Starting phenix.real_space_refine
on Mon Jul 28 14:50:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wp8_37711/07_2025/8wp8_37711.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      36      5.16       5
     C    4185      2.51       5
     N    1068      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6539
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1493
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 11, 'TRANS': 172}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 6.70, per 1000 atoms: 1.02
  Number of scatterers: 6539
  At special positions: 0
  Unit cell: (77.97, 87.63, 117.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      36     16.00
     O    1249      8.00
     N    1068      7.00
     C    4185      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG A 702 " - " ASN A  53 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A 432 "
      " NAG B 601 " - " ASN B 354 "
      " NAG B 602 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  90 "
      " NAG D   1 " - " ASN A 546 "
      " NAG E   1 " - " ASN A 103 "
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "


  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1474

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      55.0% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.147A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN A  53 " --> pdb=" O   ASN A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.565A  pdb=" N   THR A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA A  80 " --> pdb=" O   GLN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 92 through 101
      removed outlier: 3.776A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 158 through 173
      removed outlier: 3.780A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.632A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 249
      removed outlier: 3.956A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ILE A 233 " --> pdb=" O   THR A 229 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LYS A 234 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.748A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.912A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.560A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.649A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.613A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A 481 " --> pdb=" O   TRP A 477 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.653A  pdb=" N   THR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.817A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.588A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 366 through 372
      removed outlier: 3.639A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 4.245A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.701A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.609A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.227A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASP B 398 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL B 512 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454

    268 hydrogen bonds defined for protein.
    759 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: 1.78

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1185
        1.33 -     1.45: 1904
        1.45 -     1.57: 3581
        1.57 -     1.69: 0
        1.69 -     1.82: 57
  Bond restraints: 6727
  Sorted by residual:
  bond pdb=" C   PRO B 491 "
       pdb=" O   PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.239  1.205  0.034 1.27e-02 6.20e+03 7.14e+00
  bond pdb=" N   PHE B 490 "
       pdb=" CA  PHE B 490 "
    ideal  model  delta    sigma   weight residual
    1.452  1.490 -0.037 1.41e-02 5.03e+03 7.05e+00
  bond pdb=" N   LEU B 492 "
       pdb=" CA  LEU B 492 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.030 1.23e-02 6.61e+03 5.97e+00
  bond pdb=" N   PRO B 491 "
       pdb=" CA  PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.469  1.445  0.024 1.25e-02 6.40e+03 3.73e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.554 -0.035 2.00e-02 2.50e+03 3.08e+00
  ... (remaining 6722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 8846
        1.40 -     2.80: 229
        2.80 -     4.20: 46
        4.20 -     5.60: 16
        5.60 -     7.00: 5
  Bond angle restraints: 9142
  Sorted by residual:
  angle pdb=" N   PHE B 338 "
        pdb=" CA  PHE B 338 "
