Starting phenix.real_space_refine
on Tue May 13 12:02:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdi_37137/05_2025/8kdi_37137.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    6811      2.51       5
     N    1718      2.21       5
     O    1963      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10532
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 447, 3451
          Classifications: {'peptide': 447}
          Link IDs: {'PTRANS': 23, 'TRANS': 423}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1686
          Classifications: {'peptide': 217}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 205}
    Chain: "H"
      Number of atoms: 1689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1689
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 6.00, per 1000 atoms: 0.57
  Number of scatterers: 10532
  At special positions: 0
  Unit cell: (81.3285, 141.174, 148.847, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1963      8.00
     N    1718      7.00
     C    6811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.12
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.12
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.11
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 202 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 381 "
      " NAG A 702 " - " ASN A 506 "
      " NAG A 703 " - " ASN A 365 "
      " NAG A 704 " - " ASN A 424 "
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2502

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      47.4% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 5.341A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 207
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.170A  pdb=" N   GLY A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.750A  pdb=" N   GLY A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ASP A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   TYR A 250 " --> pdb=" O   GLY A 246 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 322 through 341
      removed outlier: 3.641A  pdb=" N   VAL A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 355 through 371
    Processing helix  chain 'A' and resid 384 through 395
      removed outlier: 4.256A  pdb=" N   SER A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ASN A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 407
      removed outlier: 4.270A  pdb=" N   ASP A 407 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
    Processing helix  chain 'A' and resid 440 through 444
    Processing helix  chain 'A' and resid 449 through 458
    Processing helix  chain 'A' and resid 469 through 473
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 4.039A  pdb=" N   GLU A 514 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 533
    Processing helix  chain 'A' and resid 533 through 539
    Processing helix  chain 'A' and resid 612 through 614
      No H-bonds generated for 'chain 'A' and resid 612 through 614'
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.508A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 71 through 80
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.585A  pdb=" N   ALA B  85 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.853A  pdb=" N   TYR B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU B 122 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.599A  pdb=" N   PHE B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.757A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 222
      removed outlier: 4.267A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 201 " --> pdb=" O   GLN B 197 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ALA B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 254
      removed outlier: 3.527A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 261
      removed outlier: 3.688A  pdb=" N   LEU B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN B 261 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 256 through 261'
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 272 through 298
      removed outlier: 3.746A  pdb=" N   LEU B 276 " --> pdb=" O   ARG B 272 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.711A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 345
    Processing helix  chain 'B' and resid 346 through 356
      removed outlier: 3.914A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 387
      removed outlier: 3.869A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 392 through 422
    Processing helix  chain 'B' and resid 435 through 454
      removed outlier: 4.332A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 467
      removed outlier: 3.770A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.304A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.917A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 129 through 133
    Processing helix  chain 'L' and resid 189 through 194
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.744A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.536A  pdb=" N   LYS H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 136 through 140
      removed outlier: 3.930A  pdb=" N   ASN H 140 " --> pdb=" O   ALA H 137 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 198
      removed outlier: 3.598A  pdb=" N   GLU H 198 " --> pdb=" O   TRP H 195 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401
      removed outlier: 3.649A  pdb=" N   LEU A 399 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   GLY A 379 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL A 347 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE A 466 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544
