Starting phenix.real_space_refine
on Wed Mar  4 22:51:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xgc_22180/03_2026/6xgc_22180.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      69      5.16       5
     C   10668      2.51       5
     N    2916      2.21       5
     O    3387      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17040
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2528
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 18, 'TRANS': 304}
    Chain: "B"
      Number of atoms: 1339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1339
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 1, 'TRANS': 162}
    Chain: "M"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 925
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
    Chain: "N"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 790
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    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
  Restraints were copied for chains:
    C, E, D, F, H, I, L, J, K, O
  Time building chain proxies: 3.15, per 1000 atoms: 0.18
  Number of scatterers: 17040
  At special positions: 0
  Unit cell: (124.962, 131.316, 150.378, 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      69     16.00
     O    3387      8.00
     N    2916      7.00
     C   10668      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  14 " - pdb=" SG  CYS B 137 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  29 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS D 137 " distance=1.96
    Simple disulfide: pdb=" SG  CYS E  14 " - pdb=" SG  CYS F 137 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C  52 " - pdb=" SG  CYS C 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  52 " - pdb=" SG  CYS E 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  65 " - pdb=" SG  CYS E  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 100 " - pdb=" SG  CYS C 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 100 " - pdb=" SG  CYS E 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 289 " - pdb=" SG  CYS C 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 289 " - pdb=" SG  CYS E 313 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 144 " - pdb=" SG  CYS D 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 144 " - pdb=" SG  CYS F 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  29 " - pdb=" SG  CYS L  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  29 " - pdb=" SG  CYS J  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
      " NAG K   1 " - " NAG K   2 "
      " NAG O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A 403 " - " ASN A 286 "
      " NAG A 404 " - " ASN A 297 "
      " NAG A 405 " - " ASN A  33 "
      " NAG A 406 " - " ASN A  21 "
      " NAG B 301 " - " ASN B 154 "
      " NAG C 403 " - " ASN C 286 "
      " NAG C 404 " - " ASN C 297 "
      " NAG C 405 " - " ASN C  33 "
      " NAG C 406 " - " ASN C  21 "
      " NAG D 301 " - " ASN D 154 "
      " NAG E 403 " - " ASN E 286 "
      " NAG E 404 " - " ASN E 297 "
      " NAG E 405 " - " ASN E  33 "
      " NAG E 406 " - " ASN E  21 "
      " NAG F 301 " - " ASN F 154 "
      " NAG G   1 " - " ASN A  97 "
      " NAG K   1 " - " ASN C  97 "
      " NAG O   1 " - " ASN E  97 "
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 704.4 milliseconds
  

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3924

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 54 sheets defined
      19.9% alpha, 29.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 72
    Processing helix  chain 'A' and resid 74 through 78
    Processing helix  chain 'A' and resid 107 through 115
    Processing helix  chain 'A' and resid 194 through 203
    Processing helix  chain 'B' and resid 37 through 58
    Processing helix  chain 'B' and resid 74 through 127
    Processing helix  chain 'B' and resid 145 through 155
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 4.003A  pdb=" N   TYR B 162 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLU B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   GLU B 165 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 87 through 91
    Processing helix  chain 'N' and resid 32 through 37
      removed outlier: 3.742A  pdb=" N   GLY N  37 " --> pdb=" O   SER N  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 72
    Processing helix  chain 'C' and resid 74 through 78
    Processing helix  chain 'C' and resid 107 through 115
    Processing helix  chain 'C' and resid 194 through 203
    Processing helix  chain 'D' and resid 37 through 58
    Processing helix  chain 'D' and resid 74 through 127
    Processing helix  chain 'D' and resid 145 through 155
    Processing helix  chain 'D' and resid 158 through 171
      removed outlier: 4.002A  pdb=" N   TYR D 162 " --> pdb=" O   ASP D 158 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   GLU D 164 " --> pdb=" O   PRO D 160 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   GLU D 165 " --> pdb=" O   LYS D 161 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 32 through 37
      removed outlier: 3.744A  pdb=" N   GLY L  37 " --> pdb=" O   SER L  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 72
    Processing helix  chain 'E' and resid 74 through 78
    Processing helix  chain 'E' and resid 107 through 115
    Processing helix  chain 'E' and resid 194 through 203
    Processing helix  chain 'F' and resid 37 through 58
    Processing helix  chain 'F' and resid 74 through 127
    Processing helix  chain 'F' and resid 145 through 155
    Processing helix  chain 'F' and resid 158 through 171
      removed outlier: 4.002A  pdb=" N   TYR F 162 " --> pdb=" O   ASP F 158 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU F 164 " --> pdb=" O   PRO F 160 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   GLU F 165 " --> pdb=" O   LYS F 161 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 87 through 91
    Processing helix  chain 'J' and resid 32 through 37
      removed outlier: 3.743A  pdb=" N   GLY J  37 " --> pdb=" O   SER J  33 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36
      removed outlier: 4.104A  pdb=" N   GLY B  23 " --> pdb=" O   GLY A  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41
    Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53
      removed outlier: 5.930A  pdb=" N   LEU A  51 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   CYS A 285 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61
      removed outlier: 6.553A  pdb=" N   LEU A  60 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE A  89 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124
      removed outlier: 8.041A  pdb=" N   LEU A 186 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124
    Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148
      removed outlier: 4.649A  pdb=" N   CYS A 146 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 171 through 176
    Processing sheet with id=AB2, first strand: chain 'A' and resid 289 through 290
      removed outlier: 3.686A  pdb=" N   CYS A 289 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 311
      removed outlier: 3.882A  pdb=" N   THR B  64 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.438A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 124 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ARG M  38 " --> pdb=" O   TRP M  47 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   TRP M  47 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 104
      removed outlier: 3.670A  pdb=" N   GLY M 100 " --> pdb=" O   ASN M 111 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'N' and resid 16 through 18
      removed outlier: 6.417A  pdb=" N   TRP N  43 " --> pdb=" O   LEU N  55 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 16 through 18
    Processing sheet with id=AB9, first strand: chain 'N' and resid 25 through 30
    Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 36
      removed outlier: 4.170A  pdb=" N   GLY D  23 " --> pdb=" O   GLY C  16 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26
    Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44
    Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53
      removed outlier: 5.930A  pdb=" N   LEU C  51 " --> pdb=" O   HIS C 283 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   CYS C 285 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 61
      removed outlier: 6.552A  pdb=" N   LEU C  60 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE C  89 " --> pdb=" O   ILE C 276 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'C' and resid 122 through 124
      removed outlier: 8.039A  pdb=" N   LEU C 186 " --> pdb=" O   PRO C 261 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 122 through 124
    Processing sheet with id=AC9, first strand: chain 'C' and resid 143 through 148
      removed outlier: 4.649A  pdb=" N   CYS C 146 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 171 through 176
    Processing sheet with id=AD2, first strand: chain 'C' and resid 289 through 290
      removed outlier: 3.686A  pdb=" N   CYS C 289 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 310 through 311
      removed outlier: 3.972A  pdb=" N   THR D  64 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.439A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'H' and resid 100 through 104
      removed outlier: 3.668A  pdb=" N   GLY H 100 " --> pdb=" O   ASN H 111 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'L' and resid 16 through 18
      removed outlier: 6.416A  pdb=" N   TRP L  43 " --> pdb=" O   LEU L  55 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'L' and resid 16 through 18
    Processing sheet with id=AD9, first strand: chain 'L' and resid 25 through 30
    Processing sheet with id=AE1, first strand: chain 'F' and resid 31 through 36
      removed outlier: 4.086A  pdb=" N   GLY F  23 " --> pdb=" O   GLY E  16 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'E' and resid 25 through 26
    Processing sheet with id=AE3, first strand: chain 'E' and resid 39 through 41
    Processing sheet with id=AE4, first strand: chain 'E' and resid 43 through 44
    Processing sheet with id=AE5, first strand: chain 'E' and resid 51 through 53
      removed outlier: 5.931A  pdb=" N   LEU E  51 " --> pdb=" O   HIS E 283 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   CYS E 285 " --> pdb=" O   LEU E  51 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 61
      removed outlier: 6.552A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  90 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ILE E  89 " --> pdb=" O   ILE E 276 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE6
    Processing sheet with id=AE7, first strand: chain 'E' and resid 122 through 124
      removed outlier: 8.041A  pdb=" N   LEU E 186 " --> pdb=" O   PRO E 261 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'E' and resid 122 through 124
    Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 148
      removed outlier: 4.649A  pdb=" N   CYS E 146 " --> pdb=" O   SER E 153 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'E' and resid 171 through 176
    Processing sheet with id=AF2, first strand: chain 'E' and resid 289 through 290
      removed outlier: 3.687A  pdb=" N   CYS E 289 " --> pdb=" O   ILE E 296 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'E' and resid 310 through 311
      removed outlier: 3.868A  pdb=" N   THR F  64 " --> pdb=" O   GLY E 311 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7
    Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11
      removed outlier: 6.438A  pdb=" N   GLY I  10 " --> pdb=" O   THR I 124 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'I' and resid 100 through 104
      removed outlier: 3.671A  pdb=" N   GLY I 100 " --> pdb=" O   ASN I 111 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'J' and resid 16 through 18
      removed outlier: 6.415A  pdb=" N   TRP J  43 " --> pdb=" O   LEU J  55 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'J' and resid 16 through 18
    Processing sheet with id=AF9, first strand: chain 'J' and resid 25 through 30

    738 hydrogen bonds defined for protein.