        pdb=" C   PHE B 338 "
      ideal   model   delta    sigma   weight residual
     114.31  108.01    6.30 1.29e+00 6.01e-01 2.38e+01
  angle pdb=" CA  PHE B 490 "
        pdb=" C   PHE B 490 "
        pdb=" N   PRO B 491 "
      ideal   model   delta    sigma   weight residual
     117.67  121.79   -4.12 1.01e+00 9.80e-01 1.66e+01
  angle pdb=" N   CYS B 361 "
        pdb=" CA  CYS B 361 "
        pdb=" C   CYS B 361 "
      ideal   model   delta    sigma   weight residual
     107.88  112.87   -4.99 1.41e+00 5.03e-01 1.25e+01
  angle pdb=" C   GLU A 171 "
        pdb=" N   VAL A 172 "
        pdb=" CA  VAL A 172 "
      ideal   model   delta    sigma   weight residual
     122.63  118.69    3.94 1.19e+00 7.06e-01 1.10e+01
  angle pdb=" C   LEU B 492 "
        pdb=" N   GLN B 493 "
        pdb=" CA  GLN B 493 "
      ideal   model   delta    sigma   weight residual
     121.94  127.24   -5.30 1.76e+00 3.23e-01 9.06e+00
  ... (remaining 9137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.98: 3840
       21.98 -    43.96: 235
       43.96 -    65.94: 22
       65.94 -    87.92: 23
       87.92 -   109.90: 8
  Dihedral angle restraints: 4128
    sinusoidal: 1831
      harmonic: 2297
  Sorted by residual:
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -9.72  -76.28     1      1.00e+01 1.00e-02 7.32e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.97  -71.97     1      1.00e+01 1.00e-02 6.63e+01
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.82   33.82     1      1.00e+01 1.00e-02 1.62e+01
  ... (remaining 4125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 964
       0.106 -    0.212: 17
       0.212 -    0.317: 3
       0.317 -    0.423: 0
       0.423 -    0.529: 2
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 6.99e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.91   -0.49 2.00e-01 2.50e+01 5.91e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 983 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 602 "    0.303 2.00e-02 2.50e+03   2.55e-01 8.12e+02
        pdb=" C7  NAG B 602 "   -0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG B 602 "    0.188 2.00e-02 2.50e+03
        pdb=" N2  NAG B 602 "   -0.437 2.00e-02 2.50e+03
        pdb=" O7  NAG B 602 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 601 "    0.044 2.00e-02 2.50e+03   3.66e-02 1.67e+01
        pdb=" C7  NAG B 601 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG B 601 "    0.034 2.00e-02 2.50e+03
        pdb=" N2  NAG B 601 "   -0.058 2.00e-02 2.50e+03
        pdb=" O7  NAG B 601 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 354 "    0.014 2.00e-02 2.50e+03   1.69e-02 3.56e+00
        pdb=" CG  ASN B 354 "   -0.001 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 354 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 354 "   -0.028 2.00e-02 2.50e+03
        pdb=" C1  NAG B 601 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 73
        2.66 -     3.22: 5961
        3.22 -     3.78: 9514
        3.78 -     4.34: 12755
        4.34 -     4.90: 21373
  Nonbonded interactions: 49676
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.100 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.118 2.230
  nonbonded pdb=" OG  SER B 469 "
            pdb=" OE1 GLU B 471 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   MET A 152 "
            pdb=" NH2 ARG A 161 "
     model   vdw
     2.315 3.120
  ... (remaining 49671 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 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:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.160
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
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      :  0.005   0.209   6748  Z= 0.204
  Angle     :  0.635  12.236   9193  Z= 0.313
  Chirality :  0.049   0.529    986
  Planarity :  0.008   0.255   1164
  Dihedral  : 15.475 109.902   2636
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.24 (0.31), residues: 777
  helix:  1.72 (0.29), residues: 362
  sheet: -1.07 (0.89), residues: 32
  loop : -1.32 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 203 
 HIS   0.008   0.001   HIS A 374 
 PHE   0.019   0.001   PHE B 515 
 TYR   0.013   0.001   TYR B 489 
 ARG   0.002   0.000   ARG A 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00609 (    8)
  link_NAG-ASN         : angle       4.47105 (   24)
  link_BETA1-4         : bond        0.00669 (    5)
  link_BETA1-4         : angle       2.62598 (   15)