      removed outlier: 4.042A  pdb=" N   SER A 552 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ARG A 625 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LEU A 595 " --> pdb=" O   ARG A 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574
      removed outlier: 6.362A  pdb=" N   GLY A 573 " --> pdb=" O   ILE L 100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.672A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 110 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.672A  pdb=" N   ALA L  90 " --> pdb=" O   LEU L 110 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   THR L 103 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.620A  pdb=" N   VAL L 139 " --> pdb=" O   PHE L 124 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 159 through 161
      removed outlier: 4.430A  pdb=" N   TRP L 154 " --> pdb=" O   ARG L 161 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.477A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.477A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 117 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 127 through 131
      removed outlier: 5.329A  pdb=" N   THR H 144 " --> pdb=" O   VAL H 190 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL H 190 " --> pdb=" O   THR H 144 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   GLY H 146 " --> pdb=" O   VAL H 188 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   VAL H 188 " --> pdb=" O   GLY H 146 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   LEU H 148 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   SER H 186 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   LYS H 150 " --> pdb=" O   LEU H 184 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU H 184 " --> pdb=" O   LYS H 150 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   SER H 185 " --> pdb=" O   PRO H 174 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   SER H 187 " --> pdb=" O   THR H 172 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   THR H 172 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   THR H 189 " --> pdb=" O   VAL H 170 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL H 170 " --> pdb=" O   THR H 189 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 201 through 205
      removed outlier: 3.584A  pdb=" N   LYS H 215 " --> pdb=" O   CYS H 202 " (cutoff:3.500A)

    546 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.45

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1698
        1.31 -     1.44: 3022
        1.44 -     1.58: 6015
        1.58 -     1.72: 4
        1.72 -     1.85: 58
  Bond restraints: 10797
  Sorted by residual:
  bond pdb=" CG  HIS L  97 "
       pdb=" CD2 HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.354  1.251  0.103 1.10e-02 8.26e+03 8.68e+01
  bond pdb=" CB  HIS L  97 "
       pdb=" CG  HIS L  97 "
    ideal  model  delta    sigma   weight residual
    1.497  1.412  0.085 1.40e-02 5.10e+03 3.68e+01
  bond pdb=" CB  HIS H  35 "
       pdb=" CG  HIS H  35 "
    ideal  model  delta    sigma   weight residual
    1.497  1.428  0.069 1.40e-02 5.10e+03 2.43e+01
  bond pdb=" C   GLY A 462 "
       pdb=" O   GLY A 462 "
    ideal  model  delta    sigma   weight residual
    1.229  1.190  0.040 8.20e-03 1.49e+04 2.33e+01
  bond pdb=" C   LEU A 213 "
       pdb=" N   PRO A 214 "
    ideal  model  delta    sigma   weight residual
    1.331  1.269  0.061 1.31e-02 5.83e+03 2.18e+01
  ... (remaining 10792 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.37: 14204
        4.37 -     8.74: 483
        8.74 -    13.11: 25
       13.11 -    17.48: 1
       17.48 -    21.85: 1
  Bond angle restraints: 14714
  Sorted by residual:
  angle pdb=" O   LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
      ideal   model   delta    sigma   weight residual
     121.42   99.57   21.85 1.06e+00 8.90e-01 4.25e+02
  angle pdb=" CA  LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" O   LEU A 213 "
      ideal   model   delta    sigma   weight residual
     119.76  132.87  -13.11 8.90e-01 1.26e+00 2.17e+02
  angle pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
        pdb=" CA  PRO A 214 "
      ideal   model   delta    sigma   weight residual
     119.85  111.75    8.10 1.01e+00 9.80e-01 6.43e+01
  angle pdb=" N   PRO A 214 "
        pdb=" CA  PRO A 214 "
        pdb=" CB  PRO A 214 "
      ideal   model   delta    sigma   weight residual
     103.33   95.93    7.40 9.30e-01 1.16e+00 6.34e+01
  angle pdb=" CA  LEU A 213 "
        pdb=" C   LEU A 213 "
        pdb=" N   PRO A 214 "
      ideal   model   delta    sigma   weight residual
     118.75  126.47   -7.72 9.70e-01 1.06e+00 6.33e+01
  ... (remaining 14709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5867
       17.57 -    35.14: 434
       35.14 -    52.72: 87
       52.72 -    70.29: 13
       70.29 -    87.86: 11
  Dihedral angle restraints: 6412
    sinusoidal: 2513
      harmonic: 3899
  Sorted by residual:
  dihedral pdb=" CA  SER A 410 "
           pdb=" C   SER A 410 "
           pdb=" N   THR A 411 "
           pdb=" CA  THR A 411 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  136.43   43.57     0      5.00e+00 4.00e-02 7.59e+01
  dihedral pdb=" CA  TRP A 557 "
           pdb=" C   TRP A 557 "
           pdb=" N   ASP A 558 "
           pdb=" CA  ASP A 558 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.80  -31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral pdb=" CA  GLY A 412 "
           pdb=" C   GLY A 412 "
           pdb=" N   GLU A 413 "
           pdb=" CA  GLU A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.09  -30.91     0      5.00e+00 4.00e-02 3.82e+01
  ... (remaining 6409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1368
       0.117 -    0.233: 312
       0.233 -    0.349: 16
       0.349 -    0.466: 3
       0.466 -    0.582: 1
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CA  PRO A 548 "
