Starting phenix.real_space_refine
on Fri Jun  6 09:38:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nou_49617/06_2025/9nou_49617.cif"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.028
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      49      5.16       5
     C    4799      2.51       5
     N    1266      2.21       5
     O    1405      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7519
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3611
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 24, 'TRANS': 440}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 3698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3698
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 21, 'TRANS': 436}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 112
          Unusual residues: {'NAG': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
    Chain: "A"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 98
          Unusual residues: {'NAG': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
  Time building chain proxies: 5.29, per 1000 atoms: 0.70
  Number of scatterers: 7519
  At special positions: 0
  Unit cell: (92.999, 88.061, 92.176, 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      49     16.00
     O    1405      8.00
     N    1266      7.00
     C    4799      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS A 359 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 517 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 499 " - pdb=" SG  CYS B 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 513 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 514 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 487 "
      " NAG A 602 " - " ASN A  84 "
      " NAG A 603 " - " ASN A 428 "
      " NAG A 604 " - " ASN A 312 "
      " NAG A 605 " - " ASN A 248 "
      " NAG A 606 " - " ASN A 292 "
      " NAG A 607 " - " ASN A 368 "
      " NAG B 601 " - " ASN B 475 "
      " NAG B 602 " - " ASN B 285 "
      " NAG B 603 " - " ASN B 264 "
      " NAG B 604 " - " ASN B 411 "
      " NAG B 605 " - " ASN B  85 "
      " NAG B 606 " - " ASN B 130 "
      " NAG B 607 " - " ASN B 380 "
      " NAG B 608 " - " ASN B 432 "
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1746

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 9 sheets defined
      42.5% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'B' and resid 25 through 28
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 3.541A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 3.760A  pdb=" N   ALA B 109 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LYS B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 130 through 134
      removed outlier: 3.777A  pdb=" N   GLN B 133 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 161
      removed outlier: 4.090A  pdb=" N   PHE B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   PHE B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 3.941A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 234
      removed outlier: 3.614A  pdb=" N   ALA B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 266
      removed outlier: 3.557A  pdb=" N   SER B 266 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 290
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 314 through 318
    Processing helix  chain 'B' and resid 333 through 345
    Processing helix  chain 'B' and resid 347 through 354
    Processing helix  chain 'B' and resid 370 through 374
      removed outlier: 3.517A  pdb=" N   ASP B 374 " --> pdb=" O   PRO B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 385
      removed outlier: 3.788A  pdb=" N   SER B 382 " --> pdb=" O   GLN B 379 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   ALA B 383 " --> pdb=" O   ASN B 380 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY B 384 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 408
      removed outlier: 3.645A  pdb=" N   SER B 392 " --> pdb=" O   HIS B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 425
    Processing helix  chain 'B' and resid 426 through 431
    Processing helix  chain 'B' and resid 482 through 485
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 65 through 85
      removed outlier: 3.888A  pdb=" N   TYR A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 3.664A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 213 through 228
    Processing helix  chain 'A' and resid 250 through 267
    Processing helix  chain 'A' and resid 281 through 291
      removed outlier: 3.515A  pdb=" N   GLU A 287 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 314
      No H-bonds generated for 'chain 'A' and resid 313 through 314'
    Processing helix  chain 'A' and resid 315 through 318
      removed outlier: 3.987A  pdb=" N   HIS A 318 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 315 through 318'
    Processing helix  chain 'A' and resid 334 through 342
    Processing helix  chain 'A' and resid 365 through 372
      removed outlier: 4.072A  pdb=" N   SER A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 384 through 404
    Processing helix  chain 'A' and resid 416 through 425
      removed outlier: 3.662A  pdb=" N   TRP A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31
      removed outlier: 3.541A  pdb=" N   MET B  31 " --> pdb=" O   TYR B  97 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TYR B  35 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   ASP B  98 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   LEU B  37 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   PHE B 100 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLY B  39 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   VAL B  36 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   ILE B 142 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   GLY B  38 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   GLN B 164 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 126
    Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.901A  pdb=" N   VAL B 209 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   GLU B 240 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ALA B 211 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   LEU B 242 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLY B 213 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   VAL B 270 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   PHE B 324 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ALA B 299 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   GLN B 326 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   VAL B 321 " --> pdb=" O   TRP B 459 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B 458 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ASP B 470 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL B 460 " --> pdb=" O   LEU B 468 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   LEU B 468 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 434 through 437
    Processing sheet with id=AA6, first strand: chain 'B' and resid 511 through 512
    Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.122A  pdb=" N   LEU A  35 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL A  99 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   VAL A 101 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   PHE A  39 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   ILE A 139 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   GLY A  36 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 8.915A  pdb=" N   ILE A 162 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   GLN A 161 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 233 through 240
      removed outlier: 7.195A  pdb=" N   ILE A 206 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 8.895A  pdb=" N   GLU A 238 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A 208 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   LEU A 240 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL A 210 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   TRP A 205 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 8.357A  pdb=" N   VAL A 273 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ILE A 207 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   PHE A 275 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU A 209 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL A 272 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ALA A 296 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LEU A 323 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   TRP A 298 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ILE A 325 " --> pdb=" O   TRP A 298 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA A 300 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 9.288A  pdb=" N   ILE A 327 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   PHE A 322 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE A 450 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A 474 " --> pdb=" O   TYR A 469 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 428 through 431

    280 hydrogen bonds defined for protein.