  hydrogen bonds       : bond        0.16329 (  268)
  hydrogen bonds       : angle       6.00395 (  759)
  metal coordination   : bond        0.20307 (    2)
  SS BOND              : bond        0.00152 (    6)
  SS BOND              : angle       0.62947 (   12)
  covalent geometry    : bond        0.00319 ( 6727)
  covalent geometry    : angle       0.58428 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.7688 (tp) cc_final: 0.7455 (tt)
REVERT: A  190 MET cc_start: 0.7344 (tmm) cc_final: 0.7135 (tmt)
REVERT: A  218 SER cc_start: 0.8610 (t) cc_final: 0.8227 (p)
REVERT: A  227 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6925 (mm-30)
REVERT: A  368 ASP cc_start: 0.6784 (m-30) cc_final: 0.6567 (m-30)
REVERT: A  471 ASP cc_start: 0.7591 (p0) cc_final: 0.7355 (p0)
REVERT: A  536 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6221 (tm-30)
REVERT: A  544 ILE cc_start: 0.8361 (pt) cc_final: 0.8003 (mp)
REVERT: A  547 SER cc_start: 0.7799 (t) cc_final: 0.7148 (p)
REVERT: B  420 ASP cc_start: 0.7445 (m-30) cc_final: 0.7239 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 1.1297
  time to fit residues: 231.6559
Evaluate side-chains
  169 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 401 HIS
A 535 HIS
A 572 ASN
B 339 HIS
B 409 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.148184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.124199 restraints weight = 17117.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.35
r_work: 0.3442 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6748  Z= 0.167
  Angle     :  0.648  12.407   9193  Z= 0.317
  Chirality :  0.049   0.586    986
  Planarity :  0.005   0.039   1164
  Dihedral  :  8.778  66.934   1118
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 11.21 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.31), residues: 777
  helix:  1.54 (0.29), residues: 366
  sheet: -0.68 (0.86), residues: 34
  loop : -1.26 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 203 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.016   0.002   PHE B 515 
 TYR   0.015   0.002   TYR A 385 
 ARG   0.003   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00542 (    8)
  link_NAG-ASN         : angle       3.77495 (   24)
  link_BETA1-4         : bond        0.00642 (    5)
  link_BETA1-4         : angle       2.50879 (   15)
  hydrogen bonds       : bond        0.06240 (  268)
  hydrogen bonds       : angle       4.81618 (  759)
  metal coordination   : bond        0.00803 (    2)
  SS BOND              : bond        0.00435 (    6)
  SS BOND              : angle       0.78526 (   12)
  covalent geometry    : bond        0.00381 ( 6727)
  covalent geometry    : angle       0.61088 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 175
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7527 (mp0)
REVERT: A   88 ILE cc_start: 0.8240 (pt) cc_final: 0.7712 (pp)
REVERT: A  126 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: A  149 ASN cc_start: 0.7953 (m-40) cc_final: 0.7664 (m-40)
REVERT: A  192 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7920 (mtt-85)
REVERT: A  227 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7622 (mm-30)
REVERT: A  297 MET cc_start: 0.7941 (mmm) cc_final: 0.7624 (mtp)
REVERT: A  471 ASP cc_start: 0.8061 (p0) cc_final: 0.7766 (p0)
REVERT: A  483 GLU cc_start: 0.7720 (tt0) cc_final: 0.7341 (tm-30)
REVERT: A  489 GLU cc_start: 0.8201 (pm20) cc_final: 0.7858 (pm20)
REVERT: A  536 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6982 (tm-30)
REVERT: A  544 ILE cc_start: 0.8645 (pt) cc_final: 0.8422 (mp)
REVERT: B  405 ASN cc_start: 0.8424 (p0) cc_final: 0.7969 (p0)
REVERT: B  420 ASP cc_start: 0.7922 (m-30) cc_final: 0.7631 (m-30)
  outliers start: 19
  outliers final: 7
  residues processed: 179
  average time/residue: 1.0631
  time to fit residues: 200.9813
Evaluate side-chains
  172 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
B 339 HIS
B 439 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.145586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.122523 restraints weight = 13827.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.00
r_work: 0.3435 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6748  Z= 0.188
  Angle     :  0.639  12.245   9193  Z= 0.316
  Chirality :  0.049   0.525    986
  Planarity :  0.005   0.041   1164
  Dihedral  :  6.168  52.091   1118
