Starting phenix.real_space_refine
on Fri Jul  3 08:31:30 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hps_34942/07_2026/8hps_34942.cif"
  }
  resolution = 3.51
  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=   0.016
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    8310      2.51       5
     N    2194      2.21       5
     O    2438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12984
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2153
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 14, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1994
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 16, 'TRANS': 247}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 2684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2684
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 138
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 78
    Chain: "D"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2725
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "E"
      Number of atoms: 3341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3341
          Classifications: {'peptide': 437}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "H"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.64, per 1000 atoms: 0.20
  Number of scatterers: 12984
  At special positions: 0
  Unit cell: (86.1, 86.1, 168.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     P       6     15.00
     Mg      2     11.99
     O    2438      8.00
     N    2194      7.00
     C    8310      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
    ALPHA1-1
      " GLC H   1 " - " GLC H   2 "
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 587.2 milliseconds
  

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3198

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 13 sheets defined
      56.2% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 50
      removed outlier: 3.640A  pdb=" N   SER A  19 " --> pdb=" O   ASP A  15 " (cutoff:3.500A)
      Proline residue:  A  30  - end of helix
      removed outlier: 3.699A  pdb=" N   VAL A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   TYR A  41 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      removed outlier: 3.785A  pdb=" N   SER A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
      removed outlier: 3.515A  pdb=" N   VAL A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 111
      removed outlier: 3.569A  pdb=" N   ALA A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 122
    Processing helix  chain 'A' and resid 123 through 128
    Processing helix  chain 'A' and resid 129 through 142
      removed outlier: 3.523A  pdb=" N   THR A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 161 through 190
      removed outlier: 4.010A  pdb=" N   LYS A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 193 through 202
      removed outlier: 3.514A  pdb=" N   LEU A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.518A  pdb=" N   LYS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 235
      Proline residue:  A 221  - end of helix
      removed outlier: 4.052A  pdb=" N   VAL A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 243
    Processing helix  chain 'A' and resid 253 through 263
    Processing helix  chain 'A' and resid 267 through 272
    Processing helix  chain 'A' and resid 272 through 294
      removed outlier: 3.977A  pdb=" N   ILE A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 37
      Proline residue:  B  27  - end of helix
    Processing helix  chain 'B' and resid 54 through 62
    Processing helix  chain 'B' and resid 64 through 98
      removed outlier: 3.629A  pdb=" N   ALA B  69 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 116
      removed outlier: 3.818A  pdb=" N   ILE B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 133
      removed outlier: 3.845A  pdb=" N   LEU B 121 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   THR B 123 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
      removed outlier: 3.646A  pdb=" N   GLY B 131 " --> pdb=" O   ASN B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 162
      Proline residue:  B 144  - end of helix
      Proline residue:  B 151  - end of helix
    Processing helix  chain 'B' and resid 165 through 175
      removed outlier: 3.995A  pdb=" N   GLU B 169 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.756A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 208
      removed outlier: 3.611A  pdb=" N   ASN B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 216
      removed outlier: 3.607A  pdb=" N   SER B 215 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 253 through 264
      removed outlier: 4.007A  pdb=" N   VAL B 260 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'C' and resid 46 through 55
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 96 through 108
      Proline residue:  C 104  - end of helix
    Processing helix  chain 'C' and resid 111 through 127
    Processing helix  chain 'C' and resid 135 through 139
    Processing helix  chain 'C' and resid 140 through 155
      removed outlier: 3.757A  pdb=" N   GLY C 150 " --> pdb=" O   ARG C 146 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ARG C 151 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ALA C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG C 155 " --> pdb=" O   ARG C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 188
      removed outlier: 4.335A  pdb=" N   GLN C 176 " --> pdb=" O   LYS C 172 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ALA C 179 " --> pdb=" O   VAL C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 206
      removed outlier: 3.734A  pdb=" N   ALA C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR C 204 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 229
    Processing helix  chain 'C' and resid 232 through 237
    Processing helix  chain 'C' and resid 266 through 276
    Processing helix  chain 'C' and resid 287 through 289
      No H-bonds generated for 'chain 'C' and resid 287 through 289'
    Processing helix  chain 'C' and resid 295 through 297
      No H-bonds generated for 'chain 'C' and resid 295 through 297'
    Processing helix  chain 'C' and resid 298 through 304
      removed outlier: 3.983A  pdb=" N   ILE C 303 " --> pdb=" O   GLY C 299 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ARG C 304 " --> pdb=" O   TYR C 300 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 56
    Processing helix  chain 'D' and resid 76 through 81
    Processing helix  chain 'D' and resid 96 through 108
      Proline residue:  D 104  - end of helix
    Processing helix  chain 'D' and resid 111 through 126
      removed outlier: 3.934A  pdb=" N   LYS D 124 " --> pdb=" O   GLU D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 139
    Processing helix  chain 'D' and resid 140 through 155
      removed outlier: 4.287A  pdb=" N   ARG D 146 " --> pdb=" O   GLY D 142 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA D 152 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ARG D 155 " --> pdb=" O   ARG D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
    Processing helix  chain 'D' and resid 198 through 206
      removed outlier: 3.982A  pdb=" N   THR D 204 " --> pdb=" O   THR D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 229
    Processing helix  chain 'D' and resid 232 through 239
    Processing helix  chain 'D' and resid 266 through 276
    Processing helix  chain 'D' and resid 287 through 289
      No H-bonds generated for 'chain 'D' and resid 287 through 289'
    Processing helix  chain 'D' and resid 295 through 297
      No H-bonds generated for 'chain 'D' and resid 295 through 297'
    Processing helix  chain 'D' and resid 298 through 303
