500 (mmt) cc_final: -0.0101 (mmt)
REVERT: E  212 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.4621 (ttpp)
REVERT: E  311 LEU cc_start: 0.5647 (mt) cc_final: 0.5192 (mt)
REVERT: E  325 TYR cc_start: 0.4880 (t80) cc_final: 0.4398 (t80)
  outliers start: 40
  outliers final: 28
  residues processed: 229
  average time/residue: 0.2262
  time to fit residues: 84.2161
Evaluate side-chains
  214 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  277 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  284 ASP
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  163 MET
Chi-restraints excluded: chain D residue  234 ILE
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  277 VAL
Chi-restraints excluded: chain E residue  304 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 137 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 157 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 156 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN
** B  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 194 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.233956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.202673 restraints weight = 31317.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.208615 restraints weight = 14852.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.212406 restraints weight = 8706.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4353 r_free = 0.4353    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4353 r_free = 0.4353    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5198
moved from start:          1.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  14098  Z= 0.166
  Angle     :  0.756  16.321  19190  Z= 0.374
  Chirality :  0.047   0.298   2185
  Planarity :  0.005   0.052   2395
  Dihedral  :  6.303  59.933   1953
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.10 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.30 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.21), residues: 1686
  helix:  1.63 (0.22), residues: 573
  sheet: -1.28 (0.25), residues: 390
  loop : -1.35 (0.23), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 239 
 HIS   0.007   0.001   HIS D 109 
 PHE   0.038   0.002   PHE A 187 
 TYR   0.039   0.002   TYR D 128 
 ARG   0.006   0.001   ARG C 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00775 (    5)
  link_NAG-ASN         : angle       3.52702 (   15)
  hydrogen bonds       : bond        0.03160 (  512)
  hydrogen bonds       : angle       4.70071 ( 1449)
  SS BOND              : bond        0.00371 (   10)
  SS BOND              : angle       2.61973 (   20)
  covalent geometry    : bond        0.00365 (14083)
  covalent geometry    : angle       0.74519 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 238
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4479 (mpp) cc_final: 0.2925 (tmm)
REVERT: A  154 MET cc_start: 0.6202 (mmt) cc_final: 0.5870 (mmt)
REVERT: A  163 MET cc_start: -0.0202 (mtt) cc_final: -0.2308 (tpt)
REVERT: A  227 MET cc_start: 0.5383 (tpp) cc_final: 0.4783 (tpp)
REVERT: A  246 MET cc_start: 0.5696 (tmm) cc_final: 0.5493 (tmm)
REVERT: A  273 SER cc_start: 0.8171 (t) cc_final: 0.7896 (p)
REVERT: B  203 ASN cc_start: 0.7536 (t0) cc_final: 0.6806 (t0)
REVERT: D   70 ASP cc_start: 0.4574 (OUTLIER) cc_final: 0.3119 (p0)
REVERT: D  227 MET cc_start: 0.6148 (mtt) cc_final: 0.5780 (mtp)
REVERT: E  177 MET cc_start: 0.1149 (mmt) cc_final: 0.0424 (mmt)
REVERT: E  212 LYS cc_start: 0.5745 (OUTLIER) cc_final: 0.4318 (ttpp)
  outliers start: 49
  outliers final: 29
  residues processed: 270
  average time/residue: 0.2018
  time to fit residues: 86.8704
Evaluate side-chains
  237 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 1.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  140 MET
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  405 LEU
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain D residue  215 HIS
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain D residue  418 TYR
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  135 THR
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  277 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 160 optimal weight:   20.0000
   chunk 34 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 167 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 120 optimal weight:    4.9990
   chunk 85 optimal weight:    0.5980
   chunk 91 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 ASN
B 115 ASN
C 186 GLN
C 201 HIS