    1926 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: 3.31

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5547
        1.34 -     1.46: 3563
        1.46 -     1.58: 8218
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 17418
  Sorted by residual:
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" C1  NAG K   2 "
       pdb=" O5  NAG K   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.19e+00
  bond pdb=" C1  NAG O   2 "
       pdb=" O5  NAG O   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.11e+00
  bond pdb=" C1  NAG A 403 "
       pdb=" O5  NAG A 403 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C1  NAG B 301 "
       pdb=" O5  NAG B 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  ... (remaining 17413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.94: 22761
        0.94 -     1.88: 618
        1.88 -     2.83: 189
        2.83 -     3.77: 36
        3.77 -     4.71: 12
  Bond angle restraints: 23616
  Sorted by residual:
  angle pdb=" C   LEU F 126 "
        pdb=" N   LYS F 127 "
        pdb=" CA  LYS F 127 "
      ideal   model   delta    sigma   weight residual
     121.54  126.11   -4.57 1.91e+00 2.74e-01 5.72e+00
  angle pdb=" C   LEU D 126 "
        pdb=" N   LYS D 127 "
        pdb=" CA  LYS D 127 "
      ideal   model   delta    sigma   weight residual
     121.54  126.07   -4.53 1.91e+00 2.74e-01 5.62e+00
  angle pdb=" C   LEU B 126 "
        pdb=" N   LYS B 127 "
        pdb=" CA  LYS B 127 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.45e+00
  angle pdb=" C   GLY E 165 "
        pdb=" N   ASN E 166 "
        pdb=" CA  ASN E 166 "
      ideal   model   delta    sigma   weight residual
     121.54  125.25   -3.71 1.91e+00 2.74e-01 3.78e+00
  angle pdb=" C   GLY C 165 "
        pdb=" N   ASN C 166 "
        pdb=" CA  ASN C 166 "
      ideal   model   delta    sigma   weight residual
     121.54  125.24   -3.70 1.91e+00 2.74e-01 3.75e+00
  ... (remaining 23611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 10266
       17.31 -    34.63: 270
       34.63 -    51.94: 60
       51.94 -    69.25: 3
       69.25 -    86.57: 9
  Dihedral angle restraints: 10608
    sinusoidal: 4437
      harmonic: 6171
  Sorted by residual:
  dihedral pdb=" CB  GLU C 109 "
           pdb=" CG  GLU C 109 "
           pdb=" CD  GLU C 109 "
           pdb=" OE1 GLU C 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.57   86.57     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CB  GLU A 109 "
           pdb=" CG  GLU A 109 "
           pdb=" CD  GLU A 109 "
           pdb=" OE1 GLU A 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.56   86.56     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CB  GLU E 109 "
           pdb=" CG  GLU E 109 "
           pdb=" CD  GLU E 109 "
           pdb=" OE1 GLU E 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.54   86.54     1      3.00e+01 1.11e-03 1.00e+01
  ... (remaining 10605 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1561
       0.025 -    0.050: 664
       0.050 -    0.076: 174
       0.076 -    0.101: 108
       0.101 -    0.126: 115
  Chirality restraints: 2622
  Sorted by residual:
  chirality pdb=" CA  ILE A 176 "
            pdb=" N   ILE A 176 "
            pdb=" C   ILE A 176 "
            pdb=" CB  ILE A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" C1  NAG C 406 "
            pdb=" ND2 ASN C  21 "
            pdb=" C2  NAG C 406 "
            pdb=" O5  NAG C 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  ILE E 176 "
            pdb=" N   ILE E 176 "
            pdb=" C   ILE E 176 "
            pdb=" CB  ILE E 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 2619 not shown)

  Planarity restraints: 3045
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 291 "   -0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO A 292 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 292 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 292 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 291 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO E 292 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E 292 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 292 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 291 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO C 292 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 292 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 292 "    0.019 5.00e-02 4.00e+02
  ... (remaining 3042 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1694
        2.75 -     3.29: 15900
        3.29 -     3.83: 28382
        3.83 -     4.36: 31425
        4.36 -     4.90: 56507
  Nonbonded interactions: 133908
  Sorted by model distance:
  nonbonded pdb=" OG  SER J  73 "
            pdb=" OG  SER J  80 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER N  73 "
            pdb=" OG  SER N  80 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER L  73 "
            pdb=" OG  SER L  80 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   TYR B 159 "
            pdb=" OG  SER B 163 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   TYR D 159 "
            pdb=" OG  SER D 163 "
     model   vdw
     2.287 3.040
  ... (remaining 133903 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'L'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'K'
  selection = chain 'O'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.050
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
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      :  0.002   0.073  17463  Z= 0.127
  Angle     :  0.449   6.740  23727  Z= 0.238
  Chirality :  0.040   0.126   2622
  Planarity :  0.003   0.034   3027
  Dihedral  :  8.174  86.567   6612
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.64 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.19), residues: 2133
  helix:  4.15 (0.25), residues: 351
  sheet:  1.15 (0.24), residues: 519
  loop : -0.06 (0.17), residues: 1263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  72 
 TYR   0.007   0.001   TYR F  94 
 PHE   0.005   0.001   PHE A 121 
 TRP   0.005   0.001   TRP E 133 
 HIS   0.004   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (17418)
  covalent geometry    : angle       0.43316 (23616)
  SS BOND              : bond        0.01892 (   24)
  SS BOND              : angle       0.73851 (   48)
  hydrogen bonds       : bond        0.14255 (  702)
  hydrogen bonds       : angle       5.75995 ( 1926)
  link_BETA1-4         : bond        0.00803 (    3)
  link_BETA1-4         : angle       5.49846 (    9)
  link_NAG-ASN         : bond        0.00176 (   18)
  link_NAG-ASN         : angle       0.96541 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  745 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 742
  time to evaluate  : 0.607 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.9253 (mt) cc_final: 0.8983 (mp)
REVERT: A  300 LEU cc_start: 0.8719 (mt) cc_final: 0.8299 (mt)
REVERT: B   17 MET cc_start: 0.8247 (ttp) cc_final: 0.8016 (ttp)
REVERT: B   19 ASP cc_start: 0.8801 (p0) cc_final: 0.8598 (p0)
REVERT: B   26 HIS cc_start: 0.7671 (p90) cc_final: 0.7422 (p90)
REVERT: B   38 LEU cc_start: 0.8215 (mt) cc_final: 0.7944 (mt)
REVERT: B   90 ASP cc_start: 0.6534 (m-30) cc_final: 0.6088 (m-30)
REVERT: B   99 LEU cc_start: 0.8449 (tp) cc_final: 0.8240 (tp)
REVERT: M   36 TRP cc_start: 0.8377 (m100) cc_final: 0.7698 (m100)
REVERT: M   47 TRP cc_start: 0.8490 (t60) cc_final: 0.8282 (t60)
REVERT: M   48 ILE cc_start: 0.8494 (mm) cc_final: 0.6775 (mm)
REVERT: N  105 ASN cc_start: 0.7581 (m-40) cc_final: 0.7191 (m110)
REVERT: C  204 ASN cc_start: 0.8741 (m-40) cc_final: 0.8497 (m-40)
REVERT: C  230 VAL cc_start: 0.8622 (t) cc_final: 0.8414 (p)
REVERT: C  236 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7934 (mmt-90)
