Starting phenix.real_space_refine
on Sat May 10 22:08:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jje_36345/05_2025/8jje_36345.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      40      5.16       5
     C    4245      2.51       5
     N    1079      2.21       5
     O    1305      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6670
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4881
          Classifications: {'peptide': 598}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570}
    Chain: "B"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1551
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "F"
      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: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "I"
      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: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 21
          Unusual residues: {' ZN': 1, 'NAG': 1, 'SO4': 1}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.36, per 1000 atoms: 0.80
  Number of scatterers: 6670
  At special positions: 0
  Unit cell: (93.84, 82.11, 119.646, 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      40     16.00
     O    1305      8.00
     N    1079      7.00
     C    4245      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.11
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " MAN E   4 " - " MAN E   5 "
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   4 "
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
    NAG-ASN
      " NAG A1001 " - " ASN A 432 "
  Time building additional restraints: 2.13
  Conformation dependent library (CDL) restraints added in 941.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A1002 " - pdb=" NE2 HIS A 374 "


  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      59.3% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 53
      removed outlier: 4.418A  pdb=" N   VAL A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU A  39 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.744A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 4.277A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 4.052A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.554A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.737A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 194
      removed outlier: 3.865A  pdb=" N   ARG A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 232
      removed outlier: 3.668A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 4.804A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    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 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.621A  pdb=" N   PHE A 314 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.691A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 4.491A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 413
      removed outlier: 3.534A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.682A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.595A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
    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
    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: 3.802A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.407A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 4.627A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.848A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
      removed outlier: 3.966A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    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 349 through 353
      removed outlier: 3.621A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 3.988A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 3.881A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.142A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
      removed outlier: 3.720A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.248A  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 332 through 334
      removed outlier: 6.281A  pdb=" N   MET A 332 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   THR A 362 " --> pdb=" O   MET A 332 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   THR A 334 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362
      removed outlier: 7.012A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474

    298 hydrogen bonds defined for protein.
    834 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: 1.92

  Time building geometry restraints manager: 2.39 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: 1349
