Starting phenix.real_space_refine
on Mon Apr 28 04:20:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jje_36345/04_2025/8jje_36345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jje_36345/04_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_36345/04_2025/8jje_36345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jje_36345/04_2025/8jje_36345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jje_36345/04_2025/8jje_36345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jje_36345/04_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-5669/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: 5.35, 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: 2.16
  Conformation dependent library (CDL) restraints added in 920.5 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: 0.90
  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: 1.83

  Time building geometry restraints manager: 2.44 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:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     22.960
  Find NCS groups from input model:        0.070
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.740
-------------------------------------------------------------------------------
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  : 0.767 
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: 0.2155
  time to fit residues: 39.3604
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  : 0.727 
-------------------------------------------------------------------------------
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 = 47)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129181 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  : 0.795 
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: 0.8311 (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: 0.2496
  time to fit residues: 35.3825
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  : 0.656 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 4 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 76 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.5170

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.165473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131679 restraints weight = 9807.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.61
r_work: 0.3483 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2609

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= 0.127
  Angle     :  0.613   8.129   9362  Z= 0.296
  Chirality :  0.044   0.313   1024
  Planarity :  0.004   0.055   1180
  Dihedral  :  9.491  60.586   1242
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.32 %
    Favored  : 85.67 %
  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:  0.02 (0.29), residues: 790
  helix:  0.46 (0.26), residues: 405
  sheet:  0.80 (0.81), residues: 44
  loop : -0.52 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.033   0.002   PHE B 486 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00788 (    1)
  link_NAG-ASN         : angle       4.56913 (    3)
  link_ALPHA1-6        : bond        0.00966 (    2)
  link_ALPHA1-6        : angle       1.53597 (    6)
  link_BETA1-4         : bond        0.01125 (    8)
  link_BETA1-4         : angle       2.78767 (   24)
  link_ALPHA1-3        : bond        0.01350 (    2)
  link_ALPHA1-3        : angle       2.65110 (    6)
  hydrogen bonds       : bond        0.04670 (  298)
  hydrogen bonds       : angle       4.81939 (  834)
  metal coordination   : bond        0.00194 (    2)
  SS BOND              : bond        0.00256 (    7)
  SS BOND              : angle       0.90920 (   14)
  covalent geometry    : bond        0.00265 ( 6848)
  covalent geometry    : angle       0.58629 ( 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: 21
    poor density    : 76
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8536 (tt)
REVERT: A  188 ASN cc_start: 0.8197 (m-40) cc_final: 0.7606 (t0)
REVERT: A  198 ASP cc_start: 0.8247 (p0) cc_final: 0.7989 (p0)
REVERT: A  207 TYR cc_start: 0.8280 (m-80) cc_final: 0.7686 (m-80)
REVERT: A  440 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: A  469 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8291 (Cg_endo)
REVERT: B  408 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8132 (ppt170)
REVERT: B  439 ASN cc_start: 0.8872 (t0) cc_final: 0.8636 (t0)
  outliers start: 21
  outliers final: 11
  residues processed: 95
  average time/residue: 0.2415
  time to fit residues: 31.9175
Evaluate side-chains
  77 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
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  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  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:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.2384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.149044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.114959 restraints weight = 9723.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.49
r_work: 0.3422 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   6870  Z= 0.191
  Angle     :  0.642   7.636   9362  Z= 0.311
  Chirality :  0.045   0.294   1024
  Planarity :  0.004   0.039   1180
  Dihedral  :  8.422  57.732   1242
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 12.18 %