REVERT: C  262 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8144 (ttt-90)
REVERT: C  263 TYR cc_start: 0.7903 (m-80) cc_final: 0.7634 (m-80)
REVERT: D   26 HIS cc_start: 0.7970 (p90) cc_final: 0.7307 (p90)
REVERT: D  138 PHE cc_start: 0.8338 (m-80) cc_final: 0.8079 (m-80)
REVERT: D  147 THR cc_start: 0.8975 (m) cc_final: 0.8747 (p)
REVERT: H   36 TRP cc_start: 0.8464 (m100) cc_final: 0.8224 (m100)
REVERT: H   48 ILE cc_start: 0.8495 (mm) cc_final: 0.8276 (mm)
REVERT: H   94 TYR cc_start: 0.7169 (m-80) cc_final: 0.6961 (m-10)
REVERT: L   93 ASP cc_start: 0.8351 (m-30) cc_final: 0.8081 (m-30)
REVERT: L  113 ARG cc_start: 0.6793 (tpp80) cc_final: 0.6522 (tpp-160)
REVERT: E  204 ASN cc_start: 0.8576 (m-40) cc_final: 0.8363 (m110)
REVERT: E  300 LEU cc_start: 0.8675 (mt) cc_final: 0.8473 (mt)
REVERT: F   26 HIS cc_start: 0.8135 (p90) cc_final: 0.7561 (p90)
REVERT: F   27 GLN cc_start: 0.8415 (tt0) cc_final: 0.8211 (tm-30)
REVERT: F   99 LEU cc_start: 0.8121 (tp) cc_final: 0.7505 (tt)
REVERT: F  114 ASN cc_start: 0.8663 (m-40) cc_final: 0.8397 (m110)
REVERT: I   34 MET cc_start: 0.7986 (mmm) cc_final: 0.7436 (mmt)
REVERT: I   47 TRP cc_start: 0.8378 (t60) cc_final: 0.8112 (t60)
  outliers start: 3
  outliers final: 3
  residues processed: 745
  average time/residue: 0.1341
  time to fit residues: 147.5557
Evaluate side-chains
  405 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 402
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.0980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
A 238 ASN
A 290 GLN
** B  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
M  39 GLN
N  40 HIS
N  45 GLN
N  58 ASN
N  87 GLN
C 238 ASN
C 257 ASN
C 290 GLN
D 114 ASN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 HIS
L  45 GLN
L  58 ASN
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 238 ASN
E 290 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  39 GLN
J  40 HIS
J  45 GLN
J  46 GLN
J  58 ASN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.113705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.095726 restraints weight = 35446.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097157 restraints weight = 24003.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.098448 restraints weight = 18279.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099423 restraints weight = 12812.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099507 restraints weight = 11340.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  17463  Z= 0.138
  Angle     :  0.578   6.765  23727  Z= 0.298
  Chirality :  0.043   0.225   2622
  Planarity :  0.004   0.036   3027
  Dihedral  :  5.564  56.771   2760
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.79 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.18), residues: 2133
  helix:  3.33 (0.25), residues: 360
  sheet:  1.24 (0.23), residues: 495
  loop : -0.13 (0.17), residues: 1278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 112 
 TYR   0.018   0.001   TYR M  94 
 PHE   0.019   0.002   PHE A 210 
 TRP   0.020   0.001   TRP N  43 
 HIS   0.010   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (17418)
  covalent geometry    : angle       0.56517 (23616)
  SS BOND              : bond        0.00935 (   24)
  SS BOND              : angle       1.70664 (   48)
  hydrogen bonds       : bond        0.04205 (  702)
  hydrogen bonds       : angle       4.97077 ( 1926)
  link_BETA1-4         : bond        0.00730 (    3)
  link_BETA1-4         : angle       4.59663 (    9)
  link_NAG-ASN         : bond        0.00203 (   18)
  link_NAG-ASN         : angle       1.01742 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  509 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 506
  time to evaluate  : 0.513 
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: B   19 ASP cc_start: 0.8936 (p0) cc_final: 0.8735 (p0)
REVERT: B   99 LEU cc_start: 0.8512 (tp) cc_final: 0.8236 (tp)
REVERT: B  103 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7519 (tp30)
REVERT: B  147 THR cc_start: 0.8841 (p) cc_final: 0.8444 (p)
REVERT: M   36 TRP cc_start: 0.8430 (m100) cc_final: 0.7340 (m100)
REVERT: M   46 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: M   47 TRP cc_start: 0.8528 (t60) cc_final: 0.8288 (t60)
REVERT: M   82 GLN cc_start: 0.7211 (tp40) cc_final: 0.6929 (tm-30)
REVERT: M   87 ARG cc_start: 0.7307 (ptp-110) cc_final: 0.7013 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8150 (m-30) cc_final: 0.7851 (m-30)
REVERT: M   99 ASP cc_start: 0.7715 (m-30) cc_final: 0.7404 (m-30)
REVERT: N   46 GLN cc_start: 0.8434 (tt0) cc_final: 0.8098 (tt0)
REVERT: N   93 ASP cc_start: 0.8385 (m-30) cc_final: 0.7468 (p0)
REVERT: N  105 ASN cc_start: 0.7727 (m-40) cc_final: 0.7393 (m-40)
REVERT: C  155 TYR cc_start: 0.8065 (m-80) cc_final: 0.7769 (m-80)
REVERT: C  204 ASN cc_start: 0.8947 (m-40) cc_final: 0.8558 (m-40)
REVERT: D   17 MET cc_start: 0.8180 (ttp) cc_final: 0.7959 (ttp)
REVERT: D   30 GLN cc_start: 0.8537 (mp10) cc_final: 0.8287 (mp10)
REVERT: D  114 ASN cc_start: 0.8782 (m-40) cc_final: 0.8389 (m-40)
REVERT: D  147 THR cc_start: 0.9274 (m) cc_final: 0.8617 (p)
REVERT: H   36 TRP cc_start: 0.8451 (m100) cc_final: 0.7801 (m100)
REVERT: H   48 ILE cc_start: 0.8592 (mm) cc_final: 0.7648 (mm)
REVERT: H   76 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8150 (ptpt)
REVERT: H   83 MET cc_start: 0.7640 (mtt) cc_final: 0.7090 (mtt)
REVERT: H   87 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7583 (mtm-85)
REVERT: H   94 TYR cc_start: 0.7475 (m-80) cc_final: 0.6995 (m-10)
REVERT: H   99 ASP cc_start: 0.7877 (m-30) cc_final: 0.7488 (m-30)
REVERT: L   27 ILE cc_start: 0.8944 (mt) cc_final: 0.8677 (mt)
REVERT: L   43 TRP cc_start: 0.7780 (m100) cc_final: 0.7569 (m-10)
REVERT: L   81 LEU cc_start: 0.8959 (tt) cc_final: 0.7923 (tt)
REVERT: F   17 MET cc_start: 0.8347 (tmm) cc_final: 0.8123 (tmm)
REVERT: F   26 HIS cc_start: 0.8345 (p90) cc_final: 0.7431 (p90)
REVERT: F  114 ASN cc_start: 0.8812 (m-40) cc_final: 0.8452 (m110)
REVERT: I    6 GLU cc_start: 0.8431 (mp0) cc_final: 0.8176 (mp0)
REVERT: I   34 MET cc_start: 0.8050 (mmm) cc_final: 0.7469 (mmt)
REVERT: I   47 TRP cc_start: 0.8459 (t60) cc_final: 0.7880 (t60)
REVERT: I   48 ILE cc_start: 0.8747 (mm) cc_final: 0.7854 (mt)
REVERT: I   68 PHE cc_start: 0.7968 (m-10) cc_final: 0.7544 (m-10)
REVERT: I   82 GLN cc_start: 0.7261 (tp40) cc_final: 0.6902 (tm-30)
REVERT: J   93 ASP cc_start: 0.8412 (m-30) cc_final: 0.7371 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 507
  average time/residue: 0.1121
  time to fit residues: 88.8593
Evaluate side-chains
  360 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 360
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 163 optimal weight:    0.0000
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 181 optimal weight:    3.9990
   chunk 180 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.7790

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
B 124 ASN
B 125 GLN
B 142 HIS
** M  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  84 ASN
N  45 GLN
** N  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 HIS
C 290 GLN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  45 GLN
L 105 ASN
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 238 ASN
E 257 ASN
E 290 GLN
F  62 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  45 GLN
J 105 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.107978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.090069 restraints weight = 36026.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.090658 restraints weight = 25394.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.091950 restraints weight = 20603.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.092672 restraints weight = 15425.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.093430 restraints weight = 14577.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  17463  Z= 0.205