            pdb=" N   PRO A 548 "
            pdb=" C   PRO A 548 "
            pdb=" CB  PRO A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.14    0.58 2.00e-01 2.50e+01 8.47e+00
  chirality pdb=" CA  HIS L  97 "
            pdb=" N   HIS L  97 "
            pdb=" C   HIS L  97 "
            pdb=" CB  HIS L  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.05e+00
  chirality pdb=" CA  TYR H 103 "
            pdb=" N   TYR H 103 "
            pdb=" C   TYR H 103 "
            pdb=" CB  TYR H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.93e+00
  ... (remaining 1697 not shown)

  Planarity restraints: 1845
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.088 2.00e-02 2.50e+03   7.34e-02 6.74e+01
        pdb=" C7  NAG A 702 "    0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.067 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.118 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H 100 "   -0.509 9.50e-02 1.11e+02   2.28e-01 3.21e+01
        pdb=" NE  ARG H 100 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG H 100 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG H 100 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG H 100 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 525 "    0.387 9.50e-02 1.11e+02   1.73e-01 1.86e+01
        pdb=" NE  ARG A 525 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 525 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 525 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 525 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1842 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 20
        2.60 -     3.17: 8927
        3.17 -     3.75: 15713
        3.75 -     4.32: 22987
        4.32 -     4.90: 37298
  Nonbonded interactions: 84945
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 213 "
            pdb=" CA  PRO A 214 "
     model   vdw
     2.022 2.776
  nonbonded pdb=" CB  LYS A 532 "
            pdb=" OE1 GLU B 303 "
     model   vdw
     2.074 3.440
  nonbonded pdb=" OH  TYR A 250 "
            pdb=" OE2 GLU A 471 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU A 213 "
            pdb=" C   PRO A 214 "
     model   vdw
     2.334 3.270
  nonbonded pdb=" CB  GLN L  96 "
            pdb=" OE1 GLN L  96 "
     model   vdw
     2.497 2.752
  ... (remaining 84940 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.150
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.240
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
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      :  0.013   0.103  10806  Z= 0.822
  Angle     :  1.930  21.854  14736  Z= 1.271
  Chirality :  0.092   0.582   1700
  Planarity :  0.012   0.228   1841
  Dihedral  : 13.638  87.859   3895
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.54 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  5.11 %
    Favored  : 93.42 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.20), residues: 1343
  helix: -1.68 (0.18), residues: 509
  sheet: -0.34 (0.30), residues: 270
  loop : -1.16 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.007   TRP H 110 
 HIS   0.010   0.003   HIS A 619 
 PHE   0.029   0.005   PHE L  56 
 TYR   0.029   0.005   TYR A 250 
 ARG   0.009   0.002   ARG A 562 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01216 (    4)
  link_NAG-ASN         : angle       4.84201 (   12)
  hydrogen bonds       : bond        0.18393 (  535)
  hydrogen bonds       : angle       8.28512 ( 1482)
  SS BOND              : bond        0.06864 (    5)
  SS BOND              : angle       4.60584 (   10)
  covalent geometry    : bond        0.01297 (10797)
  covalent geometry    : angle       1.92294 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 290
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 ARG cc_start: 0.4716 (mtm110) cc_final: 0.4196 (mtm180)
REVERT: A  211 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6397 (ttt180)
REVERT: A  212 GLU cc_start: 0.8021 (pm20) cc_final: 0.7666 (tt0)
REVERT: A  234 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7197 (mt0)
REVERT: A  236 HIS cc_start: 0.6447 (m-70) cc_final: 0.5929 (m-70)
REVERT: A  252 SER cc_start: 0.8897 (t) cc_final: 0.8662 (p)
REVERT: A  290 PHE cc_start: 0.8210 (t80) cc_final: 0.7911 (t80)
REVERT: A  442 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (p)
REVERT: A  457 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: A  475 ASP cc_start: 0.8306 (t0) cc_final: 0.7896 (p0)
REVERT: A  484 MET cc_start: 0.8558 (mtm) cc_final: 0.8055 (tpt)
REVERT: A  535 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.7879 (t)
REVERT: A  604 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8181 (pm20)
REVERT: A  612 GLU cc_start: 0.8156 (tt0) cc_final: 0.7838 (tp30)
REVERT: A  625 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7879 (ttp80)
REVERT: B   81 SER cc_start: 0.8610 (t) cc_final: 0.8350 (p)
REVERT: B  242 ASN cc_start: 0.6538 (m110) cc_final: 0.6177 (p0)
REVERT: B  265 GLU cc_start: 0.5906 (tm-30) cc_final: 0.5617 (tp30)
REVERT: B  268 ILE cc_start: 0.5238 (mm) cc_final: 0.4827 (tt)
REVERT: B  296 TYR cc_start: 0.7016 (m-80) cc_final: 0.6718 (m-10)
REVERT: B  349 LEU cc_start: 0.8726 (tp) cc_final: 0.8496 (tt)
REVERT: B  365 MET cc_start: 0.8348 (mtt) cc_final: 0.7948 (mmm)
REVERT: B  387 TYR cc_start: 0.7809 (m-80) cc_final: 0.7481 (m-80)
REVERT: B  444 LEU cc_start: 0.8718 (mt) cc_final: 0.8494 (tp)
REVERT: B  454 THR cc_start: 0.8275 (p) cc_final: 0.7898 (t)
REVERT: L    1 ASP cc_start: 0.7532 (m-30) cc_final: 0.6981 (p0)
REVERT: L   21 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7257 (mmt)
REVERT: L   66 ASP cc_start: 0.8502 (m-30) cc_final: 0.8131 (t0)
REVERT: L  111 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7619 (mm-30)