    771 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2394
        1.34 -     1.46: 1885
        1.46 -     1.59: 3349
        1.59 -     1.71: 0
        1.71 -     1.83: 71
  Bond restraints: 7699
  Sorted by residual:
  bond pdb=" N   VAL B 511 "
       pdb=" CA  VAL B 511 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.23e+00
  bond pdb=" N   VAL A 108 "
       pdb=" CA  VAL A 108 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.68e+00
  bond pdb=" N   VAL A 385 "
       pdb=" CA  VAL A 385 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.032 1.17e-02 7.31e+03 7.64e+00
  bond pdb=" N   VAL A 384 "
       pdb=" CA  VAL A 384 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.28e-02 6.10e+03 7.59e+00
  bond pdb=" N   PHE A 285 "
       pdb=" CA  PHE A 285 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.33e-02 5.65e+03 7.55e+00
  ... (remaining 7694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 10211
        1.90 -     3.80: 232
        3.80 -     5.71: 23
        5.71 -     7.61: 2
        7.61 -     9.51: 3
  Bond angle restraints: 10471
  Sorted by residual:
  angle pdb=" N   VAL A 384 "
        pdb=" CA  VAL A 384 "
        pdb=" C   VAL A 384 "
      ideal   model   delta    sigma   weight residual
     113.16  107.55    5.61 1.49e+00 4.50e-01 1.42e+01
  angle pdb=" N   VAL A 288 "
        pdb=" CA  VAL A 288 "
        pdb=" C   VAL A 288 "
      ideal   model   delta    sigma   weight residual
     110.62  106.35    4.27 1.14e+00 7.69e-01 1.40e+01
  angle pdb=" O   PHE A 284 "
        pdb=" C   PHE A 284 "
        pdb=" N   PHE A 285 "
      ideal   model   delta    sigma   weight residual
     122.12  118.20    3.92 1.06e+00 8.90e-01 1.36e+01
  angle pdb=" N   TYR B 128 "
        pdb=" CA  TYR B 128 "
        pdb=" C   TYR B 128 "
      ideal   model   delta    sigma   weight residual
     110.59  105.28    5.31 1.45e+00 4.76e-01 1.34e+01
  angle pdb=" CA  PHE A 284 "
        pdb=" C   PHE A 284 "
        pdb=" N   PHE A 285 "
      ideal   model   delta    sigma   weight residual
     117.30  121.38   -4.08 1.16e+00 7.43e-01 1.24e+01
  ... (remaining 10466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4094
       17.94 -    35.89: 486
       35.89 -    53.83: 158
       53.83 -    71.78: 36
       71.78 -    89.72: 10
  Dihedral angle restraints: 4784
    sinusoidal: 2092
      harmonic: 2692
  Sorted by residual:
  dihedral pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A 102 "
           pdb=" CB  CYS A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.30   69.30     1      1.00e+01 1.00e-02 6.21e+01
  dihedral pdb=" CB  CYS A 363 "
           pdb=" SG  CYS A 363 "
           pdb=" SG  CYS A 366 "
           pdb=" CB  CYS A 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.08   61.08     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" CB  CYS A 495 "
           pdb=" SG  CYS A 495 "
           pdb=" SG  CYS A 514 "
           pdb=" CB  CYS A 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.73   50.73     1      1.00e+01 1.00e-02 3.52e+01
  ... (remaining 4781 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1011
       0.061 -    0.123: 181
       0.123 -    0.184: 18
       0.184 -    0.245: 5
       0.245 -    0.307: 2
  Chirality restraints: 1217
  Sorted by residual:
  chirality pdb=" C1  NAG A 602 "
            pdb=" ND2 ASN A  84 "
            pdb=" C2  NAG A 602 "
            pdb=" O5  NAG A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" C2  NAG A 604 "
            pdb=" C1  NAG A 604 "
            pdb=" C3  NAG A 604 "
            pdb=" N2  NAG A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.19   -0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" C1  NAG B 608 "
            pdb=" ND2 ASN B 432 "
            pdb=" C2  NAG B 608 "
            pdb=" O5  NAG B 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1214 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 130 "    0.038 2.00e-02 2.50e+03   4.12e-02 2.12e+01
        pdb=" CG  ASN B 130 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 130 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 130 "   -0.065 2.00e-02 2.50e+03
        pdb=" C1  NAG B 606 "    0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 510 "    0.212 9.50e-02 1.11e+02   9.50e-02 5.54e+00
        pdb=" NE  ARG B 510 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 510 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 510 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 510 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 127 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   ALA B 127 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ALA B 127 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR B 128 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2938
        2.89 -     3.40: 6954
        3.40 -     3.90: 12905
        3.90 -     4.40: 14840
        4.40 -     4.90: 24651
  Nonbonded interactions: 62288
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 416 "
            pdb=" OE1 GLN B 418 "
     model   vdw
     2.394 3.040
  nonbonded pdb=" N   TYR B 128 "
            pdb=" O   TYR B 128 "
     model   vdw
     2.523 2.496
  nonbonded pdb=" N   GLN B 418 "
            pdb=" OE1 GLN B 418 "
     model   vdw
     2.531 3.120
  nonbonded pdb=" O   ARG B 510 "
            pdb=" N   ASP B 520 "
     model   vdw
     2.559 3.120
  nonbonded pdb=" CB  ARG A 226 "
            pdb=" NE  ARG A 226 "
     model   vdw
     2.560 2.816
  ... (remaining 62283 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 individual isotropic
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:             6.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.440
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