  Angle     :  0.603  11.140  23727  Z= 0.317
  Chirality :  0.043   0.280   2622
  Planarity :  0.004   0.051   3027
  Dihedral  :  5.526  51.659   2760
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.42 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.18), residues: 2133
  helix:  2.66 (0.26), residues: 357
  sheet:  1.34 (0.24), residues: 453
  loop : -0.36 (0.16), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG M  87 
 TYR   0.028   0.002   TYR H 112 
 PHE   0.033   0.002   PHE A 210 
 TRP   0.011   0.002   TRP C 241 
 HIS   0.009   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (17418)
  covalent geometry    : angle       0.59249 (23616)
  SS BOND              : bond        0.00263 (   24)
  SS BOND              : angle       1.44133 (   48)
  hydrogen bonds       : bond        0.04334 (  702)
  hydrogen bonds       : angle       5.06599 ( 1926)
  link_BETA1-4         : bond        0.00724 (    3)
  link_BETA1-4         : angle       4.57303 (    9)
  link_NAG-ASN         : bond        0.00174 (   18)
  link_NAG-ASN         : angle       1.03457 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  458 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 455
  time to evaluate  : 0.662 
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: symmetry clash
   revert: symmetry clash
REVERT: A  108 TYR cc_start: 0.7699 (t80) cc_final: 0.7450 (t80)
REVERT: B   19 ASP cc_start: 0.8915 (p0) cc_final: 0.8683 (p0)
REVERT: B   27 GLN cc_start: 0.8307 (tp40) cc_final: 0.8056 (tp-100)
REVERT: M   36 TRP cc_start: 0.8228 (m100) cc_final: 0.7490 (m100)
REVERT: M   47 TRP cc_start: 0.8643 (t60) cc_final: 0.8358 (t60)
REVERT: M   48 ILE cc_start: 0.8649 (mm) cc_final: 0.8235 (mm)
REVERT: M   90 ASP cc_start: 0.8164 (m-30) cc_final: 0.7700 (m-30)
REVERT: M   99 ASP cc_start: 0.7934 (m-30) cc_final: 0.7706 (m-30)
REVERT: N   46 GLN cc_start: 0.8444 (tt0) cc_final: 0.8182 (tt0)
REVERT: N   93 ASP cc_start: 0.8384 (m-30) cc_final: 0.7480 (p0)
REVERT: N  105 ASN cc_start: 0.7633 (m-40) cc_final: 0.7432 (m-40)
REVERT: C  108 TYR cc_start: 0.7807 (t80) cc_final: 0.7530 (t80)
REVERT: C  155 TYR cc_start: 0.8274 (m-80) cc_final: 0.7977 (m-80)
REVERT: C  204 ASN cc_start: 0.8992 (m-40) cc_final: 0.8661 (m-40)
REVERT: D   28 ASN cc_start: 0.8809 (p0) cc_final: 0.8566 (p0)
REVERT: D   30 GLN cc_start: 0.8578 (mp10) cc_final: 0.8317 (mp10)
REVERT: D  114 ASN cc_start: 0.8922 (m-40) cc_final: 0.8526 (m-40)
REVERT: D  147 THR cc_start: 0.9234 (m) cc_final: 0.8894 (p)
REVERT: H   36 TRP cc_start: 0.8426 (m100) cc_final: 0.7751 (m100)
REVERT: H   90 ASP cc_start: 0.8361 (m-30) cc_final: 0.7909 (m-30)
REVERT: L   27 ILE cc_start: 0.9064 (mt) cc_final: 0.8751 (mt)
REVERT: L   43 TRP cc_start: 0.7900 (m100) cc_final: 0.7388 (m-10)
REVERT: L   46 GLN cc_start: 0.8562 (tp40) cc_final: 0.7852 (tp40)
REVERT: L   81 LEU cc_start: 0.9054 (tt) cc_final: 0.7962 (tt)
REVERT: E  108 TYR cc_start: 0.8019 (t80) cc_final: 0.7744 (t80)
REVERT: F   17 MET cc_start: 0.8505 (tmm) cc_final: 0.8182 (tmm)
REVERT: F   26 HIS cc_start: 0.8444 (p90) cc_final: 0.8166 (p90)
REVERT: F   32 SER cc_start: 0.8471 (p) cc_final: 0.8269 (p)
REVERT: F  114 ASN cc_start: 0.8961 (m-40) cc_final: 0.8557 (m110)
REVERT: I    6 GLU cc_start: 0.8655 (mp0) cc_final: 0.8379 (mp0)
REVERT: I   34 MET cc_start: 0.8219 (mmm) cc_final: 0.7750 (mmt)
REVERT: I   46 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: I   48 ILE cc_start: 0.8847 (mm) cc_final: 0.8314 (mm)
REVERT: I   82 GLN cc_start: 0.7462 (tp40) cc_final: 0.6979 (tm-30)
REVERT: I   83 MET cc_start: 0.7361 (mtp) cc_final: 0.7043 (mtm)
REVERT: I   90 ASP cc_start: 0.8101 (m-30) cc_final: 0.7894 (m-30)
REVERT: J   43 TRP cc_start: 0.8088 (m100) cc_final: 0.7684 (m100)
  outliers start: 3
  outliers final: 1
  residues processed: 456
  average time/residue: 0.1122
  time to fit residues: 81.5310
Evaluate side-chains
  347 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 346
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 139 optimal weight:    0.0020
   chunk 192 optimal weight:    6.9990
   chunk 200 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9980
   chunk 190 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 257 ASN
A 290 GLN
B 125 GLN
C 257 ASN
C 290 GLN
D 125 GLN
D 142 HIS
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
F  62 GLN
F 125 GLN
F 142 HIS
I  39 GLN
** J  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.104759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.086649 restraints weight = 36480.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.087207 restraints weight = 25538.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.088474 restraints weight = 20743.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.089284 restraints weight = 15341.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.089804 restraints weight = 14454.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  17463  Z= 0.220
  Angle     :  0.651   8.613  23727  Z= 0.340
  Chirality :  0.045   0.233   2622
  Planarity :  0.004   0.036   3027
  Dihedral  :  5.284  41.058   2760
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.23 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.17), residues: 2133
  helix:  1.96 (0.26), residues: 357
  sheet:  1.25 (0.23), residues: 489
  loop : -0.64 (0.16), residues: 1287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG I  87 
 TYR   0.037   0.002   TYR I 112 
 PHE   0.015   0.002   PHE E 265 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.011   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (17418)
  covalent geometry    : angle       0.63418 (23616)
  SS BOND              : bond        0.00523 (   24)
  SS BOND              : angle       2.04783 (   48)
  hydrogen bonds       : bond        0.04429 (  702)
  hydrogen bonds       : angle       5.44321 ( 1926)
  link_BETA1-4         : bond        0.00668 (    3)
  link_BETA1-4         : angle       5.61899 (    9)
  link_NAG-ASN         : bond        0.00208 (   18)
  link_NAG-ASN         : angle       1.05955 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 440
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 TYR cc_start: 0.7860 (t80) cc_final: 0.7503 (t80)
REVERT: A  203 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: B   19 ASP cc_start: 0.8938 (p0) cc_final: 0.8652 (p0)
REVERT: B   28 ASN cc_start: 0.8982 (p0) cc_final: 0.8687 (p0)
REVERT: B   32 SER cc_start: 0.9005 (p) cc_final: 0.8672 (p)
REVERT: B   90 ASP cc_start: 0.7333 (m-30) cc_final: 0.7055 (m-30)
REVERT: B  133 ILE cc_start: 0.8980 (mt) cc_final: 0.8404 (mt)
REVERT: M   36 TRP cc_start: 0.8266 (m100) cc_final: 0.7642 (m100)
REVERT: M   46 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: M   47 TRP cc_start: 0.8590 (t60) cc_final: 0.8176 (t60)
REVERT: M   82 GLN cc_start: 0.7416 (tp40) cc_final: 0.7018 (tm-30)
REVERT: M   83 MET cc_start: 0.7987 (mtt) cc_final: 0.7617 (mtt)
REVERT: M   87 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7580 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8304 (m-30) cc_final: 0.7875 (m-30)
REVERT: M   99 ASP cc_start: 0.8284 (m-30) cc_final: 0.7625 (m-30)
REVERT: N   36 PHE cc_start: 0.7497 (t80) cc_final: 0.7289 (t80)
REVERT: N   46 GLN cc_start: 0.8526 (tt0) cc_final: 0.8239 (tt0)
REVERT: N   93 ASP cc_start: 0.8218 (m-30) cc_final: 0.7462 (p0)
REVERT: C  108 TYR cc_start: 0.7933 (t80) cc_final: 0.7699 (t80)
REVERT: C  155 TYR cc_start: 0.8295 (m-80) cc_final: 0.7978 (m-80)
REVERT: C  204 ASN cc_start: 0.9022 (m-40) cc_final: 0.8667 (m-40)
REVERT: D   19 ASP cc_start: 0.8692 (p0) cc_final: 0.8468 (p0)
REVERT: D  109 ASP cc_start: 0.7651 (m-30) cc_final: 0.7449 (m-30)