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.233240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.200620 restraints weight = 33306.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.206891 restraints weight = 15690.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.210824 restraints weight = 9139.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5470
moved from start:          1.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  14098  Z= 0.140
  Angle     :  0.735  16.262  19190  Z= 0.352
  Chirality :  0.044   0.216   2185
  Planarity :  0.004   0.040   2395
  Dihedral  :  6.077  59.984   1952
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.74 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.78 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.34 (0.21), residues: 1686
  helix:  1.74 (0.22), residues: 574
  sheet: -1.32 (0.26), residues: 393
  loop : -1.17 (0.23), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 239 
 HIS   0.008   0.001   HIS D 109 
 PHE   0.028   0.001   PHE A 295 
 TYR   0.023   0.001   TYR A 222 
 ARG   0.004   0.000   ARG A 218 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00658 (    5)
  link_NAG-ASN         : angle       3.72923 (   15)
  hydrogen bonds       : bond        0.02915 (  512)
  hydrogen bonds       : angle       4.58220 ( 1449)
  SS BOND              : bond        0.00401 (   10)
  SS BOND              : angle       1.84225 (   20)
  covalent geometry    : bond        0.00314 (14083)
  covalent geometry    : angle       0.72571 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4650 (mpp) cc_final: 0.2988 (tmm)
REVERT: A  136 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7980 (mp)
REVERT: A  154 MET cc_start: 0.6319 (mmt) cc_final: 0.6046 (mmt)
REVERT: A  210 ILE cc_start: 0.6683 (mm) cc_final: 0.6481 (mp)
REVERT: A  220 MET cc_start: 0.4992 (tpt) cc_final: 0.4356 (ppp)
REVERT: A  227 MET cc_start: 0.5547 (tpp) cc_final: 0.5100 (tpp)
REVERT: A  246 MET cc_start: 0.5708 (tmm) cc_final: 0.5479 (tmm)
REVERT: B   94 TRP cc_start: 0.5913 (t60) cc_final: 0.5651 (t60)
REVERT: B  163 MET cc_start: 0.4852 (ppp) cc_final: 0.3872 (mtp)
REVERT: B  198 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6927 (p)
REVERT: B  203 ASN cc_start: 0.7590 (t0) cc_final: 0.6852 (t0)
REVERT: B  225 ILE cc_start: 0.8463 (mt) cc_final: 0.8242 (mm)
REVERT: C  163 MET cc_start: 0.7616 (tpt) cc_final: 0.7400 (tpt)
REVERT: D   70 ASP cc_start: 0.5006 (OUTLIER) cc_final: 0.3660 (p0)
REVERT: D  111 VAL cc_start: 0.6745 (OUTLIER) cc_final: 0.6266 (m)
REVERT: E  177 MET cc_start: 0.1726 (mmt) cc_final: 0.0953 (mmt)
REVERT: E  212 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.4307 (ttpp)
  outliers start: 34
  outliers final: 20
  residues processed: 238
  average time/residue: 0.2108
  time to fit residues: 78.9959
Evaluate side-chains
  218 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain B residue  159 PHE
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  215 HIS
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain D residue  418 TYR
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 155 optimal weight:    0.9990
   chunk 13 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0370
   chunk 97 optimal weight:   10.0000
   chunk 168 optimal weight:    0.8980
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 ASN
D  66 GLN
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 200 GLN ** 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 = 0.4517 r_free = 0.4517 target = 0.232044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.196314 restraints weight = 47104.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.203592 restraints weight = 19434.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.208180 restraints weight = 10450.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4320 r_free = 0.4320    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4320 r_free = 0.4320    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5679
moved from start:          1.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14098  Z= 0.131
  Angle     :  0.714  17.858  19190  Z= 0.343
  Chirality :  0.044   0.203   2185
  Planarity :  0.005   0.120   2395
  Dihedral  :  6.074  59.908   1952
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.39 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 22.39 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.21), residues: 1686
  helix:  1.89 (0.23), residues: 568
  sheet: -1.22 (0.26), residues: 400
  loop : -1.28 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  94 
 HIS   0.005   0.001   HIS A 423 
 PHE   0.023   0.001   PHE E 131 
 TYR   0.019   0.001   TYR A  75 