    Processing helix  chain 'D' and resid 374 through 377
      removed outlier: 3.584A  pdb=" N   LEU D 377 " --> pdb=" O   THR D 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 374 through 377'
    Processing helix  chain 'E' and resid 37 through 39
      No H-bonds generated for 'chain 'E' and resid 37 through 39'
    Processing helix  chain 'E' and resid 40 through 55
      removed outlier: 4.474A  pdb=" N   ALA E  46 " --> pdb=" O   ALA E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 83
      removed outlier: 3.997A  pdb=" N   LEU E  75 " --> pdb=" O   ASP E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 104
    Processing helix  chain 'E' and resid 109 through 113
    Processing helix  chain 'E' and resid 117 through 122
    Processing helix  chain 'E' and resid 127 through 134
    Processing helix  chain 'E' and resid 165 through 180
    Processing helix  chain 'E' and resid 192 through 206
      removed outlier: 4.112A  pdb=" N   VAL E 196 " --> pdb=" O   TYR E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 223 through 243
    Processing helix  chain 'E' and resid 249 through 253
      removed outlier: 3.537A  pdb=" N   THR E 253 " --> pdb=" O   ILE E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 264
    Processing helix  chain 'E' and resid 275 through 286
      removed outlier: 3.600A  pdb=" N   SER E 279 " --> pdb=" O   TYR E 275 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 297
    Processing helix  chain 'E' and resid 313 through 326
      removed outlier: 3.538A  pdb=" N   LYS E 326 " --> pdb=" O   ASP E 322 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 359 through 371
    Processing helix  chain 'E' and resid 372 through 382
    Processing helix  chain 'E' and resid 389 through 394
    Processing helix  chain 'E' and resid 395 through 402
    Processing helix  chain 'E' and resid 404 through 414
      removed outlier: 3.582A  pdb=" N   ASN E 414 " --> pdb=" O   GLN E 410 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 423 through 436
    Processing helix  chain 'E' and resid 437 through 441
    Processing helix  chain 'E' and resid 442 through 460
    Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31
      removed outlier: 6.632A  pdb=" N   ALA C  23 " --> pdb=" O   SER C  12 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   SER C  12 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LYS C  25 " --> pdb=" O   THR C  10 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   THR C  10 " --> pdb=" O   LYS C  25 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   PHE C  27 " --> pdb=" O   ARG C   8 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   VAL C   9 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   SER C  62 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 85
      removed outlier: 6.121A  pdb=" N   ALA C  83 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   ASP C 163 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL C  85 " --> pdb=" O   ASP C 163 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   PHE C 160 " --> pdb=" O   VAL C 193 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   VAL C 195 " --> pdb=" O   PHE C 160 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   MET C 162 " --> pdb=" O   VAL C 195 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   PHE C  36 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   VAL C 210 " --> pdb=" O   PHE C  36 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE C  38 " --> pdb=" O   VAL C 210 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   MET C 212 " --> pdb=" O   ILE C  38 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   VAL C  40 " --> pdb=" O   MET C 212 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL C 209 " --> pdb=" O   ILE C 220 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ILE C 220 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL C 211 " --> pdb=" O   GLN C 218 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264
    Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 293
    Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 31
      removed outlier: 6.239A  pdb=" N   ALA D  23 " --> pdb=" O   SER D  12 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   SER D  12 " --> pdb=" O   ALA D  23 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LYS D  25 " --> pdb=" O   THR D  10 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   THR D  10 " --> pdb=" O   LYS D  25 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   PHE D  27 " --> pdb=" O   ARG D   8 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL D   9 " --> pdb=" O   SER D  62 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   SER D  62 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 85
      removed outlier: 6.296A  pdb=" N   ALA D  83 " --> pdb=" O   LEU D 161 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ASP D 163 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL D  85 " --> pdb=" O   ASP D 163 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   PHE D 160 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   VAL D 195 " --> pdb=" O   PHE D 160 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   MET D 162 " --> pdb=" O   VAL D 195 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   PHE D  36 " --> pdb=" O   ARG D 208 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   VAL D 210 " --> pdb=" O   PHE D  36 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ILE D  38 " --> pdb=" O   VAL D 210 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   MET D 212 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL D  40 " --> pdb=" O   MET D 212 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL D 209 " --> pdb=" O   ILE D 220 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ILE D 220 " --> pdb=" O   VAL D 209 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL D 211 " --> pdb=" O   GLN D 218 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 264
    Processing sheet with id=AA8, first strand: chain 'D' and resid 291 through 293
      removed outlier: 3.701A  pdb=" N   LEU D 306 " --> pdb=" O   ILE D 372 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 321 through 325
    Processing sheet with id=AB1, first strand: chain 'E' and resid 59 through 65
      removed outlier: 7.045A  pdb=" N   ILE E  30 " --> pdb=" O   GLN E  60 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ALA E  62 " --> pdb=" O   ILE E  30 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ILE E  32 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ARG E  64 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   TYR E  34 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   VAL E 353 " --> pdb=" O   VAL E 108 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 59 through 65
      removed outlier: 7.045A  pdb=" N   ILE E  30 " --> pdb=" O   GLN E  60 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ALA E  62 " --> pdb=" O   ILE E  30 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ILE E  32 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ARG E  64 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   TYR E  34 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLY E 347 " --> pdb=" O   THR E 147 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   THR E 147 " --> pdb=" O   GLY E 347 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   LEU E 349 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136
    Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 186
      removed outlier: 6.136A  pdb=" N   TRP E 184 " --> pdb=" O   ALA E 267 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU E 269 " --> pdb=" O   TRP E 184 " (cutoff:3.500A)

    699 hydrogen bonds defined for protein.