    Favored  : 83.81 %
  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: -0.07 (0.29), residues: 790
  helix:  0.46 (0.26), residues: 402
  sheet:  0.60 (0.80), residues: 44
  loop : -0.63 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.028   0.002   PHE A 369 
 TYR   0.016   0.002   TYR A 199 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00723 (    1)
  link_NAG-ASN         : angle       4.33467 (    3)
  link_ALPHA1-6        : bond        0.01048 (    2)
  link_ALPHA1-6        : angle       1.67823 (    6)
  link_BETA1-4         : bond        0.01039 (    8)
  link_BETA1-4         : angle       2.54395 (   24)
  link_ALPHA1-3        : bond        0.01178 (    2)
  link_ALPHA1-3        : angle       2.73111 (    6)
  hydrogen bonds       : bond        0.05049 (  298)
  hydrogen bonds       : angle       4.77474 (  834)
  metal coordination   : bond        0.00355 (    2)
  SS BOND              : bond        0.00273 (    7)
  SS BOND              : angle       1.02962 (   14)
  covalent geometry    : bond        0.00452 ( 6848)
  covalent geometry    : angle       0.61898 ( 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
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 SER cc_start: 0.8913 (p) cc_final: 0.8548 (m)
REVERT: A  198 ASP cc_start: 0.8304 (p0) cc_final: 0.8072 (p0)
REVERT: A  207 TYR cc_start: 0.8231 (m-80) cc_final: 0.7664 (m-80)
REVERT: A  334 THR cc_start: 0.8952 (m) cc_final: 0.8711 (m)
REVERT: A  475 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8426 (tmtt)
REVERT: B  408 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8289 (ppt170)
REVERT: B  439 ASN cc_start: 0.8915 (t0) cc_final: 0.8660 (t0)
REVERT: B  484 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7584 (mt-10)
  outliers start: 28
  outliers final: 21
  residues processed: 92
  average time/residue: 0.2239
  time to fit residues: 28.1703
Evaluate side-chains
  82 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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  114 LYS
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  270 MET
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  491 VAL
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  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:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.153855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119417 restraints weight = 9934.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.62
r_work: 0.3360 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6870  Z= 0.129
  Angle     :  0.577   7.295   9362  Z= 0.276
  Chirality :  0.043   0.276   1024
  Planarity :  0.004   0.047   1180
  Dihedral  :  7.688  55.544   1242
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.04 %
    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:  0.12 (0.29), residues: 790
  helix:  0.66 (0.26), residues: 405
  sheet:  0.58 (0.82), residues: 44
  loop : -0.60 (0.32), residues: 341

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   0.012   0.001   TYR A 252 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00834 (    1)
  link_NAG-ASN         : angle       3.91028 (    3)
  link_ALPHA1-6        : bond        0.01155 (    2)
  link_ALPHA1-6        : angle       1.58345 (    6)
  link_BETA1-4         : bond        0.01014 (    8)
  link_BETA1-4         : angle       2.39697 (   24)
  link_ALPHA1-3        : bond        0.01238 (    2)
  link_ALPHA1-3        : angle       2.65411 (    6)
  hydrogen bonds       : bond        0.04317 (  298)
  hydrogen bonds       : angle       4.60354 (  834)
  metal coordination   : bond        0.00135 (    2)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       0.77376 (   14)
  covalent geometry    : bond        0.00290 ( 6848)
  covalent geometry    : angle       0.55512 ( 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
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 SER cc_start: 0.8750 (p) cc_final: 0.8549 (m)
REVERT: A  188 ASN cc_start: 0.8357 (m-40) cc_final: 0.8050 (t0)
REVERT: A  207 TYR cc_start: 0.8150 (m-80) cc_final: 0.7573 (m-80)
REVERT: A  259 ILE cc_start: 0.8542 (pp) cc_final: 0.8303 (tt)
REVERT: A  334 THR cc_start: 0.8859 (m) cc_final: 0.8621 (m)
REVERT: A  435 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6950 (tt0)
REVERT: A  475 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8222 (tmtt)
REVERT: B  387 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8218 (mt)
REVERT: B  408 ARG cc_start: 0.8728 (ptm160) cc_final: 0.8150 (ppt170)
REVERT: B  439 ASN cc_start: 0.8965 (t0) cc_final: 0.8717 (t0)
REVERT: B  484 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7595 (mt-10)
  outliers start: 21
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1933
  time to fit residues: 25.6566
Evaluate side-chains
  83 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
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  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  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:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.153930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.119499 restraints weight = 9907.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.62
r_work: 0.3358 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6870  Z= 0.131