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.28 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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 (0.31), residues: 777
  helix:  1.65 (0.29), residues: 353
  sheet: -0.80 (0.92), residues: 34
  loop : -1.32 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 353 
 HIS   0.007   0.001   HIS A 401 
 PHE   0.020   0.002   PHE A 308 
 TYR   0.018   0.002   TYR A 385 
 ARG   0.002   0.001   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00468 (    8)
  link_NAG-ASN         : angle       3.71493 (   24)
  link_BETA1-4         : bond        0.00697 (    5)
  link_BETA1-4         : angle       2.40943 (   15)
  hydrogen bonds       : bond        0.06612 (  268)
  hydrogen bonds       : angle       4.67124 (  759)
  metal coordination   : bond        0.00301 (    2)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       0.87833 (   12)
  covalent geometry    : bond        0.00433 ( 6727)
  covalent geometry    : angle       0.60340 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A  149 ASN cc_start: 0.7921 (m-40) cc_final: 0.7652 (m-40)
REVERT: A  169 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7034 (mtt-85)
REVERT: A  227 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7465 (mm-30)
REVERT: A  249 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6521 (ttm)
REVERT: A  288 LYS cc_start: 0.8923 (mttt) cc_final: 0.8675 (mtmm)
REVERT: A  297 MET cc_start: 0.7983 (mmm) cc_final: 0.7621 (mtp)
REVERT: A  483 GLU cc_start: 0.7655 (tt0) cc_final: 0.7384 (tm-30)
REVERT: A  485 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7694 (t)
REVERT: A  527 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7622 (tp30)
REVERT: A  536 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6914 (tm-30)
REVERT: A  544 ILE cc_start: 0.8644 (pt) cc_final: 0.8387 (mp)
REVERT: B  405 ASN cc_start: 0.8518 (p0) cc_final: 0.8018 (p0)
REVERT: B  420 ASP cc_start: 0.7931 (m-30) cc_final: 0.7595 (m-30)
  outliers start: 22
  outliers final: 8
  residues processed: 171
  average time/residue: 1.1500
  time to fit residues: 206.7818
Evaluate side-chains
  164 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  169 ARG
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  443 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 71 optimal weight:    0.0470
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0770
   chunk 38 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.2234

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
B 439 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.127234 restraints weight = 11685.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.71
r_work: 0.3513 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6748  Z= 0.113
  Angle     :  0.586  12.042   9193  Z= 0.285
  Chirality :  0.044   0.486    986
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.202  52.557   1118
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.45 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.38 (0.32), residues: 777
  helix:  1.66 (0.29), residues: 368
  sheet: -0.82 (0.94), residues: 32
  loop : -1.13 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 610 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.016   0.001   PHE B 515 
 TYR   0.018   0.001   TYR A 202 
 ARG   0.010   0.001   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00639 (    8)
  link_NAG-ASN         : angle       3.62895 (   24)
  link_BETA1-4         : bond        0.00606 (    5)
  link_BETA1-4         : angle       2.02420 (   15)
  hydrogen bonds       : bond        0.04797 (  268)
  hydrogen bonds       : angle       4.38050 (  759)
  metal coordination   : bond        0.00114 (    2)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.56181 (   12)
  covalent geometry    : bond        0.00241 ( 6727)
  covalent geometry    : angle       0.55141 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8029 (ttm)
REVERT: A   75 GLU cc_start: 0.7506 (tp30) cc_final: 0.7142 (tp30)
REVERT: A   87 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8299 (mt-10)
REVERT: A  149 ASN cc_start: 0.7874 (m-40) cc_final: 0.7634 (m-40)
REVERT: A  249 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6481 (ttm)
REVERT: A  297 MET cc_start: 0.7940 (mmm) cc_final: 0.7688 (mtp)
REVERT: A  471 ASP cc_start: 0.8016 (p0) cc_final: 0.7736 (p0)
REVERT: A  483 GLU cc_start: 0.7584 (tt0) cc_final: 0.7336 (tm-30)
REVERT: A  527 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7614 (tp30)
