Starting phenix.real_space_refine
on Sun Apr 27 22:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/04_2025/8t23_40979.cif"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4121      2.51       5
     N    1075      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 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: 6451
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4904
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 30, 'TRANS': 565}
    Chain: "B"
      Number of atoms: 1467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1467
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 11, 'TRANS': 173}
          Chain breaks: 1
    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: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {'FUC': 1, 'NAG': 1}
          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: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.28, per 1000 atoms: 1.13
  Number of scatterers: 6451
  At special positions: 0
  Unit cell: (103.23, 75.48, 135.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1218      8.00
     N    1075      7.00
     C    4121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
    BETA1-6
      " NAG H   1 " - " FUC H   2 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A  53 "
      " NAG B 601 " - " ASN B 343 "
      " NAG G   1 " - " ASN A 322 "
      " NAG H   1 " - " ASN A 216 "
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 898.8 milliseconds
  

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 2 sheets defined
      45.6% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.534A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   PHE A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 66 through 83
      removed outlier: 3.646A  pdb=" N   THR A  82 " --> pdb=" O   GLN A  78 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR A  83 " --> pdb=" O   HIS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.610A  pdb=" N   ALA A  99 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 4.873A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   MET A 123 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.616A  pdb=" N   GLY A 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 157 through 163
      removed outlier: 4.367A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.577A  pdb=" N   LEU A 176 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 219 through 223
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 4.855A  pdb=" N   ALA A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.973A  pdb=" N   TYR A 252 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 306 through 317
      removed outlier: 4.388A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.956A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 382
    Processing helix  chain 'A' and resid 383 through 386
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 3.628A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 422
    Processing helix  chain 'A' and resid 431 through 435
    Processing helix  chain 'A' and resid 446 through 452
      removed outlier: 4.238A  pdb=" N   THR A 449 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 450 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      No H-bonds generated for 'chain 'A' and resid 446 through 452'
    Processing helix  chain 'A' and resid 453 through 464
      removed outlier: 4.725A  pdb=" N   ARG A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TRP A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 485
      removed outlier: 4.026A  pdb=" N   GLU A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 507
      removed outlier: 6.677A  pdb=" N   PHE A 504 " --> pdb=" O   ALA A 501 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   HIS A 505 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 506 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA A 507 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 523
      removed outlier: 3.646A  pdb=" N   GLN A 522 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 527
    Processing helix  chain 'A' and resid 528 through 533
    Processing helix  chain 'A' and resid 547 through 555
      removed outlier: 3.946A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN A 552 " --> pdb=" O   ARG A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.840A  pdb=" N   ALA A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 587
      No H-bonds generated for 'chain 'A' and resid 585 through 587'
    Processing helix  chain 'A' and resid 588 through 596
      removed outlier: 4.536A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.588A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 390'
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.008A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352
      removed outlier: 3.941A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 351 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 396 through 403
      removed outlier: 3.898A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR B 508 " --> pdb=" O   ILE B 402 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 513 " --> pdb=" O   CYS B 432 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)

    173 hydrogen bonds defined for protein.