    1974 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.16

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3007
        1.33 -     1.45: 2612
        1.45 -     1.58: 7553
        1.58 -     1.70: 10
        1.70 -     1.82: 64
  Bond restraints: 13246
  Sorted by residual:
  bond pdb=" C4  ATP D 501 "
       pdb=" C5  ATP D 501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.472 -0.084 1.00e-02 1.00e+04 7.01e+01
  bond pdb=" C4  ATP C 501 "
       pdb=" C5  ATP C 501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.87e+01
  bond pdb=" C5  ATP D 501 "
       pdb=" C6  ATP D 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.40e+01
  bond pdb=" C5  ATP C 501 "
       pdb=" C6  ATP C 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.30e+01
  bond pdb=" C5  GLC H   1 "
       pdb=" O5  GLC H   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.548 -0.138 2.00e-02 2.50e+03 4.77e+01
  ... (remaining 13241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.92: 17612
        3.92 -     7.84: 460
        7.84 -    11.76: 11
       11.76 -    15.68: 0
       15.68 -    19.59: 4
  Bond angle restraints: 18087
  Sorted by residual:
  angle pdb=" PB  ATP C 501 "
        pdb=" O3B ATP C 501 "
        pdb=" PG  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     139.87  120.28   19.59 1.00e+00 1.00e+00 3.84e+02
  angle pdb=" PB  ATP D 501 "
        pdb=" O3B ATP D 501 "
        pdb=" PG  ATP D 501 "
      ideal   model   delta    sigma   weight residual
     139.87  120.36   19.51 1.00e+00 1.00e+00 3.81e+02
  angle pdb=" PA  ATP C 501 "
        pdb=" O3A ATP C 501 "
        pdb=" PB  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     136.83  120.33   16.50 1.00e+00 1.00e+00 2.72e+02
  angle pdb=" PA  ATP D 501 "
        pdb=" O3A ATP D 501 "
        pdb=" PB  ATP D 501 "
      ideal   model   delta    sigma   weight residual
     136.83  120.51   16.32 1.00e+00 1.00e+00 2.66e+02
  angle pdb=" C5  ATP C 501 "
        pdb=" C4  ATP C 501 "
        pdb=" N3  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.65    8.15 1.00e+00 1.00e+00 6.65e+01
  ... (remaining 18082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 7377
       17.82 -    35.63: 402
       35.63 -    53.45: 75
       53.45 -    71.27: 29
       71.27 -    89.08: 8
  Dihedral angle restraints: 7891
    sinusoidal: 2935
      harmonic: 4956
  Sorted by residual:
  dihedral pdb=" CA  SER C 129 "
           pdb=" C   SER C 129 "
           pdb=" N   GLU C 130 "
           pdb=" CA  GLU C 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  ASP A 161 "
           pdb=" C   ASP A 161 "
           pdb=" N   GLN A 162 "
           pdb=" CA  GLN A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.72  -28.28     0      5.00e+00 4.00e-02 3.20e+01
  dihedral pdb=" CA  THR C 328 "
           pdb=" C   THR C 328 "
           pdb=" N   GLU C 329 "
           pdb=" CA  GLU C 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.81   28.19     0      5.00e+00 4.00e-02 3.18e+01
  ... (remaining 7888 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.930: 2149
       0.930 -    1.861: 0
       1.861 -    2.791: 0
       2.791 -    3.721: 0
       3.721 -    4.651: 1
  Chirality restraints: 2150
  Sorted by residual:
  chirality pdb=" C1  GLC H   2 "
            pdb=" C2  GLC H   2 "
            pdb=" O1  GLC H   2 "
            pdb=" O5  GLC H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.33   -2.32    4.65 2.00e-01 2.50e+01 5.41e+02
  chirality pdb=" C1  GLC H   1 "
            pdb=" C2  GLC H   1 "
            pdb=" O5  GLC H   1 "
            pdb=" O1  GLC H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.30    0.10 2.00e-02 2.50e+03 2.31e+01
  chirality pdb=" CA  THR A 130 "
            pdb=" N   THR A 130 "
            pdb=" C   THR A 130 "
            pdb=" CB  THR A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.06    0.47 2.00e-01 2.50e+01 5.47e+00
  ... (remaining 2147 not shown)

  Planarity restraints: 2313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 153 "    0.130 2.00e-02 2.50e+03   6.54e-02 1.07e+02
        pdb=" CG  TRP E 153 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 153 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 153 "   -0.054 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 153 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 153 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 153 "   -0.077 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 153 "    0.086 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 153 "   -0.037 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 153 "    0.064 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 333 "   -0.116 2.00e-02 2.50e+03   6.15e-02 7.56e+01
        pdb=" CG  TYR E 333 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 333 "    0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 333 "    0.063 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 333 "    0.033 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 333 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 333 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 333 "   -0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 424 "   -0.113 2.00e-02 2.50e+03   6.04e-02 7.30e+01
        pdb=" CG  TYR E 424 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 424 "    0.055 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 424 "    0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 424 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 424 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 424 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E 424 "   -0.089 2.00e-02 2.50e+03
  ... (remaining 2310 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 511
        2.75 -     3.29: 13991
        3.29 -     3.82: 19980
        3.82 -     4.36: 25812
        4.36 -     4.90: 42796
  Nonbonded interactions: 103090
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 250 "
            pdb=" OD1 ASP A 250 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OE1 GLN D  87 "
            pdb="MG    MG D 502 "
     model   vdw
     2.248 2.170
  nonbonded pdb=" NH1 ARG E  80 "
            pdb=" OD2 ASP E  85 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" CE2 PHE C  36 "
            pdb=" CB  LEU C 205 "
     model   vdw
     2.267 3.740
  nonbonded pdb=" OE1 GLN C  87 "
            pdb="MG    MG C 502 "
     model   vdw
     2.275 2.170
  ... (remaining 103085 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 30 through 125 or (resid 126 through 128 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 129 or (resid 130 t \ 
hrough 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ 
 through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 181 through 196 or (resid 197 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 198 through 359 or (resid 360 and (name N or name C \ 