REVERT: A  536 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6820 (tm-30)
REVERT: A  544 ILE cc_start: 0.8615 (pt) cc_final: 0.8348 (mp)
REVERT: B  405 ASN cc_start: 0.8482 (p0) cc_final: 0.7975 (p0)
REVERT: B  420 ASP cc_start: 0.7803 (m-30) cc_final: 0.7506 (m-30)
REVERT: B  468 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8232 (mp)
  outliers start: 17
  outliers final: 4
  residues processed: 158
  average time/residue: 1.0447
  time to fit residues: 174.5751
Evaluate side-chains
  154 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0050
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
B 437 ASN
B 439 ASN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.147109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123442 restraints weight = 17392.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 3.32
r_work: 0.3439 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6748  Z= 0.147
  Angle     :  0.606  11.105   9193  Z= 0.298
  Chirality :  0.046   0.478    986
  Planarity :  0.004   0.041   1164
  Dihedral  :  4.996  52.445   1118
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.76 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.36 (0.31), residues: 777
  helix:  1.65 (0.28), residues: 366
  sheet: -1.31 (0.75), residues: 44
  loop : -1.04 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 610 
 HIS   0.008   0.001   HIS A 265 
 PHE   0.015   0.002   PHE A 308 
 TYR   0.017   0.002   TYR A 202 
 ARG   0.008   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00479 (    8)
  link_NAG-ASN         : angle       3.42431 (   24)
  link_BETA1-4         : bond        0.00558 (    5)
  link_BETA1-4         : angle       1.94880 (   15)
  hydrogen bonds       : bond        0.05685 (  268)
  hydrogen bonds       : angle       4.29726 (  759)
  metal coordination   : bond        0.00203 (    2)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.71789 (   12)
  covalent geometry    : bond        0.00338 ( 6727)
  covalent geometry    : angle       0.57575 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7493 (tp30) cc_final: 0.7096 (tp30)
REVERT: A  149 ASN cc_start: 0.7901 (m-40) cc_final: 0.7571 (m-40)
REVERT: A  249 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6667 (ttm)
REVERT: A  252 TYR cc_start: 0.8139 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  297 MET cc_start: 0.7864 (mmm) cc_final: 0.7605 (mtp)
REVERT: A  483 GLU cc_start: 0.7623 (tt0) cc_final: 0.7377 (tm-30)
REVERT: A  527 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7719 (tp30)
REVERT: A  536 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6946 (tm-30)
REVERT: B  405 ASN cc_start: 0.8510 (p0) cc_final: 0.8021 (p0)
REVERT: B  420 ASP cc_start: 0.7870 (m-30) cc_final: 0.7575 (m-30)
REVERT: B  468 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (mp)
  outliers start: 22
  outliers final: 10
  residues processed: 158
  average time/residue: 1.0835
  time to fit residues: 180.8248
Evaluate side-chains
  157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  409 GLN
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 72 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 228 HIS
B 437 ASN
B 439 ASN
B 493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.147209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.125341 restraints weight = 11541.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.63
r_work: 0.3496 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6748  Z= 0.141
  Angle     :  0.601  11.609   9193  Z= 0.296
  Chirality :  0.045   0.468    986
  Planarity :  0.004   0.041   1164
  Dihedral  :  4.896  52.428   1118
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.90 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.38 (0.31), residues: 777
  helix:  1.73 (0.28), residues: 360
  sheet: -1.23 (0.74), residues: 44
  loop : -1.07 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.008   0.001   HIS A 265 
 PHE   0.015   0.001   PHE A 308 
 TYR   0.020   0.002   TYR B 423 
 ARG   0.007   0.001   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00536 (    8)
  link_NAG-ASN         : angle       3.43562 (   24)
  link_BETA1-4         : bond        0.00516 (    5)
  link_BETA1-4         : angle       1.79827 (   15)
  hydrogen bonds       : bond        0.05482 (  268)
  hydrogen bonds       : angle       4.17912 (  759)