        1.33 -     1.46: 2208
        1.46 -     1.59: 3231
        1.59 -     1.72: 0
        1.72 -     1.84: 60
  Bond restraints: 6848
  Sorted by residual:
  bond pdb=" CD  GLU A 375 "
       pdb=" OE2 GLU A 375 "
    ideal  model  delta    sigma   weight residual
    1.249  1.469 -0.220 1.90e-02 2.77e+03 1.34e+02
  bond pdb=" O3  SO4 A1003 "
       pdb=" S   SO4 A1003 "
    ideal  model  delta    sigma   weight residual
    1.499  1.396  0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" O1  SO4 A1003 "
       pdb=" S   SO4 A1003 "
    ideal  model  delta    sigma   weight residual
    1.498  1.403  0.095 2.00e-02 2.50e+03 2.27e+01
  bond pdb=" CG  HIS A 374 "
       pdb=" CD2 HIS A 374 "
    ideal  model  delta    sigma   weight residual
    1.354  1.310  0.044 1.10e-02 8.26e+03 1.57e+01
  bond pdb=" CG  HIS A 378 "
       pdb=" CD2 HIS A 378 "
    ideal  model  delta    sigma   weight residual
    1.354  1.314  0.040 1.10e-02 8.26e+03 1.34e+01
  ... (remaining 6843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 8656
        2.80 -     5.60: 633
        5.60 -     8.40: 16
        8.40 -    11.21: 3
       11.21 -    14.01: 1
  Bond angle restraints: 9309
  Sorted by residual:
  angle pdb=" CA  VAL A 172 "
        pdb=" CB  VAL A 172 "
        pdb=" CG1 VAL A 172 "
      ideal   model   delta    sigma   weight residual
     110.40  121.14  -10.74 1.70e+00 3.46e-01 3.99e+01
  angle pdb=" CA  PHE A 400 "
        pdb=" CB  PHE A 400 "
        pdb=" CG  PHE A 400 "
      ideal   model   delta    sigma   weight residual
     113.80  119.12   -5.32 1.00e+00 1.00e+00 2.83e+01
  angle pdb=" CA  ASP A 216 "
        pdb=" CB  ASP A 216 "
        pdb=" CG  ASP A 216 "
      ideal   model   delta    sigma   weight residual
     112.60  117.70   -5.10 1.00e+00 1.00e+00 2.60e+01
  angle pdb=" CA  ASN B 501 "
        pdb=" CB  ASN B 501 "
        pdb=" CG  ASN B 501 "
      ideal   model   delta    sigma   weight residual
     112.60  117.62   -5.02 1.00e+00 1.00e+00 2.52e+01
  angle pdb=" CA  ASN A 394 "
        pdb=" CB  ASN A 394 "
        pdb=" CG  ASN A 394 "
      ideal   model   delta    sigma   weight residual
     112.60  117.47   -4.87 1.00e+00 1.00e+00 2.38e+01
  ... (remaining 9304 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.28: 3956
       21.28 -    42.56: 231
       42.56 -    63.84: 42
       63.84 -    85.13: 27
       85.13 -   106.41: 13
  Dihedral angle restraints: 4269
    sinusoidal: 1940
      harmonic: 2329
  Sorted by residual:
  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
     -86.00 -175.43   89.43     1      1.00e+01 1.00e-02 9.51e+01
  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 -140.68   54.68     1      1.00e+01 1.00e-02 4.05e+01
  dihedral pdb=" CA  ILE A 544 "
           pdb=" C   ILE A 544 "
           pdb=" N   SER A 545 "
           pdb=" CA  SER A 545 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4266 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.189: 990
       0.189 -    0.377: 31
       0.377 -    0.566: 2
       0.566 -    0.755: 0
       0.755 -    0.944: 1
  Chirality restraints: 1024
  Sorted by residual:
  chirality pdb=" C1  BMA H   3 "
            pdb=" O4  NAG H   2 "
            pdb=" C2  BMA H   3 "
            pdb=" O5  BMA H   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-02 2.50e+03 4.37e+02
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.36e+01
  chirality pdb=" C1  NAG A1001 "
            pdb=" ND2 ASN A 432 "
            pdb=" C2  NAG A1001 "
            pdb=" O5  NAG A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.46   -0.94 2.00e-01 2.50e+01 2.23e+01
  ... (remaining 1021 not shown)

  Planarity restraints: 1181
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 477 "    0.083 2.00e-02 2.50e+03   3.94e-02 3.88e+01
        pdb=" CG  TRP A 477 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 477 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 477 "   -0.037 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 477 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 477 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 477 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 477 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 477 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 477 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 207 "   -0.080 2.00e-02 2.50e+03   4.16e-02 3.45e+01