    468 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: 1.45

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2064
        1.34 -     1.46: 1660
        1.46 -     1.58: 2852
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6635
  Sorted by residual:
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.486 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" CB  PRO A 389 "
       pdb=" CG  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.492  1.641 -0.149 5.00e-02 4.00e+02 8.92e+00
  bond pdb=" CG  PRO A 389 "
       pdb=" CD  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.503  1.431  0.072 3.40e-02 8.65e+02 4.45e+00
  bond pdb=" CA  LYS A 441 "
       pdb=" CB  LYS A 441 "
    ideal  model  delta    sigma   weight residual
    1.526  1.559 -0.033 1.70e-02 3.46e+03 3.83e+00
  bond pdb=" N   PRO A 389 "
       pdb=" CA  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.024 1.28e-02 6.10e+03 3.66e+00
  ... (remaining 6630 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 8877
        3.35 -     6.69: 118
        6.69 -    10.04: 10
       10.04 -    13.38: 4
       13.38 -    16.73: 3
  Bond angle restraints: 9012
  Sorted by residual:
  angle pdb=" CA  PRO A 389 "
        pdb=" N   PRO A 389 "
        pdb=" CD  PRO A 389 "
      ideal   model   delta    sigma   weight residual
     112.00   95.27   16.73 1.40e+00 5.10e-01 1.43e+02
  angle pdb=" C   ALA A 212 "
        pdb=" N   ASP A 213 "
        pdb=" CA  ASP A 213 "
      ideal   model   delta    sigma   weight residual
     122.35  132.59  -10.24 1.46e+00 4.69e-01 4.92e+01
  angle pdb=" N   PRO A 389 "
        pdb=" CD  PRO A 389 "
        pdb=" CG  PRO A 389 "
      ideal   model   delta    sigma   weight residual
     103.20   94.54    8.66 1.50e+00 4.44e-01 3.33e+01
  angle pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
        pdb=" C   ILE A 544 "
      ideal   model   delta    sigma   weight residual
     113.71  108.86    4.85 9.50e-01 1.11e+00 2.61e+01
  angle pdb=" CA  LEU A  45 "
        pdb=" CB  LEU A  45 "
        pdb=" CG  LEU A  45 "
      ideal   model   delta    sigma   weight residual
     116.30  132.29  -15.99 3.50e+00 8.16e-02 2.09e+01
  ... (remaining 9007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.55: 3535
       23.55 -    47.09: 388
       47.09 -    70.64: 62
       70.64 -    94.19: 10
       94.19 -   117.74: 6
  Dihedral angle restraints: 4001
    sinusoidal: 1708
      harmonic: 2293
  Sorted by residual:
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.30  -75.30     1      1.00e+01 1.00e-02 7.16e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.32  -74.32     1      1.00e+01 1.00e-02 7.01e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.83   48.17     1      1.00e+01 1.00e-02 3.20e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 828
       0.077 -    0.154: 113
       0.154 -    0.231: 3
       0.231 -    0.308: 1
       0.308 -    0.385: 1
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN A 216 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CB  VAL A 318 "
            pdb=" CA  VAL A 318 "
            pdb=" CG1 VAL A 318 "
            pdb=" CG2 VAL A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 943 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.144 5.00e-02 4.00e+02   2.00e-01 6.39e+01
        pdb=" N   PRO A 389 "   -0.344 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.113 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.087 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 168 "   -0.017 2.00e-02 2.50e+03   1.96e-02 9.57e+00
        pdb=" CG  TRP A 168 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 168 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 168 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 168 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 168 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 168 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 168 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 168 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 564 "    0.047 5.00e-02 4.00e+02   7.12e-02 8.12e+00
        pdb=" N   PRO A 565 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 565 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 565 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 191
        2.69 -     3.24: 6608
        3.24 -     3.79: 9892
        3.79 -     4.35: 12329
        4.35 -     4.90: 18650
  Nonbonded interactions: 47670
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 180 "
            pdb=" O   THR A 496 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG  SER A 170 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ARG A 305 "
            pdb=" NZ  LYS A 309 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" NH2 ARG B 355 "
            pdb=" OD2 ASP B 398 "
     model   vdw
     2.239 3.120
  ... (remaining 47665 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 'G' and resid 1)
  selection = (chain 'H' and resid 1)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.350