REVERT: L  124 PHE cc_start: 0.8587 (m-80) cc_final: 0.8157 (m-80)
REVERT: L  130 GLN cc_start: 0.9009 (tt0) cc_final: 0.8737 (tm-30)
REVERT: L  154 TRP cc_start: 0.8374 (m100) cc_final: 0.7891 (m100)
REVERT: H    6 GLN cc_start: 0.8811 (mt0) cc_final: 0.8501 (mt0)
REVERT: H   10 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: H  112 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7994 (pm20)
REVERT: H  178 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6804 (pt0)
REVERT: H  180 ASP cc_start: 0.8655 (m-30) cc_final: 0.8294 (p0)
  outliers start: 17
  outliers final: 3
  residues processed: 302
  average time/residue: 0.2445
  time to fit residues: 99.9691
Evaluate side-chains
  186 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 179
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain H residue   83 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 339 GLN
A 352 ASN
B 358 HIS
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN
L 172 GLN
H 140 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.154730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 117)---------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.099103 restraints weight = 14809.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.096621 restraints weight = 13048.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.096139 restraints weight = 13153.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10806  Z= 0.168
  Angle     :  0.745   7.484  14736  Z= 0.382
  Chirality :  0.046   0.182   1700
  Planarity :  0.005   0.036   1841
  Dihedral  :  7.199  53.284   1536
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.69 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1343
  helix:  0.71 (0.22), residues: 516
  sheet:  0.15 (0.31), residues: 271
  loop : -0.43 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  47 
 HIS   0.006   0.001   HIS A 556 
 PHE   0.025   0.002   PHE B 445 
 TYR   0.034   0.002   TYR H 103 
 ARG   0.007   0.001   ARG A 211 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    4)
  link_NAG-ASN         : angle       2.64037 (   12)
  hydrogen bonds       : bond        0.05080 (  535)
  hydrogen bonds       : angle       5.26975 ( 1482)
  SS BOND              : bond        0.00481 (    5)
  SS BOND              : angle       1.70113 (   10)
  covalent geometry    : bond        0.00372 (10797)
  covalent geometry    : angle       0.74054 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 LEU cc_start: 0.7436 (tt) cc_final: 0.7192 (tt)
REVERT: A  396 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7621 (mtpp)
REVERT: A  442 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8863 (p)
REVERT: A  457 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8812 (mt)
REVERT: A  528 ASP cc_start: 0.7776 (t0) cc_final: 0.7495 (t0)
REVERT: A  594 ASP cc_start: 0.7076 (m-30) cc_final: 0.6817 (m-30)
REVERT: B  294 LEU cc_start: 0.8413 (tp) cc_final: 0.8020 (tp)
REVERT: B  314 ASP cc_start: 0.7951 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  387 TYR cc_start: 0.8867 (m-80) cc_final: 0.8329 (m-80)
REVERT: B  391 LYS cc_start: 0.7960 (mmpt) cc_final: 0.7078 (ptpp)
REVERT: B  441 LEU cc_start: 0.7226 (mm) cc_final: 0.6850 (pp)
REVERT: B  454 THR cc_start: 0.7401 (p) cc_final: 0.6873 (t)
REVERT: L  129 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8178 (mt-10)
REVERT: L  154 TRP cc_start: 0.8392 (m100) cc_final: 0.8136 (m100)
REVERT: L  160 GLU cc_start: 0.6735 (tp30) cc_final: 0.6478 (tp30)
REVERT: L  189 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8521 (mmmm)
REVERT: H  198 GLU cc_start: 0.7638 (mp0) cc_final: 0.7234 (mp0)
  outliers start: 33
  outliers final: 18
  residues processed: 215
  average time/residue: 0.2411
  time to fit residues: 72.1078
Evaluate side-chains
  164 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  358 HIS
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  450 SER
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  159 SER
Chi-restraints excluded: chain L residue  189 LYS
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 116 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0170
   chunk 76 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.0620

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

Flipped N/Q/H residues before XYZ refinement:
** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  19 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.161970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.126666 restraints weight = 14944.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.126245 restraints weight = 21895.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116072 restraints weight = 20080.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10806  Z= 0.143
  Angle     :  0.670   7.419  14736  Z= 0.339
  Chirality :  0.044   0.190   1700
  Planarity :  0.005   0.038   1841
  Dihedral  :  6.282  55.331   1530
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.46 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.23), residues: 1343
  helix:  1.25 (0.22), residues: 521
  sheet:  0.40 (0.31), residues: 270
  loop : -0.32 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H  47 
 HIS   0.007   0.001   HIS B 358 
 PHE   0.027   0.002   PHE B  95 
 TYR   0.031   0.002   TYR H 103 
 ARG   0.004   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    4)
  link_NAG-ASN         : angle       2.16418 (   12)
  hydrogen bonds       : bond        0.04321 (  535)
  hydrogen bonds       : angle       4.82372 ( 1482)
  SS BOND              : bond        0.00382 (    5)
  SS BOND              : angle       1.39061 (   10)
  covalent geometry    : bond        0.00317 (10797)
  covalent geometry    : angle       0.66674 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8968 (mt)