  metal coordination   : bond        0.00188 (    2)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       0.68706 (   12)
  covalent geometry    : bond        0.00325 ( 6727)
  covalent geometry    : angle       0.57083 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7017 (tp30)
REVERT: A  121 ASN cc_start: 0.7907 (m-40) cc_final: 0.7703 (m-40)
REVERT: A  149 ASN cc_start: 0.7912 (m-40) cc_final: 0.7648 (m-40)
REVERT: A  249 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6505 (ttm)
REVERT: A  252 TYR cc_start: 0.7978 (m-80) cc_final: 0.7711 (m-80)
REVERT: A  297 MET cc_start: 0.7868 (mmm) cc_final: 0.7634 (mtp)
REVERT: A  483 GLU cc_start: 0.7548 (tt0) cc_final: 0.7288 (tm-30)
REVERT: A  527 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7599 (tp30)
REVERT: A  536 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6807 (tm-30)
REVERT: B  405 ASN cc_start: 0.8516 (p0) cc_final: 0.8022 (p0)
REVERT: B  420 ASP cc_start: 0.7746 (m-30) cc_final: 0.7454 (m-30)
  outliers start: 21
  outliers final: 8
  residues processed: 155
  average time/residue: 1.0917
  time to fit residues: 178.4888
Evaluate side-chains
  153 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  409 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0980
   chunk 16 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
B 437 ASN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.147283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.123660 restraints weight = 17329.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 3.38
r_work: 0.3435 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6748  Z= 0.136
  Angle     :  0.607  12.084   9193  Z= 0.296
  Chirality :  0.046   0.457    986
  Planarity :  0.004   0.041   1164
  Dihedral  :  4.889  52.452   1118
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.21 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.39 (0.31), residues: 777
  helix:  1.69 (0.28), residues: 366
  sheet: -1.06 (0.77), residues: 44
  loop : -1.08 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 610 
 HIS   0.011   0.001   HIS A 195 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.018   0.001   TYR B 423 
 ARG   0.007   0.001   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00637 (    8)
  link_NAG-ASN         : angle       3.49977 (   24)
  link_BETA1-4         : bond        0.00502 (    5)
  link_BETA1-4         : angle       1.74740 (   15)
  hydrogen bonds       : bond        0.05444 (  268)
  hydrogen bonds       : angle       4.07782 (  759)
  metal coordination   : bond        0.00174 (    2)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       0.73628 (   12)
  covalent geometry    : bond        0.00308 ( 6727)
  covalent geometry    : angle       0.57701 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7537 (tp30) cc_final: 0.7115 (tp30)
REVERT: A  121 ASN cc_start: 0.7936 (m-40) cc_final: 0.7709 (m-40)
REVERT: A  149 ASN cc_start: 0.7945 (m-40) cc_final: 0.7684 (m-40)
REVERT: A  150 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7571 (tm-30)
REVERT: A  249 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6710 (ttm)
REVERT: A  252 TYR cc_start: 0.7971 (m-80) cc_final: 0.7762 (m-80)
REVERT: A  297 MET cc_start: 0.7852 (mmm) cc_final: 0.7584 (mtp)
REVERT: A  483 GLU cc_start: 0.7681 (tt0) cc_final: 0.7366 (tm-30)
REVERT: A  536 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: B  405 ASN cc_start: 0.8526 (p0) cc_final: 0.8010 (p0)
REVERT: B  420 ASP cc_start: 0.7830 (m-30) cc_final: 0.7527 (m-30)
  outliers start: 19
  outliers final: 10
  residues processed: 150
  average time/residue: 1.0833
  time to fit residues: 171.4338
Evaluate side-chains
  151 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  443 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0570
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7900

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
B 437 ASN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.145773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.125092 restraints weight = 9322.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.37
r_work: 0.3502 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6748  Z= 0.165
  Angle     :  0.626  11.788   9193  Z= 0.308
  Chirality :  0.047   0.451    986
  Planarity :  0.004   0.042   1164
  Dihedral  :  4.958  52.435   1118
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.65 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.31), residues: 777