        pdb=" CG  TYR A 207 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 207 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 207 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 207 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 207 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 207 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A 207 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 374 "   -0.054 2.00e-02 2.50e+03   4.65e-02 3.24e+01
        pdb=" CG  HIS A 374 "    0.039 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 374 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 374 "    0.061 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 374 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 374 "   -0.064 2.00e-02 2.50e+03
  ... (remaining 1178 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 5
        2.44 -     3.06: 4056
        3.06 -     3.67: 9575
        3.67 -     4.29: 15004
        4.29 -     4.90: 24595
  Nonbonded interactions: 53235
  Sorted by model distance:
  nonbonded pdb="ZN    ZN A1002 "
            pdb=" O   HOH A1101 "
     model   vdw
     1.829 2.230
  nonbonded pdb="ZN    ZN A1002 "
            pdb=" O1  SO4 A1003 "
     model   vdw
     1.965 2.230
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A1002 "
     model   vdw
     2.178 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A1002 "
     model   vdw
     2.180 2.230
  nonbonded pdb=" OE2 GLU A 375 "
            pdb=" O   HOH A1101 "
     model   vdw
     2.356 3.040
  ... (remaining 53230 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 'E'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.240
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.527   6870  Z= 0.707
  Angle     :  1.557  16.375   9362  Z= 0.986
  Chirality :  0.093   0.944   1024
  Planarity :  0.014   0.225   1180
  Dihedral  : 16.243 106.406   2754
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 0.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  5.44 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.13 %
  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: -2.00 (0.26), residues: 790
  helix: -1.73 (0.20), residues: 393
  sheet:  1.63 (0.86), residues: 35
  loop : -0.99 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.012   TRP A 477 
 HIS   0.035   0.006   HIS A 374 
 PHE   0.065   0.010   PHE A 400 
 TYR   0.080   0.013   TYR A 207 
 ARG   0.023   0.003   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    1)
  link_NAG-ASN         : angle       9.72704 (    3)
  link_ALPHA1-6        : bond        0.01884 (    2)
  link_ALPHA1-6        : angle       3.31092 (    6)
  link_BETA1-4         : bond        0.03400 (    8)
  link_BETA1-4         : angle       6.16516 (   24)
  link_ALPHA1-3        : bond        0.02614 (    2)
  link_ALPHA1-3        : angle       6.03428 (    6)
  hydrogen bonds       : bond        0.20997 (  298)
  hydrogen bonds       : angle       7.80835 (  834)
  metal coordination   : bond        0.38272 (    2)
  SS BOND              : bond        0.03492 (    7)
  SS BOND              : angle       2.10476 (   14)
  covalent geometry    : bond        0.01063 ( 6848)
  covalent geometry    : angle       1.50698 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.8611 (tp40) cc_final: 0.8243 (mm110)
REVERT: A   54 ILE cc_start: 0.7943 (mt) cc_final: 0.7718 (mt)
REVERT: A  131 LYS cc_start: 0.6917 (ptpt) cc_final: 0.6580 (mtpt)
REVERT: A  152 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8258 (mmm)
REVERT: A  171 GLU cc_start: 0.7739 (tp30) cc_final: 0.7131 (tm-30)
REVERT: A  207 TYR cc_start: 0.8687 (m-80) cc_final: 0.8153 (m-80)
REVERT: A  331 SER cc_start: 0.9128 (m) cc_final: 0.8907 (p)
REVERT: A  343 CYS cc_start: 0.8237 (m) cc_final: 0.7752 (t)
REVERT: A  360 MET cc_start: 0.9072 (ttt) cc_final: 0.8854 (ttt)
REVERT: A  428 PHE cc_start: 0.7962 (t80) cc_final: 0.7730 (t80)
REVERT: A  475 LYS cc_start: 0.8365 (tttt) cc_final: 0.8147 (tmmt)
REVERT: B  346 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8163 (ptm-80)
REVERT: B  382 VAL cc_start: 0.7925 (t) cc_final: 0.7545 (t)
REVERT: B  408 ARG cc_start: 0.9037 (ptm160) cc_final: 0.8330 (ppt170)
REVERT: B  428 ASP cc_start: 0.8683 (t0) cc_final: 0.8406 (p0)
REVERT: B  484 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8405 (mt-10)
  outliers start: 13
  outliers final: 8
  residues processed: 140
  average time/residue: 0.2089
  time to fit residues: 37.8910
Evaluate side-chains
  86 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   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 540 HIS
B 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.163580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129178 restraints weight = 9603.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.59