 ARG   0.016   0.001   ARG B  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00664 (    5)
  link_NAG-ASN         : angle       3.59399 (   15)
  hydrogen bonds       : bond        0.02853 (  512)
  hydrogen bonds       : angle       4.50733 ( 1449)
  SS BOND              : bond        0.00300 (   10)
  SS BOND              : angle       1.89761 (   20)
  covalent geometry    : bond        0.00282 (14083)
  covalent geometry    : angle       0.70450 (19155)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 226
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.4610 (mpp) cc_final: 0.2884 (tmm)
REVERT: A   89 MET cc_start: 0.4403 (mtt) cc_final: 0.3686 (mmt)
REVERT: A  163 MET cc_start: -0.0097 (mtt) cc_final: -0.2047 (tpt)
REVERT: B   18 MET cc_start: 0.3524 (tpp) cc_final: 0.1996 (tpp)
REVERT: B  163 MET cc_start: 0.5500 (ppp) cc_final: 0.4751 (mtp)
REVERT: B  198 CYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6877 (p)
REVERT: B  203 ASN cc_start: 0.7688 (t0) cc_final: 0.7110 (t0)
REVERT: B  225 ILE cc_start: 0.8607 (mt) cc_final: 0.8361 (mm)
REVERT: B  246 MET cc_start: 0.4261 (pmm) cc_final: 0.2850 (ptt)
REVERT: C  154 MET cc_start: 0.7900 (pmm) cc_final: 0.6926 (ptt)
REVERT: D   70 ASP cc_start: 0.5511 (OUTLIER) cc_final: 0.4241 (p0)
REVERT: D  111 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6555 (m)
REVERT: D  116 LYS cc_start: 0.5790 (mmtm) cc_final: 0.5575 (mptt)
REVERT: E   89 TRP cc_start: 0.5685 (p90) cc_final: 0.5327 (p90)
REVERT: E  212 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4188 (ttpp)
REVERT: E  246 PHE cc_start: 0.6790 (t80) cc_final: 0.6493 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 246
  average time/residue: 0.2014
  time to fit residues: 79.0318
Evaluate side-chains
  233 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  198 CYS
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  390 ASP
Chi-restraints excluded: chain C residue  198 CYS
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   70 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  215 HIS
Chi-restraints excluded: chain D residue  234 ILE
Chi-restraints excluded: chain D residue  387 VAL
Chi-restraints excluded: chain D residue  418 TYR
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  212 LYS
Chi-restraints excluded: chain E residue  236 VAL
Chi-restraints excluded: chain E residue  244 VAL
Chi-restraints excluded: chain E residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 159 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0070
   chunk 31 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0570
   chunk 93 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 153 optimal weight:    0.9980
   chunk 142 optimal weight:    0.2980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 ASN
B 177 GLN
C 201 HIS
C 219 GLN
** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 200 GLN ** 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 = 0.4519 r_free = 0.4519 target = 0.232524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.202422 restraints weight = 44553.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.211672 restraints weight = 22378.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.211591 restraints weight = 12207.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5732
moved from start:          1.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14098  Z= 0.124
  Angle     :  0.710  17.012  19190  Z= 0.337
  Chirality :  0.044   0.240   2185
  Planarity :  0.004   0.036   2395
  Dihedral  :  6.029  59.476   1952
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.80 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 23.32 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.21), residues: 1686
  helix:  1.91 (0.23), residues: 573
  sheet: -1.03 (0.26), residues: 388
  loop : -1.28 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP D 239 
 HIS   0.007   0.001   HIS D 109 
 PHE   0.034   0.001   PHE C  99 
 TYR   0.016   0.001   TYR A 414 
 ARG   0.006   0.000   ARG A  59 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00620 (    5)
  link_NAG-ASN         : angle       3.58868 (   15)
  hydrogen bonds       : bond        0.02780 (  512)
  hydrogen bonds       : angle       4.47385 ( 1449)
  SS BOND              : bond        0.00349 (   10)
  SS BOND              : angle       1.86175 (   20)
  covalent geometry    : bond        0.00273 (14083)
  covalent geometry    : angle       0.70050 (19155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4696.82 seconds
wall clock time: 81 minutes 54.66 seconds (4914.66 seconds total)