A or name C or name O or name CB )) or resid 361 through 502))
  selection = (chain 'D' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 79 through 106 or (resid 107 through 108 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 109 through 111 or  \ 
(resid 112 through 113 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 114 through 120 or (resid 121 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 122 through 124 or (resid 125 through 128 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 129 through 145 or (resid 1 \ 
46 and (name N or name CA or name C or name O or name CB )) or resid 147 through \ 
 225 or (resid 226 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 227 through 237 or (resid 238 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 239 through 251 or (resid 252 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 253 through 263 or (resid 264 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 265 through 268 or (resid 2 \ 
69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 
 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 297 or (resid 298 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 299 through 302 or (resid 303 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 304 through 305 or (resid 306 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 307 through 310 or (resid 311 through 3 \ 
12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 
 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 380 through 389 or (resid 390 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 391 through 502))
}

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:             4.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     11.310
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
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      :  0.012   0.138  13247  Z= 0.761
  Angle     :  1.769  19.594  18090  Z= 1.214
  Chirality :  0.140   4.651   2150
  Planarity :  0.012   0.110   2313
  Dihedral  : 12.823  89.082   4693
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  5.20 %
    Favored  : 94.42 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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: -1.71 (0.18), residues: 1704
  helix: -1.33 (0.15), residues: 824
  sheet:  0.53 (0.47), residues: 112
  loop : -0.99 (0.20), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 119 
 TYR   0.116   0.018   TYR E 333 
 PHE   0.057   0.012   PHE C 234 
 TRP   0.130   0.020   TRP E 153 
 HIS   0.012   0.003   HIS C 197 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01236 /  0.76 (13246)
  covalent geometry    : angle       1.76891 /  1.21 (18087)
  hydrogen bonds       : bond        0.16739 / 11.53 (  692)
  hydrogen bonds       : angle       7.87269 /  5.70 ( 1974)
  glycosidic custom    : bond        0.02897 /  1.52 (    1)
  glycosidic custom    : angle       2.03233 /  1.23 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 336
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7366 (mmm160)
REVERT: A  289 TYR cc_start: 0.7904 (m-10) cc_final: 0.7559 (m-80)
REVERT: B   12 TRP cc_start: 0.8446 (t-100) cc_final: 0.8234 (t60)
REVERT: B  125 ILE cc_start: 0.8887 (mm) cc_final: 0.8485 (mm)
REVERT: C  100 ASN cc_start: 0.8153 (m-40) cc_final: 0.7312 (t0)
REVERT: C  220 ILE cc_start: 0.9030 (mt) cc_final: 0.8581 (mp)
REVERT: C  260 PHE cc_start: 0.6833 (p90) cc_final: 0.6374 (p90)
REVERT: C  308 PHE cc_start: 0.3849 (p90) cc_final: 0.3457 (p90)
REVERT: D   36 PHE cc_start: 0.7907 (t80) cc_final: 0.7685 (t80)
REVERT: D   84 MET cc_start: 0.8802 (ttt) cc_final: 0.8555 (ttm)
REVERT: D  199 GLN cc_start: 0.8361 (pp30) cc_final: 0.8085 (pp30)
REVERT: E   54 GLN cc_start: 0.7459 (mt0) cc_final: 0.7091 (mt0)
  outliers start: 5
  outliers final: 3
  residues processed: 338
  average time/residue: 0.1102
  time to fit residues: 52.6240
Evaluate side-chains
  228 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 225
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain B residue  118 HIS
Chi-restraints excluded: chain B residue  238 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 98 optimal weight:    0.0170
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.7420

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 150 ASN
A 261 ASN
C  99 GLN
C 325 HIS
E  39 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.153037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.116605 restraints weight = 24722.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117861 restraints weight = 12125.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120587 restraints weight = 7738.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.120621 restraints weight = 5317.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.120930 restraints weight = 4816.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13247  Z= 0.161
  Angle     :  0.706  10.733  18090  Z= 0.372
  Chirality :  0.047   0.188   2150
  Planarity :  0.005   0.041   2313
  Dihedral  :  6.198  69.847   1869
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.01 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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: -0.11 (0.20), residues: 1704
  helix:  0.26 (0.17), residues: 854
  sheet:  0.07 (0.39), residues: 160
  loop : -0.35 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 418 
 TYR   0.028   0.002   TYR E 192 
 PHE   0.024   0.002   PHE C 234 
 TRP   0.022   0.002   TRP A  80 
 HIS   0.005   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 (13246)
  covalent geometry    : angle       0.69838 /  0.37 (18087)
  hydrogen bonds       : bond        0.04952 /  3.36 (  692)
  hydrogen bonds       : angle       5.36426 /  3.93 ( 1974)
  glycosidic custom    : bond        0.00500 /  0.26 (    1)
  glycosidic custom    : angle       8.14570 /  5.47 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 250
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7570 (mmt90) cc_final: 0.7283 (mmm160)
REVERT: B   58 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8649 (mtmm)
REVERT: B  158 SER cc_start: 0.9364 (t) cc_final: 0.9003 (m)
REVERT: B  169 GLU cc_start: 0.8144 (tp30) cc_final: 0.7938 (tp30)
REVERT: C    4 ILE cc_start: 0.8960 (mp) cc_final: 0.8720 (tt)
REVERT: C  100 ASN cc_start: 0.8008 (m-40) cc_final: 0.7511 (t0)
REVERT: C  219 GLN cc_start: 0.7695 (tp40) cc_final: 0.7337 (tp40)
REVERT: C  244 MET cc_start: 0.3947 (ttm) cc_final: 0.3715 (ttp)
REVERT: C  260 PHE cc_start: 0.6627 (p90) cc_final: 0.5953 (p90)
REVERT: D  158 LYS cc_start: 0.8266 (mttt) cc_final: 0.7514 (tptt)
REVERT: D  199 GLN cc_start: 0.8206 (pp30) cc_final: 0.7968 (pp30)
REVERT: E   54 GLN cc_start: 0.7222 (mt0) cc_final: 0.6858 (mt0)
REVERT: E  263 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7253 (tp30)
REVERT: E  378 TYR cc_start: 0.7902 (t80) cc_final: 0.7605 (t80)