REVERT: D  114 ASN cc_start: 0.9041 (m-40) cc_final: 0.8457 (m-40)
REVERT: D  147 THR cc_start: 0.9280 (m) cc_final: 0.8710 (t)
REVERT: H   36 TRP cc_start: 0.8449 (m100) cc_final: 0.7971 (m100)
REVERT: H   46 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: H   48 ILE cc_start: 0.8661 (mm) cc_final: 0.8227 (mm)
REVERT: H   90 ASP cc_start: 0.8551 (m-30) cc_final: 0.8065 (m-30)
REVERT: L   43 TRP cc_start: 0.7670 (m100) cc_final: 0.6325 (m100)
REVERT: L   46 GLN cc_start: 0.8594 (tp40) cc_final: 0.7945 (tp40)
REVERT: E   77 CYS cc_start: 0.5934 (m) cc_final: 0.5706 (m)
REVERT: E  108 TYR cc_start: 0.8198 (t80) cc_final: 0.7949 (t80)
REVERT: F   17 MET cc_start: 0.8692 (tmm) cc_final: 0.8254 (tmm)
REVERT: F   19 ASP cc_start: 0.8586 (p0) cc_final: 0.8381 (p0)
REVERT: F   27 GLN cc_start: 0.8437 (tp40) cc_final: 0.8114 (tp-100)
REVERT: F   28 ASN cc_start: 0.8989 (p0) cc_final: 0.8475 (p0)
REVERT: F   30 GLN cc_start: 0.8966 (mp10) cc_final: 0.8587 (mp10)
REVERT: F   60 ASN cc_start: 0.8748 (m-40) cc_final: 0.8493 (t0)
REVERT: F   78 GLU cc_start: 0.8538 (tp30) cc_final: 0.8328 (tp30)
REVERT: F  133 ILE cc_start: 0.9024 (mt) cc_final: 0.8607 (mm)
REVERT: I    6 GLU cc_start: 0.8684 (mp0) cc_final: 0.8436 (mp0)
REVERT: I   34 MET cc_start: 0.8220 (mmm) cc_final: 0.7694 (mmt)
REVERT: I   36 TRP cc_start: 0.8757 (m100) cc_final: 0.8325 (m100)
REVERT: I   46 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: I   48 ILE cc_start: 0.8839 (mm) cc_final: 0.8565 (mt)
REVERT: I   82 GLN cc_start: 0.7594 (tp40) cc_final: 0.6875 (tm-30)
REVERT: I   90 ASP cc_start: 0.8240 (m-30) cc_final: 0.8038 (m-30)
REVERT: J   43 TRP cc_start: 0.8245 (m100) cc_final: 0.7745 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 440
  average time/residue: 0.1097
  time to fit residues: 77.4475
Evaluate side-chains
  331 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 200 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 178 optimal weight:    0.2980
   chunk 197 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 149 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 183 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  35 HIS
N  13 GLN
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 GLN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  87 GLN
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 257 ASN
E 283 HIS
E 290 GLN
F  26 HIS
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 105 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.108219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.090907 restraints weight = 35733.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.091049 restraints weight = 25536.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.092304 restraints weight = 21505.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093040 restraints weight = 15439.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.093300 restraints weight = 13593.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  17463  Z= 0.132
  Angle     :  0.618  12.341  23727  Z= 0.319
  Chirality :  0.044   0.243   2622
  Planarity :  0.004   0.060   3027
  Dihedral  :  4.899  34.676   2760
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.57 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.17), residues: 2133
  helix:  1.97 (0.26), residues: 357
  sheet:  1.19 (0.23), residues: 501
  loop : -0.61 (0.16), residues: 1275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  87 
 TYR   0.024   0.001   TYR I 112 
 PHE   0.026   0.002   PHE C 105 
 TRP   0.023   0.001   TRP C 241 
 HIS   0.015   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (17418)
  covalent geometry    : angle       0.59986 (23616)
  SS BOND              : bond        0.00819 (   24)
  SS BOND              : angle       2.36394 (   48)
  hydrogen bonds       : bond        0.04060 (  702)
  hydrogen bonds       : angle       5.33180 ( 1926)
  link_BETA1-4         : bond        0.00522 (    3)
  link_BETA1-4         : angle       4.98562 (    9)
  link_NAG-ASN         : bond        0.00179 (   18)
  link_NAG-ASN         : angle       1.04505 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 421
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 TYR cc_start: 0.7661 (t80) cc_final: 0.7419 (t80)
REVERT: A  124 PHE cc_start: 0.8034 (t80) cc_final: 0.7768 (t80)
REVERT: B   19 ASP cc_start: 0.8819 (p0) cc_final: 0.8545 (p0)
REVERT: B   28 ASN cc_start: 0.8982 (p0) cc_final: 0.8764 (p0)
REVERT: B   90 ASP cc_start: 0.7600 (m-30) cc_final: 0.6582 (m-30)
REVERT: M   36 TRP cc_start: 0.8012 (m100) cc_final: 0.7605 (m100)
REVERT: M   47 TRP cc_start: 0.8533 (t60) cc_final: 0.8274 (t60)
REVERT: M   82 GLN cc_start: 0.7572 (tp40) cc_final: 0.7009 (tm-30)
REVERT: M   83 MET cc_start: 0.7715 (mtt) cc_final: 0.7400 (mtt)
REVERT: M   87 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7760 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8113 (m-30) cc_final: 0.7776 (m-30)
REVERT: M   99 ASP cc_start: 0.8449 (m-30) cc_final: 0.8009 (m-30)
REVERT: N   46 GLN cc_start: 0.8377 (tt0) cc_final: 0.8149 (tt0)
REVERT: N   93 ASP cc_start: 0.7801 (m-30) cc_final: 0.7237 (p0)
REVERT: N   99 TRP cc_start: 0.7799 (t-100) cc_final: 0.6875 (t-100)
REVERT: N  105 ASN cc_start: 0.7608 (m-40) cc_final: 0.6878 (m-40)
REVERT: C  108 TYR cc_start: 0.7976 (t80) cc_final: 0.7611 (t80)
REVERT: C  155 TYR cc_start: 0.8222 (m-80) cc_final: 0.7885 (m-80)
REVERT: C  204 ASN cc_start: 0.8993 (m-40) cc_final: 0.8615 (m-40)
REVERT: D   19 ASP cc_start: 0.8575 (p0) cc_final: 0.8341 (p0)
REVERT: D   28 ASN cc_start: 0.8734 (p0) cc_final: 0.8400 (p0)
REVERT: D  133 ILE cc_start: 0.8868 (mp) cc_final: 0.8231 (mm)
REVERT: H   36 TRP cc_start: 0.8430 (m100) cc_final: 0.7948 (m100)
REVERT: H   46 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: H   48 ILE cc_start: 0.8681 (mm) cc_final: 0.8290 (mm)
REVERT: H   90 ASP cc_start: 0.8371 (m-30) cc_final: 0.7933 (m-30)
REVERT: L   43 TRP cc_start: 0.7381 (m100) cc_final: 0.6342 (m100)
REVERT: L   46 GLN cc_start: 0.8685 (tp40) cc_final: 0.8282 (tp-100)
REVERT: E   77 CYS cc_start: 0.5711 (m) cc_final: 0.5470 (m)
REVERT: E  155 TYR cc_start: 0.8516 (m-80) cc_final: 0.8254 (m-80)
REVERT: F   19 ASP cc_start: 0.8443 (p0) cc_final: 0.8216 (p0)
REVERT: F   27 GLN cc_start: 0.8302 (tp40) cc_final: 0.7912 (tp-100)
REVERT: F   28 ASN cc_start: 0.8891 (p0) cc_final: 0.8657 (p0)
REVERT: I    6 GLU cc_start: 0.8673 (mp0) cc_final: 0.8443 (mp0)
REVERT: I   36 TRP cc_start: 0.8702 (m100) cc_final: 0.8485 (m100)
REVERT: I   46 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: I   48 ILE cc_start: 0.9018 (mm) cc_final: 0.8350 (mm)
REVERT: I   82 GLN cc_start: 0.7660 (tp40) cc_final: 0.6876 (tm-30)
REVERT: I   90 ASP cc_start: 0.8164 (m-30) cc_final: 0.7927 (m-30)
REVERT: J   43 TRP cc_start: 0.7914 (m100) cc_final: 0.7434 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 421
  average time/residue: 0.1132
  time to fit residues: 75.8003
Evaluate side-chains
  327 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 181 optimal weight:    1.9990
   chunk 184 optimal weight:    0.9980
   chunk 191 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   chunk 177 optimal weight:    6.9990
   chunk 193 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9990
   chunk 115 optimal weight:    4.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 257 ASN
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
C 257 ASN
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
L  45 GLN
L  87 GLN