r_work: 0.3482 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6870  Z= 0.157
  Angle     :  0.699   8.703   9362  Z= 0.346
  Chirality :  0.046   0.406   1024
  Planarity :  0.004   0.038   1180
  Dihedral  : 11.999  77.301   1245
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  :  9.46 %
    Favored  : 86.96 %
  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 (0.29), residues: 790
  helix: -0.06 (0.26), residues: 404
  sheet:  1.04 (0.79), residues: 44
  loop : -0.52 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.030   0.002   PHE B 486 
 TYR   0.016   0.002   TYR B 396 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00868 (    1)
  link_NAG-ASN         : angle       5.91407 (    3)
  link_ALPHA1-6        : bond        0.00977 (    2)
  link_ALPHA1-6        : angle       1.72898 (    6)
  link_BETA1-4         : bond        0.01164 (    8)
  link_BETA1-4         : angle       3.10938 (   24)
  link_ALPHA1-3        : bond        0.01177 (    2)
  link_ALPHA1-3        : angle       2.76436 (    6)
  hydrogen bonds       : bond        0.05666 (  298)
  hydrogen bonds       : angle       5.23021 (  834)
  metal coordination   : bond        0.01745 (    2)
  SS BOND              : bond        0.00684 (    7)
  SS BOND              : angle       1.33661 (   14)
  covalent geometry    : bond        0.00330 ( 6848)
  covalent geometry    : angle       0.66806 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ASN cc_start: 0.8208 (m-40) cc_final: 0.7557 (t0)
REVERT: A  207 TYR cc_start: 0.8310 (m-80) cc_final: 0.7700 (m-80)
REVERT: A  475 LYS cc_start: 0.8395 (tttt) cc_final: 0.8181 (tmmt)
REVERT: B  408 ARG cc_start: 0.8659 (ptm160) cc_final: 0.7931 (ppt170)
REVERT: B  439 ASN cc_start: 0.8880 (t0) cc_final: 0.8651 (t0)
REVERT: B  486 PHE cc_start: 0.7407 (t80) cc_final: 0.7172 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 104
  average time/residue: 0.2014
  time to fit residues: 28.2879
Evaluate side-chains
  84 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  96 GLN
A 277 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.163393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.129271 restraints weight = 9852.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.61
r_work: 0.3470 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6870  Z= 0.155
  Angle     :  0.636   8.339   9362  Z= 0.309
  Chirality :  0.045   0.311   1024
  Planarity :  0.004   0.059   1180
  Dihedral  :  9.416  59.212   1242
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 11.60 %
    Favored  : 85.10 %
  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: -0.06 (0.29), residues: 790
  helix:  0.43 (0.26), residues: 401
  sheet:  0.72 (0.80), residues: 44
  loop : -0.60 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.033   0.002   PHE B 486 
 TYR   0.013   0.002   TYR A 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00693 (    1)
  link_NAG-ASN         : angle       4.53057 (    3)
  link_ALPHA1-6        : bond        0.00983 (    2)
  link_ALPHA1-6        : angle       1.56634 (    6)
  link_BETA1-4         : bond        0.01169 (    8)
  link_BETA1-4         : angle       2.77465 (   24)
  link_ALPHA1-3        : bond        0.01289 (    2)
  link_ALPHA1-3        : angle       2.65632 (    6)
  hydrogen bonds       : bond        0.05004 (  298)
  hydrogen bonds       : angle       4.87147 (  834)
  metal coordination   : bond        0.00261 (    2)
  SS BOND              : bond        0.00518 (    7)
  SS BOND              : angle       0.90891 (   14)
  covalent geometry    : bond        0.00345 ( 6848)
  covalent geometry    : angle       0.61111 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 ASP cc_start: 0.8340 (p0) cc_final: 0.8044 (p0)
REVERT: A  207 TYR cc_start: 0.8295 (m-80) cc_final: 0.7694 (m-80)
REVERT: A  440 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8218 (tp)
REVERT: A  469 PRO cc_start: 0.8675 (Cg_exo) cc_final: 0.8301 (Cg_endo)
REVERT: A  475 LYS cc_start: 0.8486 (tttt) cc_final: 0.8277 (ttpt)
REVERT: B  408 ARG cc_start: 0.8681 (ptm160) cc_final: 0.8105 (ppt170)
REVERT: B  439 ASN cc_start: 0.8908 (t0) cc_final: 0.8662 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1876
  time to fit residues: 24.1049
Evaluate side-chains
  79 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.163509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129334 restraints weight = 9917.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.61