  outliers start: 35
  outliers final: 19
  residues processed: 269
  average time/residue: 0.0866
  time to fit residues: 35.9497
Evaluate side-chains
  220 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  289 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 137 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 123 optimal weight:    8.9990
   chunk 157 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 152 optimal weight:    0.0770
   overall best weight:    2.1944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 150 ASN
A 162 GLN
B  56 ASN
C  99 GLN
D 367 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.148969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.112086 restraints weight = 25234.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.113302 restraints weight = 13156.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.116372 restraints weight = 8001.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.116141 restraints weight = 5548.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.116498 restraints weight = 4985.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13247  Z= 0.207
  Angle     :  0.677   8.282  18090  Z= 0.348
  Chirality :  0.046   0.196   2150
  Planarity :  0.005   0.058   2313
  Dihedral  :  5.828  77.126   1866
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.08 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.13 (0.20), residues: 1704
  helix:  0.59 (0.18), residues: 846
  sheet: -0.13 (0.36), residues: 192
  loop : -0.33 (0.24), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 174 
 TYR   0.031   0.002   TYR E 192 
 PHE   0.015   0.002   PHE B 183 
 TRP   0.022   0.002   TRP A  80 
 HIS   0.006   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00489 /  0.21 (13246)
  covalent geometry    : angle       0.67272 /  0.35 (18087)
  hydrogen bonds       : bond        0.04650 /  3.16 (  692)
  hydrogen bonds       : angle       5.16413 /  3.81 ( 1974)
  glycosidic custom    : bond        0.01207 /  0.64 (    1)
  glycosidic custom    : angle       5.62028 /  3.31 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 207
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7572 (mmt90) cc_final: 0.7181 (mmm160)
REVERT: B  169 GLU cc_start: 0.8309 (tp30) cc_final: 0.8035 (tp30)
REVERT: C    4 ILE cc_start: 0.8943 (mp) cc_final: 0.8637 (tt)
REVERT: C  100 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7423 (t0)
REVERT: C  244 MET cc_start: 0.3590 (ttm) cc_final: 0.3335 (ttp)
REVERT: C  260 PHE cc_start: 0.6645 (p90) cc_final: 0.5979 (p90)
REVERT: C  283 ILE cc_start: 0.8699 (mm) cc_final: 0.8249 (pt)
REVERT: D  151 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7513 (mtm110)
REVERT: D  158 LYS cc_start: 0.8266 (mttt) cc_final: 0.7528 (tppt)
  outliers start: 53
  outliers final: 39
  residues processed: 237
  average time/residue: 0.0960
  time to fit residues: 34.3723
Evaluate side-chains
  227 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 186
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  239 ASP
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain C residue  377 LEU
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  190 THR
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue  167 ASP
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Chi-restraints excluded: chain E residue  450 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 155 optimal weight:    1.9990
   chunk 147 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 146 optimal weight:    0.7980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 127 ASN
D  99 GLN
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.150924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.115566 restraints weight = 24555.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116808 restraints weight = 11901.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.119842 restraints weight = 7457.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.119748 restraints weight = 4998.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120062 restraints weight = 4369.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13247  Z= 0.133
  Angle     :  0.605   9.187  18090  Z= 0.307
  Chirality :  0.044   0.171   2150
  Planarity :  0.005   0.051   2313
  Dihedral  :  5.480  75.630   1866
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.76 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.40 (0.20), residues: 1704
  helix:  0.90 (0.18), residues: 842
  sheet: -0.08 (0.36), residues: 192
  loop : -0.31 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG D 178 
 TYR   0.025   0.002   TYR D  89 
 PHE   0.017   0.001   PHE B 183 
 TRP   0.015   0.001   TRP A  80 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 (13246)
  covalent geometry    : angle       0.60249 /  0.31 (18087)
  hydrogen bonds       : bond        0.03927 /  2.66 (  692)
  hydrogen bonds       : angle       4.84806 /  3.58 ( 1974)
  glycosidic custom    : bond        0.00701 /  0.37 (    1)
  glycosidic custom    : angle       4.03816 /  2.33 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 223
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7106 (mmm160)
REVERT: B  158 SER cc_start: 0.9351 (t) cc_final: 0.8892 (m)
REVERT: B  169 GLU cc_start: 0.8341 (tp30) cc_final: 0.8029 (tp30)
REVERT: B  216 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8214 (mt)
REVERT: C    4 ILE cc_start: 0.8931 (mp) cc_final: 0.8582 (tt)
REVERT: C  100 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7305 (t0)
REVERT: C  149 MET cc_start: 0.8815 (tpp) cc_final: 0.8576 (tpp)
REVERT: C  153 ILE cc_start: 0.8336 (mm) cc_final: 0.8001 (tp)
REVERT: C  201 GLU cc_start: 0.8419 (pt0) cc_final: 0.8151 (pt0)
REVERT: C  219 GLN cc_start: 0.7621 (tp40) cc_final: 0.7280 (tp40)
REVERT: C  244 MET cc_start: 0.3909 (ttm) cc_final: 0.3583 (ttp)
REVERT: C  260 PHE cc_start: 0.6556 (p90) cc_final: 0.5968 (p90)
REVERT: C  283 ILE cc_start: 0.8785 (mm) cc_final: 0.8325 (pt)
REVERT: D  151 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7454 (mtm110)
REVERT: D  158 LYS cc_start: 0.8239 (mttt) cc_final: 0.7516 (tppt)
REVERT: D  244 MET cc_start: 0.1398 (tpp) cc_final: 0.0417 (tpp)
REVERT: E  195 MET cc_start: 0.8047 (tpp) cc_final: 0.7845 (tpp)
REVERT: E  345 THR cc_start: 0.8740 (m) cc_final: 0.8395 (p)
REVERT: E  378 TYR cc_start: 0.7954 (t80) cc_final: 0.7698 (t80)
  outliers start: 43
  outliers final: 33
  residues processed: 249
  average time/residue: 0.1074
  time to fit residues: 40.2884
Evaluate side-chains
  230 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  168 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  167 ASP
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Chi-restraints excluded: chain E residue  450 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 14 optimal weight:    0.0270