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.106694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.089277 restraints weight = 36138.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.089560 restraints weight = 26184.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.090762 restraints weight = 21505.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.091462 restraints weight = 15450.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.091666 restraints weight = 13708.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  17463  Z= 0.169
  Angle     :  0.618   8.921  23727  Z= 0.321
  Chirality :  0.044   0.177   2622
  Planarity :  0.004   0.053   3027
  Dihedral  :  4.802  35.580   2760
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.17), residues: 2133
  helix:  1.83 (0.26), residues: 357
  sheet:  1.02 (0.22), residues: 516
  loop : -0.65 (0.17), residues: 1260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  87 
 TYR   0.024   0.002   TYR I 112 
 PHE   0.032   0.002   PHE L  36 
 TRP   0.022   0.002   TRP M  47 
 HIS   0.011   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (17418)
  covalent geometry    : angle       0.60145 (23616)
  SS BOND              : bond        0.00465 (   24)
  SS BOND              : angle       2.25771 (   48)
  hydrogen bonds       : bond        0.04209 (  702)
  hydrogen bonds       : angle       5.35827 ( 1926)
  link_BETA1-4         : bond        0.00245 (    3)
  link_BETA1-4         : angle       4.84908 (    9)
  link_NAG-ASN         : bond        0.00214 (   18)
  link_NAG-ASN         : angle       1.07964 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 403
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ASP cc_start: 0.8852 (p0) cc_final: 0.8602 (p0)
REVERT: B  133 ILE cc_start: 0.8763 (mp) cc_final: 0.8485 (mm)
REVERT: M   36 TRP cc_start: 0.8067 (m100) cc_final: 0.7497 (m100)
REVERT: M   47 TRP cc_start: 0.8463 (t60) cc_final: 0.8052 (t60)
REVERT: M   48 ILE cc_start: 0.8859 (mm) cc_final: 0.8226 (mm)
REVERT: M   82 GLN cc_start: 0.7620 (tp40) cc_final: 0.6951 (tm-30)
REVERT: M   83 MET cc_start: 0.7757 (mtt) cc_final: 0.7172 (mtm)
REVERT: M   90 ASP cc_start: 0.8005 (m-30) cc_final: 0.7781 (m-30)
REVERT: M   99 ASP cc_start: 0.8076 (m-30) cc_final: 0.7635 (m-30)
REVERT: N   99 TRP cc_start: 0.8045 (t-100) cc_final: 0.7059 (t-100)
REVERT: N  105 ASN cc_start: 0.7678 (m-40) cc_final: 0.6969 (m-40)
REVERT: C  108 TYR cc_start: 0.8080 (t80) cc_final: 0.7739 (t80)
REVERT: C  155 TYR cc_start: 0.8264 (m-80) cc_final: 0.7928 (m-80)
REVERT: C  204 ASN cc_start: 0.8995 (m-40) cc_final: 0.8634 (m-40)
REVERT: D   19 ASP cc_start: 0.8670 (p0) cc_final: 0.8458 (p0)
REVERT: H   34 MET cc_start: 0.7910 (mmt) cc_final: 0.7614 (mtp)
REVERT: H   90 ASP cc_start: 0.8398 (m-30) cc_final: 0.7981 (m-30)
REVERT: L   43 TRP cc_start: 0.7573 (m100) cc_final: 0.6614 (m100)
REVERT: L   46 GLN cc_start: 0.8782 (tp40) cc_final: 0.8361 (tp40)
REVERT: E   77 CYS cc_start: 0.5756 (m) cc_final: 0.5476 (m)
REVERT: E  108 TYR cc_start: 0.8148 (t80) cc_final: 0.7608 (t80)
REVERT: E  155 TYR cc_start: 0.8384 (m-80) cc_final: 0.8050 (m-80)
REVERT: F   17 MET cc_start: 0.8753 (tmm) cc_final: 0.8201 (ppp)
REVERT: F   19 ASP cc_start: 0.8490 (p0) cc_final: 0.8141 (p0)
REVERT: F   27 GLN cc_start: 0.8348 (tp40) cc_final: 0.8008 (tp-100)
REVERT: F   28 ASN cc_start: 0.8951 (p0) cc_final: 0.8687 (p0)
REVERT: F  103 GLU cc_start: 0.8510 (mp0) cc_final: 0.8269 (mp0)
REVERT: F  110 TYR cc_start: 0.9177 (t80) cc_final: 0.8969 (t80)
REVERT: I    6 GLU cc_start: 0.8730 (mp0) cc_final: 0.8517 (mp0)
REVERT: I   32 TYR cc_start: 0.8530 (m-10) cc_final: 0.8152 (m-10)
REVERT: I   46 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: I   48 ILE cc_start: 0.8798 (mm) cc_final: 0.8171 (mm)
REVERT: I   82 GLN cc_start: 0.7629 (tp40) cc_final: 0.6891 (tm-30)
REVERT: I   90 ASP cc_start: 0.8224 (m-30) cc_final: 0.7983 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 403
  average time/residue: 0.1078
  time to fit residues: 69.8880
Evaluate side-chains
  320 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 127 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0470
   chunk 180 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 198 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 171 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.9282

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
L  45 GLN
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.108309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.089640 restraints weight = 35918.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.091878 restraints weight = 24967.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.093213 restraints weight = 16467.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.093505 restraints weight = 12150.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.093714 restraints weight = 12171.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  17463  Z= 0.138
  Angle     :  0.609   7.147  23727  Z= 0.318
  Chirality :  0.044   0.158   2622
  Planarity :  0.004   0.067   3027
  Dihedral  :  4.672  33.691   2760
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.41 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.17), residues: 2133
  helix:  1.76 (0.27), residues: 357
  sheet:  1.10 (0.22), residues: 504
  loop : -0.68 (0.16), residues: 1272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  87 
 TYR   0.027   0.001   TYR M  94 
 PHE   0.031   0.002   PHE E 124 
 TRP   0.043   0.002   TRP N  43 
 HIS   0.012   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (17418)
  covalent geometry    : angle       0.59405 (23616)
  SS BOND              : bond        0.00456 (   24)
  SS BOND              : angle       1.96357 (   48)
  hydrogen bonds       : bond        0.04038 (  702)
  hydrogen bonds       : angle       5.33293 ( 1926)
  link_BETA1-4         : bond        0.00515 (    3)
  link_BETA1-4         : angle       4.78002 (    9)
  link_NAG-ASN         : bond        0.00199 (   18)
  link_NAG-ASN         : angle       1.06394 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 400
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ASP cc_start: 0.8845 (p0) cc_final: 0.8605 (p0)
REVERT: M   36 TRP cc_start: 0.7984 (m100) cc_final: 0.7583 (m100)
REVERT: M   47 TRP cc_start: 0.8457 (t60) cc_final: 0.8113 (t60)
REVERT: M   48 ILE cc_start: 0.8783 (mm) cc_final: 0.7983 (mm)
REVERT: M   82 GLN cc_start: 0.7513 (tp40) cc_final: 0.6874 (tm-30)
REVERT: M   83 MET cc_start: 0.7685 (mtt) cc_final: 0.7418 (mtm)
REVERT: M   87 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7206 (mtm-85)
REVERT: M   99 ASP cc_start: 0.8306 (m-30) cc_final: 0.7612 (m-30)
REVERT: N   46 GLN cc_start: 0.8647 (tt0) cc_final: 0.8125 (tt0)
REVERT: N   99 TRP cc_start: 0.7968 (t-100) cc_final: 0.6948 (t-100)
REVERT: N  105 ASN cc_start: 0.7644 (m-40) cc_final: 0.6977 (m-40)
REVERT: C   65 CYS cc_start: 0.6589 (m) cc_final: 0.6225 (m)
REVERT: C  108 TYR cc_start: 0.8039 (t80) cc_final: 0.7614 (t80)
REVERT: C  155 TYR cc_start: 0.8199 (m-80) cc_final: 0.7867 (m-80)
REVERT: C  204 ASN cc_start: 0.8947 (m-40) cc_final: 0.8687 (m-40)
REVERT: D   19 ASP cc_start: 0.8763 (p0) cc_final: 0.8556 (p0)
REVERT: H   36 TRP cc_start: 0.8823 (m100) cc_final: 0.8403 (m100)
REVERT: H   87 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7423 (mtm-85)
REVERT: H   90 ASP cc_start: 0.8304 (m-30) cc_final: 0.7879 (m-30)
REVERT: L   43 TRP cc_start: 0.7571 (m100) cc_final: 0.6728 (m100)
REVERT: L   55 LEU cc_start: 0.8332 (mp) cc_final: 0.8114 (mp)
REVERT: E   77 CYS cc_start: 0.5667 (m) cc_final: 0.5377 (m)
REVERT: E  108 TYR cc_start: 0.8131 (t80) cc_final: 0.7605 (t80)
REVERT: E  155 TYR cc_start: 0.8298 (m-80) cc_final: 0.7879 (m-80)
REVERT: F   17 MET cc_start: 0.8736 (tmm) cc_final: 0.8491 (tmm)
REVERT: F   27 GLN cc_start: 0.8366 (tp40) cc_final: 0.8015 (tp-100)
REVERT: F   28 ASN cc_start: 0.8921 (p0) cc_final: 0.8701 (p0)
REVERT: I    6 GLU cc_start: 0.8723 (mp0) cc_final: 0.8491 (mp0)
REVERT: I   82 GLN cc_start: 0.7530 (tp40) cc_final: 0.6782 (tm-30)