  helix:  1.66 (0.28), residues: 360
  sheet: -0.99 (0.78), residues: 44
  loop : -1.09 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.016   0.002   PHE A 308 
 TYR   0.022   0.002   TYR B 489 
 ARG   0.009   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00620 (    8)
  link_NAG-ASN         : angle       3.69513 (   24)
  link_BETA1-4         : bond        0.00492 (    5)
  link_BETA1-4         : angle       1.76660 (   15)
  hydrogen bonds       : bond        0.05942 (  268)
  hydrogen bonds       : angle       4.08887 (  759)
  metal coordination   : bond        0.00226 (    2)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       0.79387 (   12)
  covalent geometry    : bond        0.00382 ( 6727)
  covalent geometry    : angle       0.59397 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7664 (tp30) cc_final: 0.7183 (tp30)
REVERT: A  121 ASN cc_start: 0.8042 (m-40) cc_final: 0.7827 (m-40)
REVERT: A  149 ASN cc_start: 0.8041 (m-40) cc_final: 0.7789 (m-40)
REVERT: A  150 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: A  249 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6933 (ttm)
REVERT: A  252 TYR cc_start: 0.8056 (m-80) cc_final: 0.7752 (m-80)
REVERT: A  297 MET cc_start: 0.7861 (mmm) cc_final: 0.7569 (mtp)
REVERT: A  483 GLU cc_start: 0.7733 (tt0) cc_final: 0.7399 (tm-30)
REVERT: A  536 GLU cc_start: 0.7294 (tm-30) cc_final: 0.7082 (tm-30)
REVERT: B  405 ASN cc_start: 0.8590 (p0) cc_final: 0.8090 (p0)
REVERT: B  420 ASP cc_start: 0.7992 (m-30) cc_final: 0.7688 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 151
  average time/residue: 1.1184
  time to fit residues: 178.1553
Evaluate side-chains
  157 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  443 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0370
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0020
   chunk 59 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5266

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

Flipped N/Q/H residues before XYZ refinement:
B 437 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.147306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.124595 restraints weight = 14053.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.02
r_work: 0.3469 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3468
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3468 r_free = 0.3468    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3468
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6748  Z= 0.132
  Angle     :  0.600  11.364   9193  Z= 0.294
  Chirality :  0.045   0.435    986
  Planarity :  0.004   0.041   1164
  Dihedral  :  4.908  52.526   1118
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.94 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.26 (0.31), residues: 777
  helix:  1.51 (0.28), residues: 373
  sheet: -1.08 (0.78), residues: 44
  loop : -1.13 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.008   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.023   0.001   TYR B 489 
 ARG   0.009   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00623 (    8)
  link_NAG-ASN         : angle       3.50034 (   24)
  link_BETA1-4         : bond        0.00483 (    5)
  link_BETA1-4         : angle       1.67062 (   15)
  hydrogen bonds       : bond        0.05323 (  268)
  hydrogen bonds       : angle       4.02135 (  759)
  metal coordination   : bond        0.00137 (    2)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       0.68236 (   12)
  covalent geometry    : bond        0.00301 ( 6727)
  covalent geometry    : angle       0.57003 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7476 (tp30) cc_final: 0.7009 (tp30)
REVERT: A  121 ASN cc_start: 0.7934 (m-40) cc_final: 0.7715 (m-40)
REVERT: A  149 ASN cc_start: 0.7931 (m-40) cc_final: 0.7693 (m-40)
REVERT: A  150 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7563 (tm-30)
REVERT: A  249 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6613 (ttm)
REVERT: A  297 MET cc_start: 0.7856 (mmm) cc_final: 0.7579 (mtp)
REVERT: A  471 ASP cc_start: 0.8060 (p0) cc_final: 0.7788 (p0)
REVERT: A  483 GLU cc_start: 0.7620 (tt0) cc_final: 0.7318 (tm-30)
REVERT: A  536 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6857 (tm-30)
REVERT: B  405 ASN cc_start: 0.8547 (p0) cc_final: 0.8040 (p0)
REVERT: B  420 ASP cc_start: 0.7788 (m-30) cc_final: 0.7485 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 153
  average time/residue: 1.3600