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      :  0.004   0.038   7727  Z= 0.217
  Angle     :  0.691   9.907  10542  Z= 0.384
  Chirality :  0.049   0.307   1217
  Planarity :  0.005   0.095   1320
  Dihedral  : 17.487  89.720   2999
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 29.54 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.28), residues: 905
  helix:  0.81 (0.28), residues: 330
  sheet: -0.98 (0.41), residues: 143
  loop :  0.10 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 455 
 HIS   0.004   0.001   HIS B 341 
 PHE   0.024   0.002   PHE B  65 
 TYR   0.025   0.002   TYR B 394 
 ARG   0.005   0.000   ARG A 256 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00672 (   15)
  link_NAG-ASN         : angle       2.89910 (   45)
  hydrogen bonds       : bond        0.18255 (  280)
  hydrogen bonds       : angle       6.25606 (  771)
  SS BOND              : bond        0.00319 (   13)
  SS BOND              : angle       1.29377 (   26)
  covalent geometry    : bond        0.00418 ( 7699)
  covalent geometry    : angle       0.66332 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: B   32 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7761 (pptt)
REVERT: B   45 GLU cc_start: 0.6897 (mt-10) cc_final: 0.5820 (tp30)
REVERT: B   81 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7205 (mm-30)
REVERT: B   86 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7444 (ttmm)
REVERT: B   87 SER cc_start: 0.8398 (m) cc_final: 0.8125 (p)
REVERT: B  111 LYS cc_start: 0.7680 (ttmm) cc_final: 0.6992 (ttpp)
REVERT: B  122 SER cc_start: 0.7765 (t) cc_final: 0.7486 (t)
REVERT: B  123 ARG cc_start: 0.7214 (ttm170) cc_final: 0.7001 (ttm170)
REVERT: B  146 SER cc_start: 0.8349 (m) cc_final: 0.8017 (t)
REVERT: B  151 MET cc_start: 0.8090 (tpp) cc_final: 0.7848 (mmt)
REVERT: B  155 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (ttpt)
REVERT: B  178 GLU cc_start: 0.8151 (tt0) cc_final: 0.7804 (mp0)
REVERT: B  191 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7512 (ttt180)
REVERT: B  220 ARG cc_start: 0.7634 (mtp85) cc_final: 0.6789 (mtm-85)
REVERT: B  258 ASP cc_start: 0.6631 (t0) cc_final: 0.6404 (m-30)
REVERT: B  428 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7128 (tt0)
REVERT: B  469 HIS cc_start: 0.7260 (m90) cc_final: 0.6963 (m170)
REVERT: A   58 MET cc_start: 0.5038 (ttm) cc_final: 0.4579 (ttt)
REVERT: A   93 LEU cc_start: 0.7686 (mt) cc_final: 0.7235 (mm)
REVERT: A  126 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7571 (tp30)
REVERT: A  202 ARG cc_start: 0.8381 (mtm180) cc_final: 0.8093 (mtm110)
REVERT: A  221 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7273 (tp40)
  outliers start: 10
  outliers final: 3
  residues processed: 111
  average time/residue: 1.3443
  time to fit residues: 157.1433
Evaluate side-chains
  102 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain A residue  359 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.165241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.127024 restraints weight = 7635.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.17
r_work: 0.3169 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7727  Z= 0.224
  Angle     :  0.652  11.293  10542  Z= 0.321
  Chirality :  0.050   0.323   1217
  Planarity :  0.005   0.031   1320
  Dihedral  :  7.581  58.947   1316
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 23.73 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.28), residues: 905
  helix:  0.98 (0.28), residues: 328
  sheet: -0.95 (0.41), residues: 143
  loop :  0.05 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 455 
 HIS   0.005   0.001   HIS B 341 
 PHE   0.015   0.002   PHE A 338 
 TYR   0.029   0.002   TYR B 394 
 ARG   0.006   0.001   ARG B 510 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00750 (   15)
  link_NAG-ASN         : angle       2.86428 (   45)
  hydrogen bonds       : bond        0.05136 (  280)
  hydrogen bonds       : angle       4.91014 (  771)
  SS BOND              : bond        0.00298 (   13)
  SS BOND              : angle       1.09383 (   26)
  covalent geometry    : bond        0.00537 ( 7699)
  covalent geometry    : angle       0.62435 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 105
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7582 (mm-30)
REVERT: B   86 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7619 (ttmm)
REVERT: B  111 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7262 (ttpp)
REVERT: B  122 SER cc_start: 0.8060 (t) cc_final: 0.7766 (t)
REVERT: B  146 SER cc_start: 0.8462 (m) cc_final: 0.8156 (t)
REVERT: B  148 GLU cc_start: 0.7552 (mp0) cc_final: 0.7238 (pt0)
REVERT: B  151 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8067 (mmt)
REVERT: B  155 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8015 (ttpt)
REVERT: B  178 GLU cc_start: 0.8168 (tt0) cc_final: 0.7832 (mp0)
REVERT: B  191 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7671 (ttt180)
REVERT: B  220 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7219 (mtm-85)
REVERT: B  409 GLN cc_start: 0.8248 (mt0) cc_final: 0.7956 (mm110)
REVERT: B  469 HIS cc_start: 0.7531 (m90) cc_final: 0.7287 (m170)
REVERT: B  501 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7421 (mtp85)
REVERT: A   58 MET cc_start: 0.4740 (ttm) cc_final: 0.4022 (ttt)
REVERT: A   80 GLU cc_start: 0.8188 (tt0) cc_final: 0.7988 (tp30)
REVERT: A   93 LEU cc_start: 0.8164 (mt) cc_final: 0.7743 (mm)
REVERT: A  121 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8041 (mp)
REVERT: A  126 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8024 (tp30)
REVERT: A  202 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8129 (mtm180)
REVERT: A  221 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7633 (tp40)