REVERT: I   90 ASP cc_start: 0.8174 (m-30) cc_final: 0.7948 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 400
  average time/residue: 0.1117
  time to fit residues: 71.1573
Evaluate side-chains
  315 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 315
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 188 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 139 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0000
   chunk 67 optimal weight:    0.7980
   chunk 180 optimal weight:    2.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 283 HIS
E 290 GLN
** F 125 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 = 0.3495 r_free = 0.3495 target = 0.109554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.091501 restraints weight = 35967.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.092190 restraints weight = 24611.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.093623 restraints weight = 19586.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.094392 restraints weight = 13859.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.094744 restraints weight = 12551.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  17463  Z= 0.126
  Angle     :  0.611   8.259  23727  Z= 0.320
  Chirality :  0.044   0.162   2622
  Planarity :  0.004   0.060   3027
  Dihedral  :  4.561  32.892   2760
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.33 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.17), residues: 2133
  helix:  1.68 (0.26), residues: 357
  sheet:  0.98 (0.22), residues: 534
  loop : -0.59 (0.17), residues: 1242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  87 
 TYR   0.025   0.001   TYR M  94 
 PHE   0.019   0.001   PHE L  36 
 TRP   0.033   0.002   TRP N  43 
 HIS   0.010   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (17418)
  covalent geometry    : angle       0.59625 (23616)
  SS BOND              : bond        0.00450 (   24)
  SS BOND              : angle       2.04635 (   48)
  hydrogen bonds       : bond        0.04082 (  702)
  hydrogen bonds       : angle       5.24994 ( 1926)
  link_BETA1-4         : bond        0.00550 (    3)
  link_BETA1-4         : angle       4.62137 (    9)
  link_NAG-ASN         : bond        0.00169 (   18)
  link_NAG-ASN         : angle       1.03192 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 398
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ASP cc_start: 0.8875 (p0) cc_final: 0.8649 (p0)
REVERT: M   36 TRP cc_start: 0.7862 (m100) cc_final: 0.7365 (m100)
REVERT: M   47 TRP cc_start: 0.8486 (t60) cc_final: 0.7955 (t60)
REVERT: M   48 ILE cc_start: 0.8798 (mm) cc_final: 0.8083 (mm)
REVERT: M   82 GLN cc_start: 0.7469 (tp40) cc_final: 0.6807 (tm-30)
REVERT: M   83 MET cc_start: 0.7820 (mtt) cc_final: 0.7481 (mtm)
REVERT: M   87 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7077 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8244 (m-30) cc_final: 0.7790 (m-30)
REVERT: M   99 ASP cc_start: 0.8004 (m-30) cc_final: 0.7435 (m-30)
REVERT: N   46 GLN cc_start: 0.8179 (tt0) cc_final: 0.7854 (tt0)
REVERT: N   99 TRP cc_start: 0.7905 (t-100) cc_final: 0.6900 (t-100)
REVERT: N  105 ASN cc_start: 0.7578 (m-40) cc_final: 0.6882 (m-40)
REVERT: C  108 TYR cc_start: 0.8100 (t80) cc_final: 0.7604 (t80)
REVERT: C  155 TYR cc_start: 0.8241 (m-80) cc_final: 0.7904 (m-80)
REVERT: C  204 ASN cc_start: 0.8896 (m-40) cc_final: 0.8487 (m-40)
REVERT: D   27 GLN cc_start: 0.8442 (tp40) cc_final: 0.8234 (tp-100)
REVERT: H   31 THR cc_start: 0.9091 (m) cc_final: 0.8890 (t)
REVERT: H   36 TRP cc_start: 0.8744 (m100) cc_final: 0.8257 (m100)
REVERT: H   83 MET cc_start: 0.7622 (mtt) cc_final: 0.7364 (mtt)
REVERT: H   87 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7310 (mtm-85)
REVERT: H   90 ASP cc_start: 0.8113 (m-30) cc_final: 0.7842 (m-30)
REVERT: L   13 GLN cc_start: 0.7977 (mt0) cc_final: 0.7762 (pt0)
REVERT: L   43 TRP cc_start: 0.7555 (m100) cc_final: 0.7087 (m100)
REVERT: E   77 CYS cc_start: 0.5863 (m) cc_final: 0.5560 (m)
REVERT: E  108 TYR cc_start: 0.8143 (t80) cc_final: 0.7527 (t80)
REVERT: E  124 PHE cc_start: 0.7637 (t80) cc_final: 0.7396 (t80)
REVERT: E  155 TYR cc_start: 0.8345 (m-80) cc_final: 0.7883 (m-80)
REVERT: F   17 MET cc_start: 0.8691 (tmm) cc_final: 0.8366 (tmm)
REVERT: F   27 GLN cc_start: 0.8354 (tp40) cc_final: 0.8004 (tp-100)
REVERT: F   28 ASN cc_start: 0.8959 (p0) cc_final: 0.8736 (p0)
REVERT: I    6 GLU cc_start: 0.8714 (mp0) cc_final: 0.8498 (mp0)
REVERT: I   32 TYR cc_start: 0.8552 (m-10) cc_final: 0.8178 (m-10)
REVERT: I   82 GLN cc_start: 0.7465 (tp40) cc_final: 0.6711 (tm-30)
REVERT: J   87 GLN cc_start: 0.7111 (mp-120) cc_final: 0.6906 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 398
  average time/residue: 0.1098
  time to fit residues: 69.9321
Evaluate side-chains
  319 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 159 optimal weight:    0.6980
   chunk 174 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 182 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 184 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
A 283 HIS
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  46 GLN
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.108643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.091403 restraints weight = 36085.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.091150 restraints weight = 25895.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.092473 restraints weight = 22462.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.093406 restraints weight = 16105.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.093709 restraints weight = 14010.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  17463  Z= 0.135
  Angle     :  0.621  12.085  23727  Z= 0.324
  Chirality :  0.044   0.191   2622
  Planarity :  0.004   0.054   3027
  Dihedral  :  4.588  36.941   2760
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.43 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.17), residues: 2133
  helix:  1.55 (0.26), residues: 357
  sheet:  1.00 (0.22), residues: 516
  loop : -0.64 (0.16), residues: 1260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  87 
 TYR   0.022   0.001   TYR H  94 
 PHE   0.030   0.002   PHE C 210 
 TRP   0.034   0.002   TRP C 241 
 HIS   0.004   0.001   HIS F  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (17418)
  covalent geometry    : angle       0.60702 (23616)
  SS BOND              : bond        0.00486 (   24)
  SS BOND              : angle       2.04710 (   48)
  hydrogen bonds       : bond        0.04031 (  702)
  hydrogen bonds       : angle       5.21053 ( 1926)
  link_BETA1-4         : bond        0.00489 (    3)
  link_BETA1-4         : angle       4.49868 (    9)
  link_NAG-ASN         : bond        0.00184 (   18)
  link_NAG-ASN         : angle       1.01789 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 384
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   77 CYS cc_start: 0.5471 (m) cc_final: 0.5263 (m)
REVERT: A  108 TYR cc_start: 0.7215 (t80) cc_final: 0.6989 (t80)
REVERT: B   19 ASP cc_start: 0.8811 (p0) cc_final: 0.8557 (p0)
REVERT: B  135 ASN cc_start: 0.7039 (p0) cc_final: 0.6818 (p0)
REVERT: M   36 TRP cc_start: 0.7750 (m100) cc_final: 0.7436 (m100)
REVERT: M   47 TRP cc_start: 0.8422 (t60) cc_final: 0.8054 (t60)
REVERT: M   48 ILE cc_start: 0.8775 (mm) cc_final: 0.8087 (mm)
REVERT: M   82 GLN cc_start: 0.7441 (tp40) cc_final: 0.6897 (tm-30)
REVERT: M   87 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7095 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8056 (m-30) cc_final: 0.7824 (m-30)
REVERT: M   99 ASP cc_start: 0.8315 (m-30) cc_final: 0.7816 (m-30)
REVERT: N   99 TRP cc_start: 0.7961 (t-100) cc_final: 0.6936 (t-100)
REVERT: N  105 ASN cc_start: 0.7647 (m-40) cc_final: 0.6972 (m-40)