r_work: 0.3443 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6870  Z= 0.149
  Angle     :  0.606   7.378   9362  Z= 0.291
  Chirality :  0.044   0.290   1024
  Planarity :  0.004   0.038   1180
  Dihedral  :  8.180  58.663   1242
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.04 %
    Favored  : 83.67 %
  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: -0.01 (0.29), residues: 790
  helix:  0.55 (0.26), residues: 401
  sheet:  0.57 (0.80), residues: 44
  loop : -0.65 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.023   0.002   PHE A 369 
 TYR   0.013   0.002   TYR A 183 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00685 (    1)
  link_NAG-ASN         : angle       4.08654 (    3)
  link_ALPHA1-6        : bond        0.01094 (    2)
  link_ALPHA1-6        : angle       1.62678 (    6)
  link_BETA1-4         : bond        0.01015 (    8)
  link_BETA1-4         : angle       2.50353 (   24)
  link_ALPHA1-3        : bond        0.01190 (    2)
  link_ALPHA1-3        : angle       2.73806 (    6)
  hydrogen bonds       : bond        0.04555 (  298)
  hydrogen bonds       : angle       4.68471 (  834)
  metal coordination   : bond        0.00131 (    2)
  SS BOND              : bond        0.00219 (    7)
  SS BOND              : angle       1.02108 (   14)
  covalent geometry    : bond        0.00342 ( 6848)
  covalent geometry    : angle       0.58234 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 SER cc_start: 0.8759 (p) cc_final: 0.8519 (m)
REVERT: A  188 ASN cc_start: 0.8219 (m-40) cc_final: 0.7902 (t0)
REVERT: A  207 TYR cc_start: 0.8192 (m-80) cc_final: 0.7628 (m-80)
REVERT: A  259 ILE cc_start: 0.8529 (pp) cc_final: 0.8300 (tt)
REVERT: A  334 THR cc_start: 0.8933 (m) cc_final: 0.8688 (m)
REVERT: A  475 LYS cc_start: 0.8437 (tttt) cc_final: 0.8215 (ttpt)
REVERT: B  387 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: B  408 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8267 (ppt170)
REVERT: B  439 ASN cc_start: 0.8928 (t0) cc_final: 0.8681 (t0)
REVERT: B  484 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7530 (mt-10)
  outliers start: 23
  outliers final: 18
  residues processed: 97
  average time/residue: 0.1835
  time to fit residues: 24.1735
Evaluate side-chains
  90 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
A 472 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.155151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120701 restraints weight = 9922.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.65
r_work: 0.3380 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6870  Z= 0.116
  Angle     :  0.558   7.371   9362  Z= 0.268
  Chirality :  0.042   0.270   1024
  Planarity :  0.004   0.050   1180
  Dihedral  :  7.411  56.325   1242
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 13.90 %
    Favored  : 82.95 %
  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 (0.29), residues: 790
  helix:  0.73 (0.26), residues: 405
  sheet:  0.52 (0.81), residues: 44
  loop : -0.58 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 252 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00882 (    1)
  link_NAG-ASN         : angle       3.71466 (    3)
  link_ALPHA1-6        : bond        0.01188 (    2)
  link_ALPHA1-6        : angle       1.52943 (    6)
  link_BETA1-4         : bond        0.01039 (    8)
  link_BETA1-4         : angle       2.35976 (   24)
  link_ALPHA1-3        : bond        0.01252 (    2)
  link_ALPHA1-3        : angle       2.64766 (    6)
  hydrogen bonds       : bond        0.04027 (  298)
  hydrogen bonds       : angle       4.52141 (  834)
  metal coordination   : bond        0.00088 (    2)
  SS BOND              : bond        0.00237 (    7)
  SS BOND              : angle       0.78182 (   14)
  covalent geometry    : bond        0.00250 ( 6848)
  covalent geometry    : angle       0.53586 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ASN cc_start: 0.8336 (m-40) cc_final: 0.8052 (t0)
REVERT: A  198 ASP cc_start: 0.8111 (p0) cc_final: 0.7800 (p0)
REVERT: A  207 TYR cc_start: 0.8175 (m-80) cc_final: 0.7618 (m-80)
REVERT: A  259 ILE cc_start: 0.8551 (pp) cc_final: 0.8339 (tt)
REVERT: A  435 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6909 (tt0)
REVERT: A  475 LYS cc_start: 0.8407 (tttt) cc_final: 0.8182 (ttpt)
REVERT: B  408 ARG cc_start: 0.8696 (ptm160) cc_final: 0.8137 (ppt170)
REVERT: B  439 ASN cc_start: 0.8941 (t0) cc_final: 0.8694 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1761
  time to fit residues: 25.2298
Evaluate side-chains
  92 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0270