REVERT: A  477 ASN cc_start: 0.7753 (t0) cc_final: 0.7423 (t0)
  outliers start: 52
  outliers final: 18
  residues processed: 137
  average time/residue: 1.2310
  time to fit residues: 178.2150
Evaluate side-chains
  116 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0970
   chunk 82 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  55 GLN
A 460 ASN
A 488 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.167820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.129283 restraints weight = 7734.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.26
r_work: 0.3218 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7727  Z= 0.132
  Angle     :  0.578  14.891  10542  Z= 0.277
  Chirality :  0.047   0.472   1217
  Planarity :  0.004   0.027   1320
  Dihedral  :  7.275  59.849   1314
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.47 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 905
  helix:  1.37 (0.29), residues: 332
  sheet: -1.00 (0.41), residues: 144
  loop :  0.10 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.019   0.001   PHE B  65 
 TYR   0.023   0.002   TYR B 394 
 ARG   0.005   0.000   ARG B  30 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00761 (   15)
  link_NAG-ASN         : angle       3.56312 (   45)
  hydrogen bonds       : bond        0.03955 (  280)
  hydrogen bonds       : angle       4.42948 (  771)
  SS BOND              : bond        0.00200 (   13)
  SS BOND              : angle       0.96121 (   26)
  covalent geometry    : bond        0.00307 ( 7699)
  covalent geometry    : angle       0.52908 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7390 (mm-30)
REVERT: B  111 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7078 (ttpp)
REVERT: B  115 MET cc_start: 0.8518 (tpt) cc_final: 0.8205 (tpt)
REVERT: B  122 SER cc_start: 0.8159 (t) cc_final: 0.7890 (t)
REVERT: B  135 GLN cc_start: 0.7765 (tp40) cc_final: 0.7418 (mm-40)
REVERT: B  146 SER cc_start: 0.8227 (m) cc_final: 0.7920 (t)
REVERT: B  151 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7770 (mmt)
REVERT: B  191 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7517 (ttt180)
REVERT: B  220 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7137 (mtt90)
REVERT: B  221 GLN cc_start: 0.8291 (mm-40) cc_final: 0.6838 (pp30)
REVERT: B  318 MET cc_start: 0.8271 (mmm) cc_final: 0.7909 (mmp)
REVERT: B  409 GLN cc_start: 0.8022 (mt0) cc_final: 0.7818 (mm110)
REVERT: B  457 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7003 (mmpt)
REVERT: B  469 HIS cc_start: 0.7172 (m90) cc_final: 0.6894 (m170)
REVERT: B  486 ARG cc_start: 0.7674 (tpt90) cc_final: 0.7367 (tpt170)
REVERT: A   58 MET cc_start: 0.5009 (ttm) cc_final: 0.4264 (ttt)
REVERT: A   93 LEU cc_start: 0.8172 (mt) cc_final: 0.7780 (mm)
REVERT: A  126 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7659 (tp30)
REVERT: A  202 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7794 (mtm110)
REVERT: A  221 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7435 (tp40)
REVERT: A  477 ASN cc_start: 0.7442 (t0) cc_final: 0.7137 (t0)
REVERT: A  506 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5794 (ptpt)
  outliers start: 35
  outliers final: 14
  residues processed: 125
  average time/residue: 1.2987
  time to fit residues: 171.5668
Evaluate side-chains
  110 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  506 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 51 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.166254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128065 restraints weight = 7719.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.24
r_work: 0.3208 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7727  Z= 0.144
  Angle     :  0.582  11.848  10542  Z= 0.280
  Chirality :  0.047   0.392   1217
  Planarity :  0.004   0.027   1320
  Dihedral  :  7.052  59.791   1307
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 24.10 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.28), residues: 905
  helix:  1.44 (0.29), residues: 334
  sheet: -0.99 (0.41), residues: 144
  loop :  0.14 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.013   0.001   PHE A 338 
 TYR   0.025   0.002   TYR B 394 
 ARG   0.006   0.000   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00709 (   15)
  link_NAG-ASN         : angle       3.35092 (   45)
  hydrogen bonds       : bond        0.03956 (  280)
  hydrogen bonds       : angle       4.36525 (  771)
  SS BOND              : bond        0.00194 (   13)
  SS BOND              : angle       1.04341 (   26)
  covalent geometry    : bond        0.00336 ( 7699)
  covalent geometry    : angle       0.53821 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 95
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7411 (mm-30)
REVERT: B  111 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7088 (ttpp)
REVERT: B  115 MET cc_start: 0.8520 (tpt) cc_final: 0.8257 (tpt)
REVERT: B  122 SER cc_start: 0.8306 (t) cc_final: 0.8025 (t)
REVERT: B  135 GLN cc_start: 0.7762 (tp40) cc_final: 0.7418 (mm-40)
REVERT: B  146 SER cc_start: 0.8184 (m) cc_final: 0.7888 (t)
REVERT: B  191 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7522 (ttt180)
REVERT: B  220 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7174 (mtt90)
REVERT: B  221 GLN cc_start: 0.8271 (mm-40) cc_final: 0.6827 (pp30)
REVERT: B  318 MET cc_start: 0.8332 (mmm) cc_final: 0.8121 (mmp)
REVERT: B  409 GLN cc_start: 0.8026 (mt0) cc_final: 0.7798 (mm110)
REVERT: B  469 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.7015 (m170)
REVERT: B  486 ARG cc_start: 0.7639 (tpt90) cc_final: 0.7324 (tpt170)
REVERT: A   58 MET cc_start: 0.5151 (ttm) cc_final: 0.4401 (ttt)
REVERT: A   93 LEU cc_start: 0.8247 (mt) cc_final: 0.8012 (mt)