   chunk 151 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0570
   chunk 75 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 137 optimal weight:    5.9990
   chunk 159 optimal weight:    0.7980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.149292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.113314 restraints weight = 24659.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.114367 restraints weight = 12298.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117175 restraints weight = 7851.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116933 restraints weight = 5457.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.117133 restraints weight = 4846.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13247  Z= 0.113
  Angle     :  0.573   7.733  18090  Z= 0.289
  Chirality :  0.043   0.177   2150
  Planarity :  0.004   0.047   2313
  Dihedral  :  5.198  72.175   1866
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.29 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.60 (0.20), residues: 1704
  helix:  1.11 (0.18), residues: 835
  sheet: -0.03 (0.35), residues: 196
  loop : -0.26 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 178 
 TYR   0.024   0.001   TYR D  89 
 PHE   0.019   0.001   PHE B 183 
 TRP   0.018   0.001   TRP B 166 
 HIS   0.003   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 (13246)
  covalent geometry    : angle       0.57144 /  0.29 (18087)
  hydrogen bonds       : bond        0.03557 /  2.40 (  692)
  hydrogen bonds       : angle       4.65024 /  3.44 ( 1974)
  glycosidic custom    : bond        0.00441 /  0.23 (    1)
  glycosidic custom    : angle       3.02289 /  1.72 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 221
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7431 (mmt90) cc_final: 0.6961 (mmm160)
REVERT: A  147 TYR cc_start: 0.8593 (p90) cc_final: 0.8225 (p90)
REVERT: B  216 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8068 (mp)
REVERT: C    4 ILE cc_start: 0.8946 (mp) cc_final: 0.8533 (tt)
REVERT: C  100 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7325 (t0)
REVERT: C  153 ILE cc_start: 0.8268 (mm) cc_final: 0.7958 (tp)
REVERT: C  201 GLU cc_start: 0.8501 (pt0) cc_final: 0.8157 (pt0)
REVERT: C  244 MET cc_start: 0.3514 (ttm) cc_final: 0.3240 (ttp)
REVERT: C  260 PHE cc_start: 0.6651 (p90) cc_final: 0.6204 (p90)
REVERT: C  283 ILE cc_start: 0.8613 (mm) cc_final: 0.8185 (pt)
REVERT: D  151 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7403 (mtm110)
REVERT: D  158 LYS cc_start: 0.8265 (mttt) cc_final: 0.7546 (tppt)
REVERT: D  178 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7994 (mtt180)
REVERT: E  345 THR cc_start: 0.8733 (m) cc_final: 0.8392 (p)
REVERT: E  378 TYR cc_start: 0.7951 (t80) cc_final: 0.7685 (t80)
  outliers start: 42
  outliers final: 30
  residues processed: 242
  average time/residue: 0.1046
  time to fit residues: 38.3996
Evaluate side-chains
  229 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Chi-restraints excluded: chain E residue  450 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 112 optimal weight:    9.9990
   chunk 76 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 95 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.2782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.147463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.111412 restraints weight = 24594.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.112109 restraints weight = 12789.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.115122 restraints weight = 8152.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.114969 restraints weight = 5454.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.115209 restraints weight = 4920.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13247  Z= 0.141
  Angle     :  0.597   8.426  18090  Z= 0.299
  Chirality :  0.043   0.182   2150
  Planarity :  0.005   0.059   2313
  Dihedral  :  5.161  73.392   1866
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.82 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.64 (0.20), residues: 1704
  helix:  1.18 (0.18), residues: 838
  sheet:  0.04 (0.36), residues: 196
  loop : -0.31 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 178 
 TYR   0.025   0.001   TYR D  89 
 PHE   0.017   0.001   PHE C 234 
 TRP   0.012   0.001   TRP A  80 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 (13246)
  covalent geometry    : angle       0.59582 /  0.30 (18087)
  hydrogen bonds       : bond        0.03715 /  2.51 (  692)
  hydrogen bonds       : angle       4.65210 /  3.44 ( 1974)
  glycosidic custom    : bond        0.00430 /  0.23 (    1)
  glycosidic custom    : angle       2.95362 /  1.66 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 206
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7394 (mmt90) cc_final: 0.6941 (mmm160)
REVERT: A  147 TYR cc_start: 0.8620 (p90) cc_final: 0.8292 (p90)
REVERT: B  216 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: B  240 GLU cc_start: 0.6939 (mp0) cc_final: 0.6655 (mp0)
REVERT: C    4 ILE cc_start: 0.8944 (mp) cc_final: 0.8517 (tt)
REVERT: C  100 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7380 (t0)
REVERT: C  244 MET cc_start: 0.3607 (ttm) cc_final: 0.3332 (ttp)
REVERT: C  283 ILE cc_start: 0.8639 (mm) cc_final: 0.8202 (pt)
REVERT: D  151 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7411 (mtm110)
REVERT: D  158 LYS cc_start: 0.8209 (mttt) cc_final: 0.7554 (tppt)
REVERT: E   93 LEU cc_start: 0.8466 (mt) cc_final: 0.8222 (mt)
REVERT: E  345 THR cc_start: 0.8755 (m) cc_final: 0.8461 (p)
REVERT: E  378 TYR cc_start: 0.8008 (t80) cc_final: 0.7797 (t80)
  outliers start: 44
  outliers final: 36
  residues processed: 234
  average time/residue: 0.1031
  time to fit residues: 36.6163
Evaluate side-chains
  228 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  167 ASP
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Chi-restraints excluded: chain E residue  450 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0070
   chunk 25 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 132 optimal weight:    5.9990
   overall best weight:    1.2604

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.147997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.110484 restraints weight = 25131.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.111264 restraints weight = 13254.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.114620 restraints weight = 8584.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.114360 restraints weight = 5584.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.114580 restraints weight = 5032.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13247  Z= 0.139
  Angle     :  0.596   7.472  18090  Z= 0.300
  Chirality :  0.043   0.175   2150
  Planarity :  0.004   0.046   2313
  Dihedral  :  5.109  73.597   1866