  time to fit residues: 219.7504
Evaluate side-chains
  154 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  443 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B 437 ASN
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.147298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126430 restraints weight = 9466.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.41
r_work: 0.3523 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6748  Z= 0.131
  Angle     :  0.598  11.820   9193  Z= 0.293
  Chirality :  0.045   0.426    986
  Planarity :  0.004   0.041   1164
  Dihedral  :  4.865  52.635   1118
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.09 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.30 (0.31), residues: 777
  helix:  1.58 (0.28), residues: 373
  sheet: -1.08 (0.78), residues: 42
  loop : -1.13 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 610 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.022   0.001   TYR B 423 
 ARG   0.009   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00617 (    8)
  link_NAG-ASN         : angle       3.38949 (   24)
  link_BETA1-4         : bond        0.00519 (    5)
  link_BETA1-4         : angle       1.66344 (   15)
  hydrogen bonds       : bond        0.05248 (  268)
  hydrogen bonds       : angle       3.97000 (  759)
  metal coordination   : bond        0.00149 (    2)
  SS BOND              : bond        0.00321 (    6)
  SS BOND              : angle       0.62363 (   12)
  covalent geometry    : bond        0.00298 ( 6727)
  covalent geometry    : angle       0.56997 ( 9142)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7668 (tp30) cc_final: 0.7212 (tp30)
REVERT: A  121 ASN cc_start: 0.8010 (m-40) cc_final: 0.7809 (m-40)
REVERT: A  149 ASN cc_start: 0.8039 (m-40) cc_final: 0.7818 (m-40)
REVERT: A  150 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: A  249 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6979 (ttm)
REVERT: A  252 TYR cc_start: 0.8068 (m-80) cc_final: 0.7706 (m-80)
REVERT: A  297 MET cc_start: 0.7838 (mmm) cc_final: 0.7577 (mtp)
REVERT: A  455 MET cc_start: 0.7555 (tmm) cc_final: 0.7340 (ttm)
REVERT: A  471 ASP cc_start: 0.8160 (p0) cc_final: 0.7901 (p0)
REVERT: A  483 GLU cc_start: 0.7800 (tt0) cc_final: 0.7447 (tm-30)
REVERT: A  536 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7105 (tm-30)
REVERT: B  405 ASN cc_start: 0.8575 (p0) cc_final: 0.8088 (p0)
REVERT: B  420 ASP cc_start: 0.7951 (m-30) cc_final: 0.7654 (m-30)
  outliers start: 13
  outliers final: 11
  residues processed: 148
  average time/residue: 1.3840
  time to fit residues: 216.7889
Evaluate side-chains
  152 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  507 SER
Chi-restraints excluded: chain B residue  347 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 10 optimal weight:    0.4980
   chunk 37 optimal weight:    0.0010
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
B 437 ASN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.147504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.124802 restraints weight = 14074.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 3.04
r_work: 0.3478 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6748  Z= 0.127
  Angle     :  0.591  11.363   9193  Z= 0.289
  Chirality :  0.045   0.417    986
  Planarity :  0.004   0.040   1164
  Dihedral  :  4.811  52.665   1118
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 20.09 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.31), residues: 777
  helix:  1.62 (0.28), residues: 372
  sheet: -1.11 (0.77), residues: 42
  loop : -1.16 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 610 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.024   0.001   TYR B 489 
 ARG   0.009   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (    8)
  link_NAG-ASN         : angle       3.33078 (   24)
  link_BETA1-4         : bond        0.00504 (    5)
  link_BETA1-4         : angle       1.62884 (   15)
  hydrogen bonds       : bond        0.05087 (  268)
  hydrogen bonds       : angle       3.95695 (  759)
  metal coordination   : bond        0.00146 (    2)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       0.61631 (   12)
  covalent geometry    : bond        0.00289 ( 6727)
  covalent geometry    : angle       0.56313 ( 9142)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6068.27 seconds
wall clock time: 106 minutes 9.02 seconds (6369.02 seconds total)