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.730
  Find NCS groups from input model:        0.060
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4948
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.149   6647  Z= 0.209
  Angle     :  1.032  19.045   9042  Z= 0.540
  Chirality :  0.051   0.385    946
  Planarity :  0.009   0.200   1164
  Dihedral  : 19.217 117.737   2511
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.87 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 31.48 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.28), residues: 775
  helix: -1.63 (0.31), residues: 257
  sheet:  2.48 (1.14), residues: 24
  loop : -2.66 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 168 
 HIS   0.008   0.001   HIS A 505 
 PHE   0.020   0.002   PHE B 338 
 TYR   0.015   0.001   TYR A 510 
 ARG   0.008   0.001   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01295 (    4)
  link_NAG-ASN         : angle       6.53667 (   12)
  link_BETA1-4         : bond        0.00233 (    1)
  link_BETA1-4         : angle       1.35764 (    3)
  hydrogen bonds       : bond        0.15776 (  173)
  hydrogen bonds       : angle       6.45848 (  468)
  link_BETA1-6         : bond        0.00809 (    1)
  link_BETA1-6         : angle       1.93647 (    3)
  SS BOND              : bond        0.00539 (    6)
  SS BOND              : angle       1.15684 (   12)
  covalent geometry    : bond        0.00462 ( 6635)
  covalent geometry    : angle       1.00443 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6107 (mt) cc_final: 0.5829 (mm)
REVERT: A   62 MET cc_start: 0.4429 (mpp) cc_final: 0.4108 (pmm)
REVERT: A  123 MET cc_start: -0.0391 (tpt) cc_final: -0.0686 (tpt)
REVERT: A  202 TYR cc_start: 0.7222 (m-10) cc_final: 0.6390 (t80)
REVERT: A  379 ILE cc_start: 0.8955 (tt) cc_final: 0.8683 (mm)
REVERT: A  382 ASP cc_start: 0.8908 (t70) cc_final: 0.8393 (p0)
REVERT: A  408 MET cc_start: 0.3341 (mmp) cc_final: 0.2561 (mmm)
REVERT: A  474 MET cc_start: -0.1394 (ptt) cc_final: -0.2041 (ptt)
REVERT: A  497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6257 (t80)
REVERT: A  515 TYR cc_start: 0.6070 (m-80) cc_final: 0.5712 (m-80)
REVERT: A  539 LEU cc_start: 0.6118 (tp) cc_final: 0.5859 (mp)
  outliers start: 4
  outliers final: 1
  residues processed: 127
  average time/residue: 0.1825
  time to fit residues: 30.7704
Evaluate side-chains
  82 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 TYR
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 58 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0010
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.3980
   overall best weight:    0.2344

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.146012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.127510 restraints weight = 41722.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.129459 restraints weight = 36294.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.130636 restraints weight = 29187.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5112
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6647  Z= 0.144
  Angle     :  0.817  18.296   9042  Z= 0.399
  Chirality :  0.051   0.504    946
  Planarity :  0.006   0.066   1164
  Dihedral  : 11.473 104.694    982
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 26.65 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.30), residues: 775
  helix: -1.21 (0.32), residues: 259
  sheet:  1.82 (1.13), residues: 24
  loop : -2.45 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 211 
 HIS   0.006   0.001   HIS A 417 
 PHE   0.023   0.002   PHE B 490 
 TYR   0.016   0.001   TYR A 180 
 ARG   0.005   0.001   ARG A 245 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01213 (    4)
  link_NAG-ASN         : angle       6.10575 (   12)
  link_BETA1-4         : bond        0.00371 (    1)
  link_BETA1-4         : angle       1.51220 (    3)
  hydrogen bonds       : bond        0.04018 (  173)
  hydrogen bonds       : angle       5.76154 (  468)
  link_BETA1-6         : bond        0.01477 (    1)
  link_BETA1-6         : angle       2.29494 (    3)
  SS BOND              : bond        0.00371 (    6)
  SS BOND              : angle       1.30363 (   12)
  covalent geometry    : bond        0.00309 ( 6635)
  covalent geometry    : angle       0.78423 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ILE cc_start: 0.6995 (mm) cc_final: 0.6713 (mt)
REVERT: A  203 TRP cc_start: 0.6057 (t-100) cc_final: 0.4614 (m-10)
REVERT: A  211 TRP cc_start: 0.5753 (p90) cc_final: 0.3103 (m100)
REVERT: A  252 TYR cc_start: 0.2775 (OUTLIER) cc_final: 0.1779 (p90)
REVERT: A  279 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.5040 (m-10)
REVERT: A  345 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7338 (t70)
REVERT: A  376 MET cc_start: 0.8852 (tpt) cc_final: 0.8009 (ptt)
REVERT: A  382 ASP cc_start: 0.9116 (t70) cc_final: 0.8461 (p0)
REVERT: A  400 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7689 (t80)