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.13 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.63 (0.20), residues: 1704
  helix:  1.20 (0.18), residues: 838
  sheet:  0.01 (0.34), residues: 214
  loop : -0.34 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 178 
 TYR   0.027   0.001   TYR D  89 
 PHE   0.010   0.001   PHE E 291 
 TRP   0.012   0.001   TRP A  80 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 (13246)
  covalent geometry    : angle       0.59479 /  0.30 (18087)
  hydrogen bonds       : bond        0.03637 /  2.45 (  692)
  hydrogen bonds       : angle       4.64669 /  3.45 ( 1974)
  glycosidic custom    : bond        0.00342 /  0.18 (    1)
  glycosidic custom    : angle       2.58975 /  1.45 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 206
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7427 (mmt90) cc_final: 0.6987 (mmm160)
REVERT: A  147 TYR cc_start: 0.8599 (p90) cc_final: 0.8289 (p90)
REVERT: B   58 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8789 (mtpp)
REVERT: B  216 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: B  240 GLU cc_start: 0.7000 (mp0) cc_final: 0.6770 (mp0)
REVERT: C  100 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7479 (t0)
REVERT: C  153 ILE cc_start: 0.8387 (mm) cc_final: 0.8061 (tp)
REVERT: C  244 MET cc_start: 0.3551 (ttm) cc_final: 0.3305 (ttp)
REVERT: C  283 ILE cc_start: 0.8575 (mm) cc_final: 0.8157 (pt)
REVERT: D  151 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7415 (mtm110)
REVERT: D  158 LYS cc_start: 0.8222 (mttt) cc_final: 0.7582 (tppt)
REVERT: E  345 THR cc_start: 0.8750 (m) cc_final: 0.8475 (p)
REVERT: E  378 TYR cc_start: 0.7987 (t80) cc_final: 0.7741 (t80)
  outliers start: 52
  outliers final: 40
  residues processed: 240
  average time/residue: 0.1030
  time to fit residues: 37.5435
Evaluate side-chains
  232 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 189
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   51 CYS
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  167 ASP
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 145 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.148487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.111207 restraints weight = 24919.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.111838 restraints weight = 13203.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.114097 restraints weight = 8845.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.114387 restraints weight = 6491.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.114672 restraints weight = 5290.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13247  Z= 0.126
  Angle     :  0.608  12.328  18090  Z= 0.302
  Chirality :  0.043   0.178   2150
  Planarity :  0.004   0.046   2313
  Dihedral  :  5.033  72.856   1866
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.04 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.68 (0.20), residues: 1704
  helix:  1.22 (0.18), residues: 838
  sheet:  0.17 (0.36), residues: 201
  loop : -0.34 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 130 
 TYR   0.027   0.001   TYR D  89 
 PHE   0.034   0.001   PHE C 234 
 TRP   0.011   0.001   TRP A  80 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (13246)
  covalent geometry    : angle       0.60765 /  0.30 (18087)
  hydrogen bonds       : bond        0.03504 /  2.36 (  692)
  hydrogen bonds       : angle       4.62432 /  3.44 ( 1974)
  glycosidic custom    : bond        0.00212 /  0.11 (    1)
  glycosidic custom    : angle       2.40353 /  1.32 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 202
  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: A  110 ARG cc_start: 0.7367 (mmt90) cc_final: 0.6898 (mmm160)
REVERT: A  147 TYR cc_start: 0.8618 (p90) cc_final: 0.8345 (p90)
REVERT: A  173 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7270 (mt-10)
REVERT: A  237 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: B   58 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8799 (mtpp)
REVERT: B  216 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8102 (mp)
REVERT: B  240 GLU cc_start: 0.6993 (mp0) cc_final: 0.6791 (mp0)
REVERT: C  100 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7492 (t0)
REVERT: C  153 ILE cc_start: 0.8385 (mm) cc_final: 0.8041 (tp)
REVERT: C  164 GLN cc_start: 0.7861 (mp10) cc_final: 0.7649 (mp10)
REVERT: C  244 MET cc_start: 0.3438 (ttm) cc_final: 0.3185 (ttp)
REVERT: C  283 ILE cc_start: 0.8519 (mm) cc_final: 0.8108 (pt)
REVERT: D  151 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7432 (mtm110)
REVERT: D  158 LYS cc_start: 0.8217 (mttt) cc_final: 0.7551 (tppt)
  outliers start: 45
  outliers final: 38
  residues processed: 229
  average time/residue: 0.1051
  time to fit residues: 36.5216
Evaluate side-chains
  235 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 193
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   64 ASP
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   51 CYS
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 GLN
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Chi-restraints excluded: chain E residue  450 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 134 optimal weight:    0.2980
   chunk 138 optimal weight:    0.9990
   chunk 156 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   chunk 82 optimal weight:    0.0670
   chunk 100 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0670
   overall best weight:    0.4256

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.150245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.112971 restraints weight = 24978.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.113717 restraints weight = 13282.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117082 restraints weight = 8552.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.116786 restraints weight = 5726.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116941 restraints weight = 4902.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13247  Z= 0.112
  Angle     :  0.598  12.848  18090  Z= 0.296
  Chirality :  0.042   0.193   2150
  Planarity :  0.004   0.046   2313
  Dihedral  :  4.890  71.730   1866
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.50 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.76 (0.20), residues: 1704
  helix:  1.28 (0.18), residues: 839
  sheet:  0.25 (0.36), residues: 203
  loop : -0.32 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 130 
 TYR   0.026   0.001   TYR D  89 
 PHE   0.010   0.001   PHE C 260 
 TRP   0.008   0.001   TRP A  80 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 (13246)
  covalent geometry    : angle       0.59745 /  0.30 (18087)
  hydrogen bonds       : bond        0.03303 /  2.21 (  692)
  hydrogen bonds       : angle       4.55174 /  3.38 ( 1974)
  glycosidic custom    : bond        0.00201 /  0.11 (    1)