REVERT: A  475 ASP cc_start: 0.7437 (t0) cc_final: 0.7226 (t0)
REVERT: B  145 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8002 (mp10)
REVERT: B  294 LEU cc_start: 0.7766 (tp) cc_final: 0.7451 (tp)
REVERT: B  387 TYR cc_start: 0.8769 (m-80) cc_final: 0.8419 (m-80)
REVERT: B  391 LYS cc_start: 0.7642 (mmpt) cc_final: 0.6973 (ptpp)
REVERT: B  454 THR cc_start: 0.6879 (p) cc_final: 0.6514 (t)
REVERT: L  189 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7659 (tptm)
REVERT: H   73 ASP cc_start: 0.6817 (t0) cc_final: 0.6573 (t70)
REVERT: H  129 TYR cc_start: 0.7951 (m-80) cc_final: 0.7552 (m-80)
  outliers start: 28
  outliers final: 14
  residues processed: 178
  average time/residue: 0.2287
  time to fit residues: 57.6485
Evaluate side-chains
  152 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  159 SER
Chi-restraints excluded: chain L residue  189 LYS
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 91 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
B 293 ASN
B 304 GLN
H  43 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.160225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.125644 restraints weight = 14775.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.125164 restraints weight = 21776.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.122205 restraints weight = 21474.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10806  Z= 0.200
  Angle     :  0.677   8.592  14736  Z= 0.340
  Chirality :  0.045   0.209   1700
  Planarity :  0.004   0.042   1841
  Dihedral  :  5.875  56.278   1527
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.41 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.23), residues: 1343
  helix:  1.49 (0.23), residues: 521
  sheet:  0.41 (0.31), residues: 279
  loop : -0.34 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H  47 
 HIS   0.009   0.001   HIS L  97 
 PHE   0.030   0.002   PHE B 445 
 TYR   0.035   0.002   TYR H 103 
 ARG   0.003   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    4)
  link_NAG-ASN         : angle       1.82211 (   12)
  hydrogen bonds       : bond        0.04161 (  535)
  hydrogen bonds       : angle       4.67946 ( 1482)
  SS BOND              : bond        0.00388 (    5)
  SS BOND              : angle       1.27370 (   10)
  covalent geometry    : bond        0.00467 (10797)
  covalent geometry    : angle       0.67447 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8932 (mt)
REVERT: B  294 LEU cc_start: 0.6964 (tp) cc_final: 0.6737 (tp)
REVERT: B  391 LYS cc_start: 0.7834 (mmpt) cc_final: 0.7194 (ptpp)
REVERT: L  189 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7996 (tptm)
REVERT: L  191 GLU cc_start: 0.6213 (tp30) cc_final: 0.5897 (tp30)
REVERT: H   73 ASP cc_start: 0.7057 (t0) cc_final: 0.6796 (t70)
  outliers start: 38
  outliers final: 23
  residues processed: 167
  average time/residue: 0.2102
  time to fit residues: 50.8879
Evaluate side-chains
  144 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  189 LYS
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 123 optimal weight:    0.0670
   chunk 9 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0000
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8128

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
L  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.161906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.126335 restraints weight = 14854.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.125728 restraints weight = 25958.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119880 restraints weight = 22812.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10806  Z= 0.120
  Angle     :  0.631  12.366  14736  Z= 0.312
  Chirality :  0.043   0.187   1700
  Planarity :  0.004   0.043   1841
  Dihedral  :  5.599  55.591   1525
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.32 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1343
  helix:  1.67 (0.23), residues: 522
  sheet:  0.53 (0.31), residues: 281
  loop : -0.31 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP L 169 
 HIS   0.004   0.001   HIS L  97 
 PHE   0.020   0.001   PHE B 403 
 TYR   0.027   0.001   TYR H 103 
 ARG   0.007   0.000   ARG H  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00216 (    4)
  link_NAG-ASN         : angle       1.99394 (   12)
  hydrogen bonds       : bond        0.03733 (  535)
  hydrogen bonds       : angle       4.53755 ( 1482)
  SS BOND              : bond        0.00294 (    5)
  SS BOND              : angle       0.94411 (   10)
  covalent geometry    : bond        0.00262 (10797)
  covalent geometry    : angle       0.62808 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8820 (p)
REVERT: A  457 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (mt)
REVERT: A  507 MET cc_start: 0.8110 (mtm) cc_final: 0.7677 (ttm)
REVERT: B  145 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8077 (mp10)
REVERT: B  208 LEU cc_start: 0.7961 (tp) cc_final: 0.7708 (tp)
REVERT: B  294 LEU cc_start: 0.7549 (tp) cc_final: 0.7132 (tp)
REVERT: B  386 LEU cc_start: 0.8873 (mt) cc_final: 0.8615 (mt)
REVERT: B  391 LYS cc_start: 0.7958 (mmpt) cc_final: 0.7144 (ptpp)
REVERT: B  483 LYS cc_start: 0.6684 (mmpt) cc_final: 0.6418 (mmmt)
REVERT: L  189 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8148 (tptm)
REVERT: L  191 GLU cc_start: 0.6692 (tp30) cc_final: 0.6405 (tp30)
REVERT: H   40 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7376 (mtp-110)
REVERT: H  166 LEU cc_start: 0.7803 (mt) cc_final: 0.7588 (mp)
REVERT: H  216 LYS cc_start: 0.8034 (tptp) cc_final: 0.7656 (tptp)
  outliers start: 40
  outliers final: 25
  residues processed: 165
  average time/residue: 0.2136
  time to fit residues: 51.1004
Evaluate side-chains
  147 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue  189 LYS