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0030
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.4248

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.156602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122283 restraints weight = 9903.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.63
r_work: 0.3394 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6870  Z= 0.109
  Angle     :  0.548   7.213   9362  Z= 0.263
  Chirality :  0.041   0.265   1024
  Planarity :  0.004   0.051   1180
  Dihedral  :  6.965  53.113   1242
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.33 %
    Favored  : 82.09 %
  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 (0.30), residues: 790
  helix:  0.93 (0.27), residues: 406
  sheet:  0.46 (0.81), residues: 44
  loop : -0.56 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 587 
 ARG   0.001   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00807 (    1)
  link_NAG-ASN         : angle       3.42449 (    3)
  link_ALPHA1-6        : bond        0.01208 (    2)
  link_ALPHA1-6        : angle       1.46270 (    6)
  link_BETA1-4         : bond        0.00978 (    8)
  link_BETA1-4         : angle       2.27503 (   24)
  link_ALPHA1-3        : bond        0.01237 (    2)
  link_ALPHA1-3        : angle       2.57753 (    6)
  hydrogen bonds       : bond        0.03788 (  298)
  hydrogen bonds       : angle       4.43778 (  834)
  metal coordination   : bond        0.00076 (    2)
  SS BOND              : bond        0.00166 (    7)
  SS BOND              : angle       0.75076 (   14)
  covalent geometry    : bond        0.00236 ( 6848)
  covalent geometry    : angle       0.52762 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8128 (m-80) cc_final: 0.7581 (m-80)
REVERT: A  347 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7910 (p)
REVERT: A  435 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6875 (tt0)
REVERT: A  475 LYS cc_start: 0.8394 (tttt) cc_final: 0.8164 (ttpt)
REVERT: B  408 ARG cc_start: 0.8691 (ptm160) cc_final: 0.8153 (ppt170)
  outliers start: 25
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1813
  time to fit residues: 24.2838
Evaluate side-chains
  90 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.154718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120271 restraints weight = 9908.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.64
r_work: 0.3371 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6870  Z= 0.143
  Angle     :  0.587  12.265   9362  Z= 0.285
  Chirality :  0.043   0.262   1024
  Planarity :  0.004   0.053   1180
  Dihedral  :  6.860  48.629   1242
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.04 %
    Favored  : 81.38 %
  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:  0.35 (0.30), residues: 790
  helix:  0.93 (0.27), residues: 406
  sheet:  0.54 (0.82), residues: 44
  loop : -0.58 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.022   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 587 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00550 (    1)
  link_NAG-ASN         : angle       3.39848 (    3)
  link_ALPHA1-6        : bond        0.01149 (    2)
  link_ALPHA1-6        : angle       1.42151 (    6)
  link_BETA1-4         : bond        0.00976 (    8)
  link_BETA1-4         : angle       2.23166 (   24)
  link_ALPHA1-3        : bond        0.01164 (    2)
  link_ALPHA1-3        : angle       2.49800 (    6)
  hydrogen bonds       : bond        0.04085 (  298)
  hydrogen bonds       : angle       4.53459 (  834)
  metal coordination   : bond        0.00114 (    2)
  SS BOND              : bond        0.00639 (    7)
  SS BOND              : angle       1.55148 (   14)
  covalent geometry    : bond        0.00334 ( 6848)
  covalent geometry    : angle       0.56648 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8104 (m-80) cc_final: 0.7542 (m-80)
REVERT: A  228 HIS cc_start: 0.7978 (t70) cc_final: 0.7683 (m-70)
REVERT: A  347 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8089 (p)
REVERT: A  435 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6838 (tt0)
REVERT: A  475 LYS cc_start: 0.8428 (tttt) cc_final: 0.8198 (ttpt)
REVERT: B  387 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8181 (mt)
REVERT: B  408 ARG cc_start: 0.8680 (ptm160) cc_final: 0.8148 (ppt170)
  outliers start: 25
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1733
  time to fit residues: 22.6284
Evaluate side-chains
  91 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0970
   chunk 67 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