REVERT: A  121 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: A  126 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7842 (tp30)
REVERT: A  202 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7789 (mtm110)
REVERT: A  221 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7441 (tp40)
REVERT: A  474 GLN cc_start: 0.8429 (tt0) cc_final: 0.8117 (tt0)
REVERT: A  477 ASN cc_start: 0.7302 (t0) cc_final: 0.7021 (t0)
REVERT: A  493 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8355 (t)
  outliers start: 42
  outliers final: 27
  residues processed: 126
  average time/residue: 1.1522
  time to fit residues: 154.0458
Evaluate side-chains
  122 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0670
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 78 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
B 145 HIS
B 332 HIS
** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.166394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.128397 restraints weight = 7613.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.23
r_work: 0.3204 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7727  Z= 0.140
  Angle     :  0.569  11.295  10542  Z= 0.274
  Chirality :  0.046   0.338   1217
  Planarity :  0.004   0.027   1320
  Dihedral  :  6.731  59.235   1307
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 23.98 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.28), residues: 905
  helix:  1.45 (0.29), residues: 336
  sheet: -0.99 (0.40), residues: 149
  loop :  0.18 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.013   0.001   PHE A 338 
 TYR   0.025   0.002   TYR B 394 
 ARG   0.005   0.000   ARG A 317 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00767 (   15)
  link_NAG-ASN         : angle       3.15139 (   45)
  hydrogen bonds       : bond        0.03844 (  280)
  hydrogen bonds       : angle       4.25639 (  771)
  SS BOND              : bond        0.00193 (   13)
  SS BOND              : angle       1.10435 (   26)
  covalent geometry    : bond        0.00329 ( 7699)
  covalent geometry    : angle       0.52930 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 101
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 MET cc_start: 0.8447 (ttt) cc_final: 0.8217 (ttt)
REVERT: B   81 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7435 (mm-30)
REVERT: B  111 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7044 (ttpp)
REVERT: B  115 MET cc_start: 0.8537 (tpt) cc_final: 0.8235 (tpt)
REVERT: B  122 SER cc_start: 0.8383 (t) cc_final: 0.8083 (t)
REVERT: B  135 GLN cc_start: 0.7781 (tp40) cc_final: 0.7464 (mm-40)
REVERT: B  146 SER cc_start: 0.8078 (m) cc_final: 0.7817 (t)
REVERT: B  151 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7025 (mpp)
REVERT: B  155 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7842 (ttpt)
REVERT: B  191 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7524 (ttt180)
REVERT: B  220 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7171 (mtm-85)
REVERT: B  221 GLN cc_start: 0.8244 (mm-40) cc_final: 0.6796 (pp30)
REVERT: B  409 GLN cc_start: 0.8033 (mt0) cc_final: 0.7794 (mm110)
REVERT: B  455 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7826 (t0)
REVERT: B  457 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7075 (mtpt)
REVERT: B  469 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.7036 (m170)
REVERT: B  486 ARG cc_start: 0.7611 (tpt90) cc_final: 0.7305 (tpt170)
REVERT: A   58 MET cc_start: 0.5213 (ttm) cc_final: 0.4562 (ttt)
REVERT: A   93 LEU cc_start: 0.8313 (mt) cc_final: 0.8103 (mt)
REVERT: A  126 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7843 (tp30)
REVERT: A  221 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7459 (tp40)
REVERT: A  287 GLU cc_start: 0.8401 (tp30) cc_final: 0.7629 (tp30)
REVERT: A  422 GLU cc_start: 0.8271 (tt0) cc_final: 0.7981 (tt0)
REVERT: A  477 ASN cc_start: 0.7210 (t0) cc_final: 0.6918 (t0)
REVERT: A  506 LYS cc_start: 0.5428 (OUTLIER) cc_final: 0.5183 (ptpt)
  outliers start: 42
  outliers final: 27
  residues processed: 131
  average time/residue: 1.0584
  time to fit residues: 147.5236
Evaluate side-chains
  129 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain B residue  489 THR
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 THR
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0570
   chunk 15 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.164389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.126309 restraints weight = 7654.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.23
r_work: 0.3186 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7727  Z= 0.167
  Angle     :  0.591  10.640  10542  Z= 0.288
  Chirality :  0.047   0.348   1217
  Planarity :  0.004   0.030   1320
  Dihedral  :  6.698  59.816   1307
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 23.73 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.28), residues: 905
  helix:  1.40 (0.29), residues: 333
  sheet: -0.99 (0.40), residues: 150
  loop :  0.17 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.015   0.002   PHE A 338 
 TYR   0.028   0.002   TYR B 394 
 ARG   0.005   0.001   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00746 (   15)
  link_NAG-ASN         : angle       3.09230 (   45)
  hydrogen bonds       : bond        0.04143 (  280)
  hydrogen bonds       : angle       4.37869 (  771)
  SS BOND              : bond        0.00226 (   13)
  SS BOND              : angle       1.24112 (   26)
  covalent geometry    : bond        0.00396 ( 7699)
  covalent geometry    : angle       0.55344 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 98
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7569 (mm-30)
REVERT: B  111 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7217 (ttpp)