  Angle     :  0.567   7.247   9362  Z= 0.273
  Chirality :  0.042   0.274   1024
  Planarity :  0.004   0.052   1180
  Dihedral  :  7.231  51.707   1242
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.33 %
    Favored  : 82.38 %
  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:  0.24 (0.30), residues: 790
  helix:  0.80 (0.26), residues: 406
  sheet:  0.52 (0.82), residues: 44
  loop : -0.60 (0.32), residues: 340

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   0.010   0.001   TYR A 252 
 ARG   0.001   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00812 (    1)
  link_NAG-ASN         : angle       3.59638 (    3)
  link_ALPHA1-6        : bond        0.01187 (    2)
  link_ALPHA1-6        : angle       1.51645 (    6)
  link_BETA1-4         : bond        0.00994 (    8)
  link_BETA1-4         : angle       2.30274 (   24)
  link_ALPHA1-3        : bond        0.01225 (    2)
  link_ALPHA1-3        : angle       2.59903 (    6)
  hydrogen bonds       : bond        0.04209 (  298)
  hydrogen bonds       : angle       4.54277 (  834)
  metal coordination   : bond        0.00095 (    2)
  SS BOND              : bond        0.00232 (    7)
  SS BOND              : angle       0.82298 (   14)
  covalent geometry    : bond        0.00296 ( 6848)
  covalent geometry    : angle       0.54639 ( 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
  93 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 ASN cc_start: 0.8325 (m-40) cc_final: 0.8019 (t0)
REVERT: A  207 TYR cc_start: 0.8110 (m-80) cc_final: 0.7557 (m-80)
REVERT: B  387 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: B  408 ARG cc_start: 0.8707 (ptm160) cc_final: 0.8121 (ppt170)
REVERT: B  439 ASN cc_start: 0.8998 (t0) cc_final: 0.8748 (t0)
REVERT: B  484 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7605 (mt-10)
  outliers start: 23
  outliers final: 19
  residues processed: 89
  average time/residue: 0.1796
  time to fit residues: 22.6799
Evaluate side-chains
  90 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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  270 MET
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 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  452 LEU
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:    4.9990
   chunk 40 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0060
   chunk 73 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.6000

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.154770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.120273 restraints weight = 9847.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.64
r_work: 0.3371 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6870  Z= 0.127
  Angle     :  0.586  12.790   9362  Z= 0.283
  Chirality :  0.043   0.282   1024
  Planarity :  0.004   0.053   1180
  Dihedral  :  7.051  48.659   1242
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  0.32 (0.30), residues: 790
  helix:  0.88 (0.27), residues: 406
  sheet:  0.53 (0.81), residues: 44
  loop : -0.56 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.019   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 252 
 ARG   0.001   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00575 (    1)
  link_NAG-ASN         : angle       3.51185 (    3)
  link_ALPHA1-6        : bond        0.01204 (    2)
  link_ALPHA1-6        : angle       1.46297 (    6)
  link_BETA1-4         : bond        0.00992 (    8)
  link_BETA1-4         : angle       2.25987 (   24)
  link_ALPHA1-3        : bond        0.01209 (    2)
  link_ALPHA1-3        : angle       2.53870 (    6)
  hydrogen bonds       : bond        0.04011 (  298)
  hydrogen bonds       : angle       4.52498 (  834)
  metal coordination   : bond        0.00074 (    2)
  SS BOND              : bond        0.00686 (    7)
  SS BOND              : angle       1.91108 (   14)
  covalent geometry    : bond        0.00293 ( 6848)
  covalent geometry    : angle       0.56364 ( 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
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8102 (m-80) cc_final: 0.7554 (m-80)
REVERT: A  435 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6826 (tt0)
REVERT: B  386 LYS cc_start: 0.8324 (ptmt) cc_final: 0.8101 (pttp)
REVERT: B  387 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (mt)
REVERT: B  408 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8154 (ppt170)
REVERT: B  439 ASN cc_start: 0.9057 (t0) cc_final: 0.8815 (t0)
REVERT: B  484 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7566 (mt-10)
  outliers start: 25
  outliers final: 19
  residues processed: 95
  average time/residue: 0.1903
  time to fit residues: 25.1632
Evaluate side-chains
  92 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
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  270 MET
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  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  517 LEU
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:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0010
   overall best weight:    0.5386

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.155749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.121359 restraints weight = 9903.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.66