A 429 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122201 restraints weight = 9904.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.65
r_work: 0.3398 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6870  Z= 0.111
  Angle     :  0.553   9.479   9362  Z= 0.268
  Chirality :  0.041   0.260   1024
  Planarity :  0.004   0.057   1180
  Dihedral  :  6.640  47.482   1242
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.76 %
    Favored  : 81.81 %
  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:  0.45 (0.30), residues: 790
  helix:  1.04 (0.27), residues: 407
  sheet:  0.41 (0.81), residues: 44
  loop : -0.56 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 587 
 ARG   0.001   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (    1)
  link_NAG-ASN         : angle       3.27983 (    3)
  link_ALPHA1-6        : bond        0.01180 (    2)
  link_ALPHA1-6        : angle       1.37099 (    6)
  link_BETA1-4         : bond        0.00983 (    8)
  link_BETA1-4         : angle       2.17434 (   24)
  link_ALPHA1-3        : bond        0.01165 (    2)
  link_ALPHA1-3        : angle       2.46264 (    6)
  hydrogen bonds       : bond        0.03666 (  298)
  hydrogen bonds       : angle       4.41660 (  834)
  metal coordination   : bond        0.00049 (    2)
  SS BOND              : bond        0.00902 (    7)
  SS BOND              : angle       1.62818 (   14)
  covalent geometry    : bond        0.00245 ( 6848)
  covalent geometry    : angle       0.53139 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8062 (m-80) cc_final: 0.7525 (m-80)
REVERT: A  228 HIS cc_start: 0.7923 (t70) cc_final: 0.7518 (t-170)
REVERT: A  347 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.7973 (p)
REVERT: A  435 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6799 (tt0)
REVERT: A  469 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8232 (Cg_endo)
REVERT: A  475 LYS cc_start: 0.8367 (tttt) cc_final: 0.8124 (ttpt)
REVERT: B  387 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8148 (mt)
REVERT: B  408 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8134 (ppt170)
REVERT: B  484 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7160 (mt-10)
  outliers start: 24
  outliers final: 20
  residues processed: 97
  average time/residue: 0.1777
  time to fit residues: 23.8772
Evaluate side-chains
  94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
A 429 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.154697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120583 restraints weight = 10002.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 2.66
r_work: 0.3375 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6870  Z= 0.143
  Angle     :  0.572   9.061   9362  Z= 0.279
  Chirality :  0.042   0.250   1024
  Planarity :  0.004   0.056   1180
  Dihedral  :  6.547  48.124   1241
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.76 %
    Favored  : 81.66 %
  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:  0.40 (0.30), residues: 790
  helix:  0.98 (0.27), residues: 407
  sheet:  0.43 (0.81), residues: 44
  loop : -0.57 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.020   0.001   PHE A 369 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00455 (    1)
  link_NAG-ASN         : angle       3.17050 (    3)
  link_ALPHA1-6        : bond        0.01169 (    2)
  link_ALPHA1-6        : angle       1.38748 (    6)
  link_BETA1-4         : bond        0.00993 (    8)
  link_BETA1-4         : angle       2.14871 (   24)
  link_ALPHA1-3        : bond        0.01142 (    2)
  link_ALPHA1-3        : angle       2.43012 (    6)
  hydrogen bonds       : bond        0.04027 (  298)
  hydrogen bonds       : angle       4.49940 (  834)
  metal coordination   : bond        0.00124 (    2)
  SS BOND              : bond        0.00703 (    7)
  SS BOND              : angle       1.50917 (   14)
  covalent geometry    : bond        0.00334 ( 6848)
  covalent geometry    : angle       0.55310 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8091 (p0) cc_final: 0.7850 (p0)
REVERT: A  207 TYR cc_start: 0.8083 (m-80) cc_final: 0.7539 (m-80)
REVERT: A  224 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7889 (mp0)
REVERT: A  228 HIS cc_start: 0.7838 (t70) cc_final: 0.7461 (t-170)
REVERT: A  347 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8016 (p)
REVERT: A  469 PRO cc_start: 0.8466 (Cg_exo) cc_final: 0.8237 (Cg_endo)
REVERT: A  475 LYS cc_start: 0.8371 (tttt) cc_final: 0.8139 (ttpt)
REVERT: B  366 SER cc_start: 0.8625 (t) cc_final: 0.8234 (p)