REVERT: B  122 SER cc_start: 0.8398 (t) cc_final: 0.8061 (t)
REVERT: B  135 GLN cc_start: 0.7924 (tp40) cc_final: 0.7622 (mm-40)
REVERT: B  146 SER cc_start: 0.8176 (m) cc_final: 0.7889 (t)
REVERT: B  155 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7954 (ttpt)
REVERT: B  191 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7517 (ttt180)
REVERT: B  220 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7254 (mtt90)
REVERT: B  221 GLN cc_start: 0.8371 (mm-40) cc_final: 0.6869 (pp30)
REVERT: B  409 GLN cc_start: 0.8130 (mt0) cc_final: 0.7809 (mm110)
REVERT: B  452 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8157 (mtt)
REVERT: B  455 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8130 (t0)
REVERT: B  457 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7162 (mtpt)
REVERT: B  469 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7239 (m170)
REVERT: B  486 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7394 (tpt170)
REVERT: A   58 MET cc_start: 0.4984 (ttm) cc_final: 0.4363 (ttt)
REVERT: A  126 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7979 (tp30)
REVERT: A  221 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7555 (tp40)
REVERT: A  287 GLU cc_start: 0.8531 (tp30) cc_final: 0.8308 (tp30)
REVERT: A  422 GLU cc_start: 0.8470 (tt0) cc_final: 0.8169 (tt0)
REVERT: A  477 ASN cc_start: 0.7429 (t0) cc_final: 0.7151 (t0)
REVERT: A  493 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.7992 (m)
REVERT: A  506 LYS cc_start: 0.5577 (pttp) cc_final: 0.5222 (ptpt)
  outliers start: 43
  outliers final: 26
  residues processed: 130
  average time/residue: 1.0978
  time to fit residues: 152.0313
Evaluate side-chains
  123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 90
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 488 HIS
A 247 GLN
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.164477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.126614 restraints weight = 7587.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.21
r_work: 0.3181 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7727  Z= 0.164
  Angle     :  0.584  10.731  10542  Z= 0.284
  Chirality :  0.047   0.348   1217
  Planarity :  0.004   0.030   1320
  Dihedral  :  6.638  59.421   1307
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.60 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.28), residues: 905
  helix:  1.53 (0.29), residues: 327
  sheet: -0.93 (0.40), residues: 146
  loop :  0.25 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.015   0.002   PHE A 338 
 TYR   0.027   0.002   TYR B 394 
 ARG   0.008   0.000   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00692 (   15)
  link_NAG-ASN         : angle       2.96033 (   45)
  hydrogen bonds       : bond        0.04036 (  280)
  hydrogen bonds       : angle       4.36190 (  771)
  SS BOND              : bond        0.00203 (   13)
  SS BOND              : angle       1.23553 (   26)
  covalent geometry    : bond        0.00388 ( 7699)
  covalent geometry    : angle       0.54993 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7543 (mm-30)
REVERT: B  111 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7162 (ttpp)
REVERT: B  122 SER cc_start: 0.8431 (t) cc_final: 0.8107 (t)
REVERT: B  135 GLN cc_start: 0.7914 (tp40) cc_final: 0.7622 (mm-40)
REVERT: B  146 SER cc_start: 0.8113 (m) cc_final: 0.7863 (t)
REVERT: B  155 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8036 (ttpt)
REVERT: B  191 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7527 (ttt180)
REVERT: B  220 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7258 (mtt90)
REVERT: B  221 GLN cc_start: 0.8343 (mm-40) cc_final: 0.6839 (pp30)
REVERT: B  315 MET cc_start: 0.8239 (tpt) cc_final: 0.7825 (tpt)
REVERT: B  409 GLN cc_start: 0.8137 (mt0) cc_final: 0.7805 (mm110)
REVERT: B  452 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8177 (mtt)
REVERT: B  455 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8156 (t0)
REVERT: B  457 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7172 (mtpt)
REVERT: B  469 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7225 (m170)
REVERT: B  486 ARG cc_start: 0.7783 (tpt90) cc_final: 0.7429 (tpt170)
REVERT: A   58 MET cc_start: 0.4956 (ttm) cc_final: 0.4322 (ttt)
REVERT: A  126 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7979 (tp30)
REVERT: A  221 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7555 (tp40)
REVERT: A  287 GLU cc_start: 0.8546 (tp30) cc_final: 0.8342 (tp30)
REVERT: A  422 GLU cc_start: 0.8478 (tt0) cc_final: 0.8189 (tt0)
REVERT: A  474 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8164 (tt0)
REVERT: A  477 ASN cc_start: 0.7422 (t0) cc_final: 0.7083 (m-40)
REVERT: A  479 GLN cc_start: 0.7366 (mt0) cc_final: 0.6835 (mm-40)
REVERT: A  493 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8353 (t)
REVERT: A  506 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.5141 (ptpt)
  outliers start: 41
  outliers final: 27
  residues processed: 127
  average time/residue: 1.0538
  time to fit residues: 143.0772
Evaluate side-chains
  128 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  405 CYS
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.164318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.126421 restraints weight = 7681.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.22
r_work: 0.3185 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7727  Z= 0.161
  Angle     :  0.585  10.923  10542  Z= 0.285
  Chirality :  0.047   0.355   1217
  Planarity :  0.004   0.030   1320
  Dihedral  :  6.648  59.641   1307
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.72 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.29), residues: 905
  helix:  1.57 (0.29), residues: 327