REVERT: A  402 GLU cc_start: 0.7108 (mp0) cc_final: 0.6767 (mp0)
REVERT: A  462 MET cc_start: 0.7043 (ppp) cc_final: 0.6726 (ppp)
REVERT: A  539 LEU cc_start: 0.5705 (tp) cc_final: 0.5492 (mp)
REVERT: A  566 TRP cc_start: 0.7458 (p-90) cc_final: 0.6990 (p-90)
REVERT: A  579 MET cc_start: 0.6576 (ppp) cc_final: 0.5330 (ppp)
  outliers start: 29
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1759
  time to fit residues: 26.9916
Evaluate side-chains
  91 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  542 CYS
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 51 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0980
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.2196

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.145999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.127457 restraints weight = 41320.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.129100 restraints weight = 34311.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.130062 restraints weight = 29239.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5221
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6647  Z= 0.133
  Angle     :  0.786  18.114   9042  Z= 0.378
  Chirality :  0.049   0.509    946
  Planarity :  0.006   0.065   1164
  Dihedral  : 10.684 101.367    980
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 26.94 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.30), residues: 775
  helix: -0.82 (0.34), residues: 245
  sheet:  1.71 (1.08), residues: 24
  loop : -2.38 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 211 
 HIS   0.007   0.001   HIS A 417 
 PHE   0.034   0.002   PHE A  72 
 TYR   0.014   0.001   TYR A 217 
 ARG   0.009   0.001   ARG A 572 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01341 (    4)
  link_NAG-ASN         : angle       6.10865 (   12)
  link_BETA1-4         : bond        0.00132 (    1)
  link_BETA1-4         : angle       1.54343 (    3)
  hydrogen bonds       : bond        0.03754 (  173)
  hydrogen bonds       : angle       5.67289 (  468)
  link_BETA1-6         : bond        0.01352 (    1)
  link_BETA1-6         : angle       2.63483 (    3)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       1.08568 (   12)
  covalent geometry    : bond        0.00284 ( 6635)
  covalent geometry    : angle       0.75182 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LYS cc_start: -0.0670 (OUTLIER) cc_final: -0.1144 (pttm)
REVERT: A   93 ILE cc_start: 0.6839 (mm) cc_final: 0.6298 (pt)
REVERT: A  123 MET cc_start: -0.0856 (tpt) cc_final: -0.1241 (tpt)
REVERT: A  150 ASP cc_start: 0.9098 (p0) cc_final: 0.8198 (t0)
REVERT: A  171 GLU cc_start: 0.9027 (pp20) cc_final: 0.8626 (pm20)
REVERT: A  252 TYR cc_start: 0.2611 (OUTLIER) cc_final: 0.1740 (p90)
REVERT: A  279 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.4907 (m-10)
REVERT: A  345 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7541 (t70)
REVERT: A  381 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.4146 (p90)
REVERT: A  382 ASP cc_start: 0.9142 (t70) cc_final: 0.8334 (p0)
REVERT: A  400 PHE cc_start: 0.8339 (t80) cc_final: 0.7921 (t80)
REVERT: A  462 MET cc_start: 0.7293 (ppp) cc_final: 0.6856 (ppp)
REVERT: A  544 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.6114 (pt)
REVERT: A  566 TRP cc_start: 0.7482 (p-90) cc_final: 0.7109 (p-90)
REVERT: A  579 MET cc_start: 0.6834 (ppp) cc_final: 0.6046 (ppp)
  outliers start: 30
  outliers final: 16
  residues processed: 101
  average time/residue: 0.2810
  time to fit residues: 39.1019
Evaluate side-chains
  96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0980
   chunk 72 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0370
   chunk 29 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.3658

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.145154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.126812 restraints weight = 42436.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.127754 restraints weight = 35846.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.128876 restraints weight = 30959.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5319
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6647  Z= 0.127
  Angle     :  0.754  17.889   9042  Z= 0.361
  Chirality :  0.048   0.502    946
  Planarity :  0.005   0.062   1164
  Dihedral  :  9.518  92.121    980
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 27.09 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.31), residues: 775
  helix: -0.77 (0.35), residues: 244
  sheet:  2.15 (1.14), residues: 24
  loop : -2.27 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 211 
 HIS   0.007   0.001   HIS A 555 
 PHE   0.027   0.002   PHE A 452 
 TYR   0.013   0.001   TYR A  41 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01270 (    4)
  link_NAG-ASN         : angle       6.10569 (   12)
  link_BETA1-4         : bond        0.00104 (    1)
  link_BETA1-4         : angle       1.69137 (    3)
  hydrogen bonds       : bond        0.03339 (  173)