REVERT: B  387 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8165 (mt)
REVERT: B  408 ARG cc_start: 0.8617 (ptm160) cc_final: 0.8113 (ppt170)
  outliers start: 25
  outliers final: 20
  residues processed: 91
  average time/residue: 0.1716
  time to fit residues: 22.0328
Evaluate side-chains
  91 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 72 optimal weight:    0.0670
   chunk 23 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
A 429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.157036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.122971 restraints weight = 10076.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.65
r_work: 0.3406 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   6870  Z= 0.110
  Angle     :  0.546   8.056   9362  Z= 0.264
  Chirality :  0.041   0.251   1024
  Planarity :  0.004   0.061   1180
  Dihedral  :  6.278  47.310   1241
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.04 %
    Favored  : 81.81 %
  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:  0.57 (0.30), residues: 790
  helix:  1.14 (0.26), residues: 407
  sheet:  0.41 (0.82), residues: 44
  loop : -0.50 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 587 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00529 (    1)
  link_NAG-ASN         : angle       3.08380 (    3)
  link_ALPHA1-6        : bond        0.01131 (    2)
  link_ALPHA1-6        : angle       1.33964 (    6)
  link_BETA1-4         : bond        0.00983 (    8)
  link_BETA1-4         : angle       2.09068 (   24)
  link_ALPHA1-3        : bond        0.01140 (    2)
  link_ALPHA1-3        : angle       2.38281 (    6)
  hydrogen bonds       : bond        0.03547 (  298)
  hydrogen bonds       : angle       4.40696 (  834)
  metal coordination   : bond        0.00100 (    2)
  SS BOND              : bond        0.00633 (    7)
  SS BOND              : angle       1.33434 (   14)
  covalent geometry    : bond        0.00245 ( 6848)
  covalent geometry    : angle       0.52749 ( 9309)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8115 (m-80) cc_final: 0.7522 (m-80)
REVERT: A  224 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7791 (mp0)
REVERT: A  228 HIS cc_start: 0.7827 (t70) cc_final: 0.7457 (t-170)
REVERT: A  347 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.7959 (p)
REVERT: A  455 MET cc_start: 0.7829 (tmm) cc_final: 0.7109 (tmm)
REVERT: A  475 LYS cc_start: 0.8411 (tttt) cc_final: 0.8157 (ttpt)
REVERT: B  366 SER cc_start: 0.8667 (t) cc_final: 0.8282 (p)
REVERT: B  387 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: B  408 ARG cc_start: 0.8530 (ptm160) cc_final: 0.8054 (ppt170)
  outliers start: 22
  outliers final: 19
  residues processed: 95
  average time/residue: 0.1717
  time to fit residues: 23.1286
Evaluate side-chains
  93 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  488 CYS
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.155712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.121497 restraints weight = 10006.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.68
r_work: 0.3386 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6870  Z= 0.125
  Angle     :  0.561   7.437   9362  Z= 0.272
  Chirality :  0.042   0.248   1024
  Planarity :  0.004   0.066   1180
  Dihedral  :  6.170  47.847   1241
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.76 %
    Favored  : 81.09 %
  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:  0.58 (0.30), residues: 790
  helix:  1.14 (0.26), residues: 407
  sheet:  0.50 (0.82), residues: 44
  loop : -0.50 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 587 
 ARG   0.002   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00537 (    1)
  link_NAG-ASN         : angle       3.00118 (    3)
  link_ALPHA1-6        : bond        0.01114 (    2)
  link_ALPHA1-6        : angle       1.35342 (    6)
  link_BETA1-4         : bond        0.00980 (    8)
  link_BETA1-4         : angle       2.07353 (   24)
  link_ALPHA1-3        : bond        0.01091 (    2)
  link_ALPHA1-3        : angle       2.37339 (    6)
  hydrogen bonds       : bond        0.03762 (  298)
  hydrogen bonds       : angle       4.42405 (  834)
  metal coordination   : bond        0.00062 (    2)
  SS BOND              : bond        0.00606 (    7)
  SS BOND              : angle       1.34917 (   14)
  covalent geometry    : bond        0.00290 ( 6848)
  covalent geometry    : angle       0.54295 ( 9309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3161.58 seconds
wall clock time: 56 minutes 1.90 seconds (3361.90 seconds total)