r_work: 0.3387 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6870  Z= 0.119
  Angle     :  0.565  10.110   9362  Z= 0.274
  Chirality :  0.042   0.255   1024
  Planarity :  0.004   0.057   1180
  Dihedral  :  6.783  47.682   1242
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.19 %
    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:  0.38 (0.30), residues: 790
  helix:  0.97 (0.27), residues: 407
  sheet:  0.47 (0.81), residues: 44
  loop : -0.59 (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   0.018   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 252 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00738 (    1)
  link_NAG-ASN         : angle       3.44651 (    3)
  link_ALPHA1-6        : bond        0.01182 (    2)
  link_ALPHA1-6        : angle       1.41420 (    6)
  link_BETA1-4         : bond        0.00982 (    8)
  link_BETA1-4         : angle       2.20962 (   24)
  link_ALPHA1-3        : bond        0.01187 (    2)
  link_ALPHA1-3        : angle       2.47471 (    6)
  hydrogen bonds       : bond        0.03848 (  298)
  hydrogen bonds       : angle       4.45651 (  834)
  metal coordination   : bond        0.00085 (    2)
  SS BOND              : bond        0.00781 (    7)
  SS BOND              : angle       1.50435 (   14)
  covalent geometry    : bond        0.00268 ( 6848)
  covalent geometry    : angle       0.54453 ( 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
  98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.762 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8073 (m-80) cc_final: 0.7531 (m-80)
REVERT: A  228 HIS cc_start: 0.7863 (t70) cc_final: 0.7579 (m170)
REVERT: A  347 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7920 (p)
REVERT: A  435 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6829 (tt0)
REVERT: A  475 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8317 (tmtt)
REVERT: B  387 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8100 (mt)
REVERT: B  408 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8146 (ppt170)
REVERT: B  484 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7555 (mt-10)
  outliers start: 22
  outliers final: 17
  residues processed: 94
  average time/residue: 0.2442
  time to fit residues: 31.2504
Evaluate side-chains
  89 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
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  270 MET
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  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  517 LEU
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:    0.7980
   chunk 8 optimal weight:    0.0070
   chunk 18 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0170
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
A 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.156895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122574 restraints weight = 9916.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.65
r_work: 0.3400 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   6870  Z= 0.110
  Angle     :  0.545   8.623   9362  Z= 0.265
  Chirality :  0.041   0.262   1024
  Planarity :  0.004   0.062   1180
  Dihedral  :  6.408  47.517   1241
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.33 %
    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:  0.43 (0.30), residues: 790
  helix:  1.08 (0.27), residues: 407
  sheet:  0.39 (0.80), residues: 44
  loop : -0.66 (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   0.017   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 587 
 ARG   0.003   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00527 (    1)
  link_NAG-ASN         : angle       3.23479 (    3)
  link_ALPHA1-6        : bond        0.01133 (    2)
  link_ALPHA1-6        : angle       1.37297 (    6)
  link_BETA1-4         : bond        0.00968 (    8)
  link_BETA1-4         : angle       2.14379 (   24)
  link_ALPHA1-3        : bond        0.01148 (    2)
  link_ALPHA1-3        : angle       2.41746 (    6)
  hydrogen bonds       : bond        0.03652 (  298)
  hydrogen bonds       : angle       4.37567 (  834)
  metal coordination   : bond        0.00054 (    2)
  SS BOND              : bond        0.00701 (    7)
  SS BOND              : angle       1.32325 (   14)
  covalent geometry    : bond        0.00242 ( 6848)
  covalent geometry    : angle       0.52542 ( 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
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A  198 ASP cc_start: 0.8060 (p0) cc_final: 0.7815 (p0)
REVERT: A  207 TYR cc_start: 0.8056 (m-80) cc_final: 0.7522 (m-80)
REVERT: A  228 HIS cc_start: 0.8015 (t70) cc_final: 0.7650 (m170)
REVERT: A  347 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7910 (p)
REVERT: A  435 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6819 (tt0)
REVERT: A  469 PRO cc_start: 0.8483 (Cg_exo) cc_final: 0.8228 (Cg_endo)
REVERT: A  475 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8304 (tmtt)
REVERT: B  366 SER cc_start: 0.8596 (t) cc_final: 0.8208 (p)
REVERT: B  387 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8098 (mt)
REVERT: B  408 ARG cc_start: 0.8657 (ptm160) cc_final: 0.8144 (ppt170)
REVERT: B  484 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7487 (mt-10)