REVERT: C  108 TYR cc_start: 0.8030 (t80) cc_final: 0.7688 (t80)
REVERT: C  155 TYR cc_start: 0.8309 (m-80) cc_final: 0.7960 (m-80)
REVERT: C  204 ASN cc_start: 0.8909 (m-40) cc_final: 0.8542 (m-40)
REVERT: D   27 GLN cc_start: 0.8382 (tp40) cc_final: 0.8153 (tp-100)
REVERT: H   36 TRP cc_start: 0.8609 (m100) cc_final: 0.8240 (m100)
REVERT: H   87 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7405 (mtm-85)
REVERT: H   90 ASP cc_start: 0.8049 (m-30) cc_final: 0.7754 (m-30)
REVERT: E   77 CYS cc_start: 0.5740 (m) cc_final: 0.5399 (m)
REVERT: E  108 TYR cc_start: 0.8116 (t80) cc_final: 0.7650 (t80)
REVERT: E  124 PHE cc_start: 0.7693 (t80) cc_final: 0.7491 (t80)
REVERT: E  155 TYR cc_start: 0.8318 (m-80) cc_final: 0.7878 (m-80)
REVERT: F   17 MET cc_start: 0.8686 (tmm) cc_final: 0.8364 (tmm)
REVERT: F   27 GLN cc_start: 0.8309 (tp40) cc_final: 0.7962 (tp-100)
REVERT: F   28 ASN cc_start: 0.8944 (p0) cc_final: 0.8716 (p0)
REVERT: F  114 ASN cc_start: 0.8904 (m-40) cc_final: 0.8457 (m110)
REVERT: I   82 GLN cc_start: 0.7493 (tp40) cc_final: 0.6775 (tm-30)
REVERT: I   90 ASP cc_start: 0.7964 (m-30) cc_final: 0.7722 (m-30)
REVERT: J   43 TRP cc_start: 0.7660 (m100) cc_final: 0.7446 (m100)
REVERT: J   93 ASP cc_start: 0.7702 (m-30) cc_final: 0.7410 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 384
  average time/residue: 0.1085
  time to fit residues: 67.0624
Evaluate side-chains
  316 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 154 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 209 optimal weight:    0.9990
   chunk 201 optimal weight:   10.0000
   chunk 191 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 131 optimal weight:   10.0000
   chunk 188 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  46 GLN
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  46 GLN
J  87 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.106601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.089369 restraints weight = 36111.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.089274 restraints weight = 26207.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.090733 restraints weight = 22666.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.091106 restraints weight = 15615.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.091493 restraints weight = 14986.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17463  Z= 0.175
  Angle     :  0.641   9.394  23727  Z= 0.335
  Chirality :  0.045   0.178   2622
  Planarity :  0.004   0.050   3027
  Dihedral  :  4.740  38.799   2760
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.27 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.17), residues: 2133
  helix:  1.36 (0.26), residues: 357
  sheet:  0.97 (0.22), residues: 510
  loop : -0.68 (0.16), residues: 1266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  87 
 TYR   0.021   0.002   TYR H 112 
 PHE   0.029   0.002   PHE A 124 
 TRP   0.036   0.002   TRP C 241 
 HIS   0.009   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (17418)
  covalent geometry    : angle       0.62721 (23616)
  SS BOND              : bond        0.00528 (   24)
  SS BOND              : angle       2.12239 (   48)
  hydrogen bonds       : bond        0.04240 (  702)
  hydrogen bonds       : angle       5.29052 ( 1926)
  link_BETA1-4         : bond        0.00424 (    3)
  link_BETA1-4         : angle       4.43407 (    9)
  link_NAG-ASN         : bond        0.00227 (   18)
  link_NAG-ASN         : angle       1.05452 (   54)

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

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

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4266 Ramachandran restraints generated.
    2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 380
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 ASN cc_start: 0.7035 (p0) cc_final: 0.6766 (p0)
REVERT: M   82 GLN cc_start: 0.7534 (tp40) cc_final: 0.6918 (tm-30)
REVERT: M   87 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7182 (mtm-85)
REVERT: M   90 ASP cc_start: 0.8401 (m-30) cc_final: 0.7940 (m-30)
REVERT: M   99 ASP cc_start: 0.8327 (m-30) cc_final: 0.7811 (m-30)
REVERT: N   93 ASP cc_start: 0.8068 (m-30) cc_final: 0.7006 (p0)
REVERT: N   99 TRP cc_start: 0.8080 (t-100) cc_final: 0.7060 (t-100)
REVERT: N  105 ASN cc_start: 0.7589 (m-40) cc_final: 0.7013 (m-40)
REVERT: C  108 TYR cc_start: 0.8044 (t80) cc_final: 0.7617 (t80)
REVERT: C  204 ASN cc_start: 0.8970 (m-40) cc_final: 0.8661 (m-40)
REVERT: D   27 GLN cc_start: 0.8528 (tp40) cc_final: 0.8312 (tp-100)
REVERT: H   36 TRP cc_start: 0.8615 (m100) cc_final: 0.8336 (m100)
REVERT: H   90 ASP cc_start: 0.8114 (m-30) cc_final: 0.7884 (m-30)
REVERT: E   77 CYS cc_start: 0.5788 (m) cc_final: 0.5453 (m)
REVERT: E  108 TYR cc_start: 0.8162 (t80) cc_final: 0.7616 (t80)
REVERT: E  155 TYR cc_start: 0.8338 (m-80) cc_final: 0.7870 (m-80)
REVERT: E  241 TRP cc_start: 0.9109 (p-90) cc_final: 0.8855 (p-90)
REVERT: F   17 MET cc_start: 0.8767 (tmm) cc_final: 0.8345 (tmm)
REVERT: F   27 GLN cc_start: 0.8366 (tp40) cc_final: 0.8039 (tp-100)
REVERT: F  114 ASN cc_start: 0.8970 (m-40) cc_final: 0.8502 (m110)
REVERT: I   82 GLN cc_start: 0.7588 (tp40) cc_final: 0.6821 (tm-30)
REVERT: I   90 ASP cc_start: 0.8038 (m-30) cc_final: 0.7785 (m-30)
REVERT: J   43 TRP cc_start: 0.7634 (m100) cc_final: 0.7394 (m100)
REVERT: J   99 TRP cc_start: 0.7625 (t-100) cc_final: 0.7316 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 380
  average time/residue: 0.1087
  time to fit residues: 65.6911
Evaluate side-chains
  308 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 157 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 144 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 140 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 135 optimal weight:    5.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 290 GLN
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 GLN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 290 GLN
F 125 GLN
J  46 GLN
J  87 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.108032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.090134 restraints weight = 35858.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.090963 restraints weight = 26017.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.092367 restraints weight = 20644.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.092879 restraints weight = 13983.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.093144 restraints weight = 13521.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17463  Z= 0.137
  Angle     :  0.623   8.180  23727  Z= 0.326
  Chirality :  0.044   0.184   2622
  Planarity :  0.004   0.046   3027
  Dihedral  :  4.606  37.898   2760
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.17), residues: 2133
  helix:  1.53 (0.26), residues: 357
  sheet:  0.93 (0.22), residues: 516
  loop : -0.68 (0.16), residues: 1260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  87 
 TYR   0.019   0.001   TYR H 112 
 PHE   0.024   0.002   PHE A 124 
 TRP   0.042   0.002   TRP C 241 
 HIS   0.008   0.001   HIS I  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (17418)
  covalent geometry    : angle       0.61042 (23616)
  SS BOND              : bond        0.00471 (   24)
  SS BOND              : angle       1.88136 (   48)
  hydrogen bonds       : bond        0.04119 (  702)
  hydrogen bonds       : angle       5.22727 ( 1926)
  link_BETA1-4         : bond        0.00539 (    3)
  link_BETA1-4         : angle       4.46533 (    9)
  link_NAG-ASN         : bond        0.00197 (   18)
  link_NAG-ASN         : angle       1.06821 (   54)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2579.48 seconds
wall clock time: 45 minutes 33.08 seconds (2733.08 seconds total)