  sheet: -1.00 (0.40), residues: 152
  loop :  0.29 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.015   0.002   PHE A 338 
 TYR   0.027   0.002   TYR B 394 
 ARG   0.008   0.001   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00690 (   15)
  link_NAG-ASN         : angle       2.89392 (   45)
  hydrogen bonds       : bond        0.04023 (  280)
  hydrogen bonds       : angle       4.35757 (  771)
  SS BOND              : bond        0.00206 (   13)
  SS BOND              : angle       1.09995 (   26)
  covalent geometry    : bond        0.00383 ( 7699)
  covalent geometry    : angle       0.55237 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7544 (mm-30)
REVERT: B  111 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7163 (ttpp)
REVERT: B  122 SER cc_start: 0.8345 (t) cc_final: 0.8020 (t)
REVERT: B  135 GLN cc_start: 0.7925 (tp40) cc_final: 0.7633 (mm-40)
REVERT: B  146 SER cc_start: 0.8105 (m) cc_final: 0.7850 (t)
REVERT: B  155 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7954 (ttpt)
REVERT: B  191 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7510 (ttt180)
REVERT: B  220 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7272 (mtt90)
REVERT: B  221 GLN cc_start: 0.8342 (mm-40) cc_final: 0.6863 (pp30)
REVERT: B  409 GLN cc_start: 0.8159 (mt0) cc_final: 0.7822 (mm110)
REVERT: B  452 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8148 (mtt)
REVERT: B  455 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8132 (t0)
REVERT: B  457 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7205 (mtpt)
REVERT: B  469 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7228 (m170)
REVERT: B  470 ASP cc_start: 0.7422 (m-30) cc_final: 0.7149 (t70)
REVERT: B  486 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7434 (tpt170)
REVERT: A   58 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.4324 (ttt)
REVERT: A  126 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7981 (tp30)
REVERT: A  221 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7566 (tp40)
REVERT: A  422 GLU cc_start: 0.8461 (tt0) cc_final: 0.8170 (tt0)
REVERT: A  474 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8136 (tt0)
REVERT: A  477 ASN cc_start: 0.7436 (t0) cc_final: 0.7074 (m-40)
REVERT: A  479 GLN cc_start: 0.7363 (mt0) cc_final: 0.6808 (mm-40)
REVERT: A  493 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8364 (t)
REVERT: A  506 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.5132 (ptpt)
  outliers start: 41
  outliers final: 26
  residues processed: 126
  average time/residue: 1.1211
  time to fit residues: 150.1645
Evaluate side-chains
  130 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  191 ARG
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  405 CYS
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.164921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.127114 restraints weight = 7753.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.23
r_work: 0.3189 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7727  Z= 0.149
  Angle     :  0.570  11.168  10542  Z= 0.277
  Chirality :  0.046   0.362   1217
  Planarity :  0.004   0.031   1320
  Dihedral  :  6.532  59.547   1306
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 25.22 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.29), residues: 905
  helix:  1.65 (0.29), residues: 327
  sheet: -0.99 (0.40), residues: 152
  loop :  0.32 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.014   0.001   PHE A 338 
 TYR   0.025   0.002   TYR B 394 
 ARG   0.008   0.000   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00670 (   15)
  link_NAG-ASN         : angle       2.75471 (   45)
  hydrogen bonds       : bond        0.03882 (  280)
  hydrogen bonds       : angle       4.31573 (  771)
  SS BOND              : bond        0.00188 (   13)
  SS BOND              : angle       1.16690 (   26)
  covalent geometry    : bond        0.00352 ( 7699)
  covalent geometry    : angle       0.53978 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 95
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7418 (mm-30)
REVERT: B  111 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7032 (ttpp)
REVERT: B  122 SER cc_start: 0.8427 (t) cc_final: 0.8144 (t)
REVERT: B  135 GLN cc_start: 0.7796 (tp40) cc_final: 0.7493 (mm-40)
REVERT: B  146 SER cc_start: 0.8061 (m) cc_final: 0.7798 (t)
REVERT: B  155 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7827 (ttpt)
REVERT: B  220 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7256 (mtt90)
REVERT: B  221 GLN cc_start: 0.8199 (mm-40) cc_final: 0.6817 (pp30)
REVERT: B  409 GLN cc_start: 0.8066 (mt0) cc_final: 0.7798 (mm110)
REVERT: B  452 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8107 (mtt)
REVERT: B  455 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7877 (t0)
REVERT: B  457 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7114 (mtpt)
REVERT: B  469 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.7130 (m170)
REVERT: B  470 ASP cc_start: 0.7168 (m-30) cc_final: 0.6965 (t70)
REVERT: B  486 ARG cc_start: 0.7651 (tpt90) cc_final: 0.7325 (tpt170)
REVERT: A   58 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4634 (ttt)
REVERT: A  126 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7820 (tp30)
REVERT: A  221 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7477 (tp40)
REVERT: A  422 GLU cc_start: 0.8287 (tt0) cc_final: 0.7994 (tt0)
REVERT: A  474 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8066 (tt0)
REVERT: A  477 ASN cc_start: 0.7255 (t0) cc_final: 0.6957 (m-40)
REVERT: A  479 GLN cc_start: 0.7198 (mt0) cc_final: 0.6767 (mm-40)
REVERT: A  493 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (t)
REVERT: A  497 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7250 (mmmt)