  glycosidic custom    : angle       1.97259 /  1.08 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 214
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7264 (mmt90) cc_final: 0.6745 (mmm160)
REVERT: A  147 TYR cc_start: 0.8623 (p90) cc_final: 0.8355 (p90)
REVERT: A  173 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7340 (mt-10)
REVERT: A  237 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8467 (tt)
REVERT: B  216 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: C    4 ILE cc_start: 0.9304 (mt) cc_final: 0.9087 (mt)
REVERT: C  100 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7525 (t0)
REVERT: C  149 MET cc_start: 0.8830 (tpp) cc_final: 0.8579 (tpp)
REVERT: C  153 ILE cc_start: 0.8257 (mm) cc_final: 0.7893 (tp)
REVERT: C  207 ASP cc_start: 0.8223 (t0) cc_final: 0.7932 (m-30)
REVERT: C  244 MET cc_start: 0.3279 (ttm) cc_final: 0.3051 (ttp)
REVERT: D  151 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7371 (mtm110)
REVERT: D  158 LYS cc_start: 0.8183 (mttt) cc_final: 0.7522 (tppt)
REVERT: E  263 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7214 (tp30)
REVERT: E  378 TYR cc_start: 0.7987 (t80) cc_final: 0.7593 (t80)
  outliers start: 41
  outliers final: 31
  residues processed: 234
  average time/residue: 0.1051
  time to fit residues: 36.8686
Evaluate side-chains
  234 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 198
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  151 ARG
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  178 ARG
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0770
   chunk 25 optimal weight:    4.9990
   chunk 126 optimal weight:    0.6980
   chunk 121 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.149917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.113258 restraints weight = 25204.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.114018 restraints weight = 13205.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.117185 restraints weight = 8514.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.116995 restraints weight = 5688.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117176 restraints weight = 4924.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13247  Z= 0.117
  Angle     :  0.615  12.879  18090  Z= 0.303
  Chirality :  0.043   0.331   2150
  Planarity :  0.004   0.046   2313
  Dihedral  :  4.861  71.553   1866
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.04 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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 (0.21), residues: 1704
  helix:  1.32 (0.19), residues: 838
  sheet:  0.22 (0.36), residues: 205
  loop : -0.28 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 151 
 TYR   0.029   0.001   TYR E 192 
 PHE   0.009   0.001   PHE E 291 
 TRP   0.008   0.001   TRP A  80 
 HIS   0.003   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (13246)
  covalent geometry    : angle       0.61440 /  0.30 (18087)
  hydrogen bonds       : bond        0.03309 /  2.21 (  692)
  hydrogen bonds       : angle       4.54359 /  3.38 ( 1974)
  glycosidic custom    : bond        0.00004 /  0.00 (    1)
  glycosidic custom    : angle       2.00273 /  1.09 (    3)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.9256 (tp) cc_final: 0.9017 (tt)
REVERT: A  110 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6793 (mmm160)
REVERT: A  138 TYR cc_start: 0.8786 (t80) cc_final: 0.8461 (t80)
REVERT: B  216 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8064 (mp)
REVERT: C  100 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7534 (t0)
REVERT: C  149 MET cc_start: 0.8838 (tpp) cc_final: 0.8570 (tpp)
REVERT: C  153 ILE cc_start: 0.8318 (mm) cc_final: 0.7939 (tp)
REVERT: C  207 ASP cc_start: 0.8257 (t0) cc_final: 0.7942 (m-30)
REVERT: C  244 MET cc_start: 0.3267 (ttm) cc_final: 0.3044 (ttp)
REVERT: D  158 LYS cc_start: 0.8200 (mttt) cc_final: 0.7543 (tppt)
REVERT: E  263 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7206 (tp30)
REVERT: E  378 TYR cc_start: 0.7976 (t80) cc_final: 0.7630 (t80)
  outliers start: 37
  outliers final: 27
  residues processed: 230
  average time/residue: 0.0999
  time to fit residues: 34.8668
Evaluate side-chains
  227 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 197
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ASP
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 HIS
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue  100 ASN
Chi-restraints excluded: chain C residue  213 LEU
Chi-restraints excluded: chain C residue  250 THR
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  256 VAL
Chi-restraints excluded: chain D residue  269 MET
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   95 VAL
Chi-restraints excluded: chain E residue  263 GLU
Chi-restraints excluded: chain E residue  339 ASP
Chi-restraints excluded: chain E residue  428 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 169
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 166 optimal weight:    1.9990
   chunk 124 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9990
   chunk 149 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 143 optimal weight:    0.9980
   overall best weight:    0.8182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.150044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.112557 restraints weight = 25181.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.114089 restraints weight = 12939.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.116768 restraints weight = 8150.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.116500 restraints weight = 5834.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.116802 restraints weight = 5354.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13247  Z= 0.123
  Angle     :  0.618  12.570  18090  Z= 0.306
  Chirality :  0.044   0.335   2150
  Planarity :  0.004   0.046   2313
  Dihedral  :  4.863  71.957   1866
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.57 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.16 %
    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:  0.83 (0.21), residues: 1704
  helix:  1.35 (0.19), residues: 837
  sheet:  0.22 (0.36), residues: 205
  loop : -0.28 (0.24), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 151 
 TYR   0.030   0.001   TYR E 192 
 PHE   0.009   0.001   PHE C 260 
 TRP   0.009   0.001   TRP B 207 
 HIS   0.004   0.001   HIS E 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 (13246)
  covalent geometry    : angle       0.61751 /  0.31 (18087)
  hydrogen bonds       : bond        0.03354 /  2.24 (  692)
  hydrogen bonds       : angle       4.59195 /  3.42 ( 1974)
  glycosidic custom    : bond        0.00159 /  0.08 (    1)
  glycosidic custom    : angle       2.05550 /  1.12 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2199.14 seconds
wall clock time: 38 minutes 46.36 seconds (2326.36 seconds total)