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Chi-restraints excluded: chain H residue  204 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 124 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 129 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN
H  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.127486 restraints weight = 14890.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126856 restraints weight = 21915.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.123975 restraints weight = 19932.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10806  Z= 0.135
  Angle     :  0.636  12.628  14736  Z= 0.315
  Chirality :  0.043   0.188   1700
  Planarity :  0.004   0.042   1841
  Dihedral  :  5.439  56.973   1525
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.32 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.23), residues: 1343
  helix:  1.77 (0.23), residues: 522
  sheet:  0.63 (0.31), residues: 285
  loop : -0.37 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP L 169 
 HIS   0.005   0.001   HIS L  97 
 PHE   0.024   0.002   PHE B 445 
 TYR   0.029   0.001   TYR L 146 
 ARG   0.007   0.001   ARG A 209 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    4)
  link_NAG-ASN         : angle       1.60070 (   12)
  hydrogen bonds       : bond        0.03629 (  535)
  hydrogen bonds       : angle       4.48890 ( 1482)
  SS BOND              : bond        0.00350 (    5)
  SS BOND              : angle       3.35880 (   10)
  covalent geometry    : bond        0.00306 (10797)
  covalent geometry    : angle       0.62873 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 124
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8935 (p)
REVERT: A  457 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8874 (mt)
REVERT: A  507 MET cc_start: 0.7900 (mtm) cc_final: 0.7502 (ttm)
REVERT: B  145 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7810 (mp10)
REVERT: B  294 LEU cc_start: 0.7147 (tp) cc_final: 0.6814 (tp)
REVERT: B  391 LYS cc_start: 0.7823 (mmpt) cc_final: 0.7259 (ptpp)
REVERT: H  115 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (tt)
REVERT: H  129 TYR cc_start: 0.7931 (m-80) cc_final: 0.7706 (m-10)
REVERT: H  217 ILE cc_start: 0.7627 (mm) cc_final: 0.7312 (mm)
  outliers start: 47
  outliers final: 30
  residues processed: 160
  average time/residue: 0.2129
  time to fit residues: 49.3340
Evaluate side-chains
  145 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  181 MET
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.161880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.135288 restraints weight = 14990.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134577 restraints weight = 26022.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.131386 restraints weight = 22851.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10806  Z= 0.127
  Angle     :  0.628  10.923  14736  Z= 0.305
  Chirality :  0.043   0.267   1700
  Planarity :  0.004   0.040   1841
  Dihedral  :  5.381  56.750   1525
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.54 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.23), residues: 1343
  helix:  1.83 (0.23), residues: 521
  sheet:  0.69 (0.31), residues: 285
  loop : -0.34 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 169 
 HIS   0.004   0.001   HIS L  97 
 PHE   0.025   0.002   PHE B 402 
 TYR   0.025   0.001   TYR H 103 
 ARG   0.004   0.000   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    4)
  link_NAG-ASN         : angle       1.47394 (   12)
  hydrogen bonds       : bond        0.03500 (  535)
  hydrogen bonds       : angle       4.41684 ( 1482)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       1.98424 (   10)
  covalent geometry    : bond        0.00288 (10797)
  covalent geometry    : angle       0.62525 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 125
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.8251 (p) cc_final: 0.7963 (t)
REVERT: A  442 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8973 (p)
REVERT: A  457 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8807 (mt)
REVERT: A  507 MET cc_start: 0.8022 (mtm) cc_final: 0.7604 (ttm)
REVERT: A  572 VAL cc_start: 0.9420 (t) cc_final: 0.9128 (m)
REVERT: B  294 LEU cc_start: 0.7259 (tp) cc_final: 0.6897 (tp)
REVERT: B  391 LYS cc_start: 0.7760 (mmpt) cc_final: 0.7213 (ptpp)
REVERT: H  115 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8755 (tt)
REVERT: H  129 TYR cc_start: 0.7831 (m-80) cc_final: 0.7576 (m-10)
  outliers start: 41
  outliers final: 31
  residues processed: 153
  average time/residue: 0.2145
  time to fit residues: 47.1839
Evaluate side-chains
  149 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ARG
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  442 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  451 PHE
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
B 304 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.159628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128520 restraints weight = 14825.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.118626 restraints weight = 21013.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116857 restraints weight = 29737.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10806  Z= 0.222
  Angle     :  0.678  12.380  14736  Z= 0.332
  Chirality :  0.045   0.267   1700
  Planarity :  0.004   0.048   1841
  Dihedral  :  5.488  56.624   1525
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.49 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1343
  helix:  1.66 (0.23), residues: 520
  sheet:  0.65 (0.31), residues: 287
  loop : -0.38 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  47 
 HIS   0.009   0.001   HIS L  97 
 PHE   0.021   0.002   PHE A 541 