REVERT: A  506 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4917 (ptpt)
  outliers start: 40
  outliers final: 26
  residues processed: 123
  average time/residue: 1.0612
  time to fit residues: 139.1478
Evaluate side-chains
  130 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  405 CYS
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0770
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.166379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128955 restraints weight = 7684.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.22
r_work: 0.3215 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7727  Z= 0.124
  Angle     :  0.547  11.041  10542  Z= 0.265
  Chirality :  0.045   0.355   1217
  Planarity :  0.004   0.056   1320
  Dihedral  :  6.417  57.802   1306
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 25.96 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 905
  helix:  1.75 (0.29), residues: 330
  sheet: -0.98 (0.40), residues: 150
  loop :  0.38 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.013   0.001   PHE A 338 
 TYR   0.023   0.002   TYR B 394 
 ARG   0.014   0.001   ARG A 317 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00647 (   15)
  link_NAG-ASN         : angle       2.64935 (   45)
  hydrogen bonds       : bond        0.03589 (  280)
  hydrogen bonds       : angle       4.20036 (  771)
  SS BOND              : bond        0.00165 (   13)
  SS BOND              : angle       0.99565 (   26)
  covalent geometry    : bond        0.00288 ( 7699)
  covalent geometry    : angle       0.51818 (10471)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 98
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7433 (mm-30)
REVERT: B  111 LYS cc_start: 0.7643 (ttmm) cc_final: 0.6948 (ttpp)
REVERT: B  122 SER cc_start: 0.8465 (t) cc_final: 0.8186 (t)
REVERT: B  135 GLN cc_start: 0.7763 (tp40) cc_final: 0.7434 (mm-40)
REVERT: B  146 SER cc_start: 0.7898 (m) cc_final: 0.7662 (t)
REVERT: B  155 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7809 (ttpt)
REVERT: B  220 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7215 (mtt90)
REVERT: B  221 GLN cc_start: 0.8160 (mm-40) cc_final: 0.6774 (pp30)
REVERT: B  315 MET cc_start: 0.8142 (tpt) cc_final: 0.7776 (tpt)
REVERT: B  409 GLN cc_start: 0.8037 (mt0) cc_final: 0.7771 (mm110)
REVERT: B  452 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8061 (mtt)
REVERT: B  455 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7878 (t0)
REVERT: B  457 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7135 (mtpt)
REVERT: B  469 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.7063 (m170)
REVERT: B  470 ASP cc_start: 0.7113 (m-30) cc_final: 0.6901 (t70)
REVERT: B  486 ARG cc_start: 0.7654 (tpt90) cc_final: 0.7327 (tpt170)
REVERT: A   58 MET cc_start: 0.5198 (OUTLIER) cc_final: 0.4599 (ttt)
REVERT: A  126 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7808 (tp30)
REVERT: A  221 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7496 (tp40)
REVERT: A  292 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6438 (m-40)
REVERT: A  422 GLU cc_start: 0.8232 (tt0) cc_final: 0.7954 (tt0)
REVERT: A  474 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8049 (tt0)
REVERT: A  477 ASN cc_start: 0.7162 (t0) cc_final: 0.6903 (m-40)
REVERT: A  479 GLN cc_start: 0.7261 (mt0) cc_final: 0.6827 (mm-40)
REVERT: A  493 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  497 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7247 (mmmt)
REVERT: A  506 LYS cc_start: 0.5231 (OUTLIER) cc_final: 0.4918 (ptpt)
  outliers start: 35
  outliers final: 21
  residues processed: 123
  average time/residue: 1.1333
  time to fit residues: 148.5554
Evaluate side-chains
  127 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 ASP
Chi-restraints excluded: chain B residue  132 THR
Chi-restraints excluded: chain B residue  155 LYS
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 GLU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  452 MET
Chi-restraints excluded: chain B residue  455 ASP
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  469 HIS
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  405 CYS
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0970
   chunk 79 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 460 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.165219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127503 restraints weight = 7679.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.22
r_work: 0.3195 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7727  Z= 0.147
  Angle     :  0.569  11.291  10542  Z= 0.277
  Chirality :  0.046   0.366   1217
  Planarity :  0.004   0.032   1320
  Dihedral  :  6.492  59.474   1306
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 25.46 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.29), residues: 905
  helix:  1.73 (0.29), residues: 328
  sheet: -1.04 (0.39), residues: 162
  loop :  0.39 (0.33), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 455 
 HIS   0.004   0.001   HIS A 400 
 PHE   0.014   0.001   PHE A 338 
 TYR   0.025   0.002   TYR B 394 
 ARG   0.008   0.000   ARG A 254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00657 (   15)
  link_NAG-ASN         : angle       2.63041 (   45)
  hydrogen bonds       : bond        0.03843 (  280)
  hydrogen bonds       : angle       4.26791 (  771)
  SS BOND              : bond        0.00174 (   13)
  SS BOND              : angle       1.12283 (   26)
  covalent geometry    : bond        0.00349 ( 7699)
  covalent geometry    : angle       0.54162 (10471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5506.73 seconds
wall clock time: 94 minutes 48.75 seconds (5688.75 seconds total)