  outliers start: 23
  outliers final: 18
  residues processed: 96
  average time/residue: 0.2864
  time to fit residues: 40.1898
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  270 MET
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  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  452 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain B residue  517 LEU
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:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0040
   chunk 66 optimal weight:    0.3980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.156883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.122527 restraints weight = 10076.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.67
r_work: 0.3403 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6870  Z= 0.111
  Angle     :  0.547   8.021   9362  Z= 0.265
  Chirality :  0.041   0.246   1024
  Planarity :  0.004   0.057   1180
  Dihedral  :  6.246  47.536   1241
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.62 %
    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:  0.47 (0.30), residues: 790
  helix:  1.11 (0.27), residues: 407
  sheet:  0.39 (0.80), residues: 44
  loop : -0.62 (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   0.014   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 587 
 ARG   0.002   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    1)
  link_NAG-ASN         : angle       3.16317 (    3)
  link_ALPHA1-6        : bond        0.01157 (    2)
  link_ALPHA1-6        : angle       1.35990 (    6)
  link_BETA1-4         : bond        0.00983 (    8)
  link_BETA1-4         : angle       2.10887 (   24)
  link_ALPHA1-3        : bond        0.01117 (    2)
  link_ALPHA1-3        : angle       2.38560 (    6)
  hydrogen bonds       : bond        0.03596 (  298)
  hydrogen bonds       : angle       4.35572 (  834)
  metal coordination   : bond        0.00062 (    2)
  SS BOND              : bond        0.00644 (    7)
  SS BOND              : angle       1.23016 (   14)
  covalent geometry    : bond        0.00248 ( 6848)
  covalent geometry    : angle       0.52809 ( 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: 23
    poor density    : 76
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8121 (m-80) cc_final: 0.7520 (m-80)
REVERT: A  228 HIS cc_start: 0.7994 (t70) cc_final: 0.7634 (m170)
REVERT: A  347 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.7917 (p)
REVERT: A  435 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6815 (tt0)
REVERT: A  455 MET cc_start: 0.7815 (tmm) cc_final: 0.6922 (tmm)
REVERT: A  475 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8299 (tmtt)
REVERT: B  366 SER cc_start: 0.8655 (t) cc_final: 0.8267 (p)
REVERT: B  387 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8134 (mt)
REVERT: B  408 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8120 (ppt170)
REVERT: B  484 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7490 (mt-10)
  outliers start: 23
  outliers final: 16
  residues processed: 94
  average time/residue: 0.2167
  time to fit residues: 30.1380
Evaluate side-chains
  86 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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  270 MET
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 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  492 LEU
Chi-restraints excluded: chain B residue  515 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0010
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.4786

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.156873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122736 restraints weight = 9947.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.67
r_work: 0.3404 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6870  Z= 0.112
  Angle     :  0.560   8.551   9362  Z= 0.267
  Chirality :  0.041   0.250   1024
  Planarity :  0.004   0.057   1180
  Dihedral  :  5.971  47.527   1238
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.05 %
    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:  0.51 (0.30), residues: 790
  helix:  1.15 (0.27), residues: 407
  sheet:  0.38 (0.80), residues: 44
  loop : -0.61 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 302 
 HIS   0.004   0.001   HIS B 519 
 PHE   0.015   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        0.00508 (    1)
  link_NAG-ASN         : angle       3.01535 (    3)
  link_ALPHA1-6        : bond        0.01122 (    2)
  link_ALPHA1-6        : angle       1.35186 (    6)
  link_BETA1-4         : bond        0.00977 (    8)
  link_BETA1-4         : angle       2.07458 (   24)
  link_ALPHA1-3        : bond        0.01105 (    2)
  link_ALPHA1-3        : angle       2.36373 (    6)
  hydrogen bonds       : bond        0.03560 (  298)
  hydrogen bonds       : angle       4.34821 (  834)
  metal coordination   : bond        0.00057 (    2)
  SS BOND              : bond        0.00591 (    7)
  SS BOND              : angle       1.21396 (   14)
  covalent geometry    : bond        0.00252 ( 6848)
  covalent geometry    : angle       0.54217 ( 9309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3711.73 seconds
wall clock time: 68 minutes 25.65 seconds (4105.65 seconds total)