 TYR   0.030   0.002   TYR H 103 
 ARG   0.005   0.001   ARG B 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00193 (    4)
  link_NAG-ASN         : angle       1.49982 (   12)
  hydrogen bonds       : bond        0.03727 (  535)
  hydrogen bonds       : angle       4.50891 ( 1482)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       1.72190 (   10)
  covalent geometry    : bond        0.00529 (10797)
  covalent geometry    : angle       0.67559 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 115
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8895 (mt)
REVERT: A  572 VAL cc_start: 0.9396 (t) cc_final: 0.9147 (m)
REVERT: B  145 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8031 (mp10)
REVERT: B  294 LEU cc_start: 0.7511 (tp) cc_final: 0.7041 (tp)
REVERT: B  391 LYS cc_start: 0.7832 (mmpt) cc_final: 0.7163 (ptpp)
REVERT: H  115 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8875 (tt)
  outliers start: 46
  outliers final: 36
  residues processed: 152
  average time/residue: 0.2171
  time to fit residues: 48.3484
Evaluate side-chains
  149 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 111
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  211 ARG
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  561 GLU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  211 ILE
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  103 TYR
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 131 optimal weight:    9.9990
   chunk 123 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 75 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
L 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.161903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136944 restraints weight = 14988.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.130159 restraints weight = 21913.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129016 restraints weight = 28768.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10806  Z= 0.128
  Angle     :  0.644  11.790  14736  Z= 0.311
  Chirality :  0.043   0.251   1700
  Planarity :  0.004   0.042   1841
  Dihedral  :  5.333  55.906   1525
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.87 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1343
  helix:  1.80 (0.23), residues: 520
  sheet:  0.70 (0.31), residues: 287
  loop : -0.42 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 195 
 HIS   0.004   0.001   HIS L  97 
 PHE   0.018   0.001   PHE A 541 
 TYR   0.024   0.001   TYR H 103 
 ARG   0.003   0.000   ARG B 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    4)
  link_NAG-ASN         : angle       1.40293 (   12)
  hydrogen bonds       : bond        0.03454 (  535)
  hydrogen bonds       : angle       4.39664 ( 1482)
  SS BOND              : bond        0.00257 (    5)
  SS BOND              : angle       1.28026 (   10)
  covalent geometry    : bond        0.00290 (10797)
  covalent geometry    : angle       0.64203 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6520 (ptm160)
REVERT: A  457 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8816 (mt)
REVERT: A  572 VAL cc_start: 0.9409 (t) cc_final: 0.9159 (m)
REVERT: B  141 ARG cc_start: 0.7173 (mtp85) cc_final: 0.6633 (mtp85)
REVERT: B  145 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7895 (mp10)
REVERT: B  294 LEU cc_start: 0.7244 (tp) cc_final: 0.6863 (tp)
REVERT: B  387 TYR cc_start: 0.8288 (m-80) cc_final: 0.8002 (m-80)
REVERT: B  391 LYS cc_start: 0.7766 (mmpt) cc_final: 0.7176 (ptpp)
REVERT: B  421 ARG cc_start: 0.6350 (tpp80) cc_final: 0.6132 (mmp80)
REVERT: H  115 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8798 (tt)
  outliers start: 33
  outliers final: 26
  residues processed: 148
  average time/residue: 0.2253
  time to fit residues: 47.6344
Evaluate side-chains
  143 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ARG
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  469 LEU
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  199 THR
Chi-restraints excluded: chain H residue  200 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0980
   chunk 78 optimal weight:    7.9990
   chunk 103 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.162447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135031 restraints weight = 14848.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.130823 restraints weight = 23485.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128199 restraints weight = 26959.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.4845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10806  Z= 0.115
  Angle     :  0.631   8.911  14736  Z= 0.306
  Chirality :  0.042   0.243   1700
  Planarity :  0.004   0.041   1841
  Dihedral  :  5.270  55.431   1525
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.31 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.23), residues: 1343
  helix:  1.76 (0.23), residues: 523
  sheet:  0.79 (0.32), residues: 285
  loop : -0.38 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP H 195 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.023   0.002   PHE B 402 
 TYR   0.024   0.001   TYR H 103 
 ARG   0.004   0.000   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00242 (    4)
  link_NAG-ASN         : angle       1.37280 (   12)
  hydrogen bonds       : bond        0.03317 (  535)
  hydrogen bonds       : angle       4.32142 ( 1482)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       1.12756 (   10)
  covalent geometry    : bond        0.00252 (10797)
  covalent geometry    : angle       0.62993 (14714)

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

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

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2686 Ramachandran restraints generated.
    1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7060 (ptm160)
REVERT: A  475 ASP cc_start: 0.7545 (t0) cc_final: 0.7274 (t0)
REVERT: A  507 MET cc_start: 0.8024 (mtm) cc_final: 0.7598 (ttm)
REVERT: A  572 VAL cc_start: 0.9425 (t) cc_final: 0.9138 (m)
REVERT: A  609 LEU cc_start: 0.8599 (mt) cc_final: 0.8136 (mt)
REVERT: B  243 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6605 (tp)
REVERT: B  294 LEU cc_start: 0.7292 (tp) cc_final: 0.6901 (tp)
REVERT: B  387 TYR cc_start: 0.8342 (m-80) cc_final: 0.8064 (m-80)
REVERT: B  391 LYS cc_start: 0.7776 (mmpt) cc_final: 0.7184 (ptpp)
REVERT: B  421 ARG cc_start: 0.6398 (tpp80) cc_final: 0.6154 (mmp80)
REVERT: H  115 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8730 (tt)
  outliers start: 30
  outliers final: 23
  residues processed: 155
  average time/residue: 0.2330
  time to fit residues: 51.3697
Evaluate side-chains
  147 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ARG
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  431 CYS
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  426 GLU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  497 GLN
Chi-restraints excluded: chain H residue   72 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  200 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2826 > 50:
  distance: 37 - 53:  33.433
  distance: 41 - 61:  21.576
  distance: 47 - 65:  32.934
  distance: 51 - 53:  31.765
  distance: 52 - 76:  19.732
  distance: 53 - 54:  30.776
  distance: 54 - 55:  24.986
  distance: 54 - 57:  23.125
  distance: 55 - 56:  17.952
  distance: 55 - 61:  26.264
  distance: 56 - 83:  36.616
  distance: 57 - 58:   7.458
  distance: 57 - 59:  20.512
  distance: 58 - 60:   8.955
  distance: 61 - 62:  19.895
  distance: 63 - 64:  10.786
  distance: 63 - 65:  18.595
  distance: 64 - 91:  23.317
  distance: 65 - 66:  23.392
  distance: 66 - 67:  23.372
  distance: 66 - 69:  15.051
  distance: 67 - 68:  18.763
  distance: 67 - 76:  29.809
  distance: 68 - 99:  24.233
  distance: 69 - 70:  32.991
  distance: 70 - 71:  30.228
  distance: 70 - 72:  32.469
  distance: 71 - 73:  11.533
  distance: 73 - 75:  21.012
  distance: 76 - 77:  24.429
  distance: 77 - 78:  35.186
  distance: 77 - 80:  25.121
  distance: 78 - 79:  31.434
  distance: 78 - 83:  13.981
  distance: 79 - 107:  43.754
  distance: 80 - 82:  25.827
  distance: 83 - 84:   5.893
  distance: 84 - 87:   5.504
  distance: 85 - 86:   4.661
  distance: 85 - 91:  13.942
  distance: 87 - 88:  15.974
  distance: 87 - 89:  18.789
  distance: 88 - 90:  10.865
  distance: 91 - 92:  24.335
  distance: 92 - 93:  25.035
  distance: 92 - 95:  39.584
  distance: 93 - 94:  24.512
  distance: 93 - 99:  21.693
  distance: 95 - 96:  11.523
  distance: 95 - 97:  40.613
  distance: 96 - 98:   4.999
  distance: 99 - 100:  20.361
  distance: 100 - 101:  29.398
  distance: 100 - 103:  44.702
  distance: 101 - 107:  11.682
  distance: 103 - 104:  39.615
  distance: 104 - 105:  29.517
  distance: 108 - 109:  24.738
  distance: 108 - 111:  15.801
  distance: 109 - 110:   5.431
  distance: 109 - 113:  17.511
  distance: 111 - 112:  39.409
  distance: 113 - 114:  42.821
  distance: 114 - 115:  25.140
  distance: 115 - 116:   5.653
  distance: 115 - 117:   5.918
  distance: 116 - 139:  29.570
  distance: 117 - 118:  35.767
  distance: 118 - 119:  36.933
  distance: 118 - 121:   5.717
  distance: 119 - 120:  44.582
  distance: 119 - 125:  22.815
  distance: 120 - 146:  30.237
  distance: 122 - 123:  22.946
  distance: 122 - 124:   4.092