  hydrogen bonds       : angle       5.66138 (  468)
  link_BETA1-6         : bond        0.01366 (    1)
  link_BETA1-6         : angle       2.79788 (    3)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       0.81028 (   12)
  covalent geometry    : bond        0.00269 ( 6635)
  covalent geometry    : angle       0.71861 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.6934 (mm) cc_final: 0.6318 (pt)
REVERT: A  150 ASP cc_start: 0.9154 (p0) cc_final: 0.8250 (t0)
REVERT: A  171 GLU cc_start: 0.9037 (pp20) cc_final: 0.8676 (pm20)
REVERT: A  203 TRP cc_start: 0.6567 (t-100) cc_final: 0.4871 (m-10)
REVERT: A  252 TYR cc_start: 0.2914 (OUTLIER) cc_final: 0.2231 (p90)
REVERT: A  279 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.4962 (m-10)
REVERT: A  345 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7696 (t70)
REVERT: A  376 MET cc_start: 0.8818 (tpt) cc_final: 0.8003 (ptp)
REVERT: A  382 ASP cc_start: 0.9090 (t70) cc_final: 0.8467 (p0)
REVERT: A  400 PHE cc_start: 0.8381 (t80) cc_final: 0.7873 (t80)
REVERT: A  462 MET cc_start: 0.7488 (ppp) cc_final: 0.7112 (ppp)
REVERT: A  579 MET cc_start: 0.6743 (ppp) cc_final: 0.6150 (ppp)
REVERT: B  486 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6495 (t80)
  outliers start: 29
  outliers final: 19
  residues processed: 99
  average time/residue: 0.3199
  time to fit residues: 42.7569
Evaluate side-chains
  96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0670
   chunk 48 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 38 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0020
   chunk 74 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0270
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.146200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.133953 restraints weight = 39673.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.133708 restraints weight = 36520.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.134088 restraints weight = 35013.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5095
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6647  Z= 0.124
  Angle     :  0.728  17.828   9042  Z= 0.351
  Chirality :  0.048   0.487    946
  Planarity :  0.005   0.063   1164
  Dihedral  :  8.411  84.015    980
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.82 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.31), residues: 775
  helix: -0.67 (0.35), residues: 246
  sheet:  2.20 (1.04), residues: 24
  loop : -2.25 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 566 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.042   0.002   PHE A  72 
 TYR   0.021   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 514 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01258 (    4)
  link_NAG-ASN         : angle       6.05090 (   12)
  link_BETA1-4         : bond        0.00222 (    1)
  link_BETA1-4         : angle       1.66814 (    3)
  hydrogen bonds       : bond        0.03300 (  173)
  hydrogen bonds       : angle       5.61464 (  468)
  link_BETA1-6         : bond        0.01464 (    1)
  link_BETA1-6         : angle       2.94730 (    3)
  SS BOND              : bond        0.00296 (    6)
  SS BOND              : angle       0.76225 (   12)
  covalent geometry    : bond        0.00260 ( 6635)
  covalent geometry    : angle       0.69149 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.6784 (mm) cc_final: 0.6200 (pt)
REVERT: A  171 GLU cc_start: 0.8718 (pp20) cc_final: 0.8457 (pm20)
REVERT: A  203 TRP cc_start: 0.6026 (t-100) cc_final: 0.4711 (m-10)
REVERT: A  252 TYR cc_start: 0.2541 (OUTLIER) cc_final: 0.2118 (p90)
REVERT: A  279 TYR cc_start: 0.5566 (OUTLIER) cc_final: 0.4640 (m-10)
REVERT: A  376 MET cc_start: 0.8517 (tpt) cc_final: 0.7859 (ptt)
REVERT: A  381 TYR cc_start: 0.5504 (OUTLIER) cc_final: 0.3719 (p90)
REVERT: A  382 ASP cc_start: 0.9084 (t70) cc_final: 0.8314 (p0)
REVERT: A  462 MET cc_start: 0.7135 (ppp) cc_final: 0.6832 (ppp)
REVERT: A  579 MET cc_start: 0.6789 (ppp) cc_final: 0.5103 (tpp)
  outliers start: 32
  outliers final: 20
  residues processed: 99
  average time/residue: 0.2104
  time to fit residues: 28.6042
Evaluate side-chains
  93 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0770
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.144495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.125675 restraints weight = 40778.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.127663 restraints weight = 32730.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.128849 restraints weight = 27351.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5315
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6647  Z= 0.134
  Angle     :  0.770  18.571   9042  Z= 0.367
  Chirality :  0.048   0.500    946
  Planarity :  0.005   0.066   1164
  Dihedral  :  7.929  74.058    980
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 27.67 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.31), residues: 775
  helix: -0.65 (0.35), residues: 245
  sheet:  2.50 (1.00), residues: 24
  loop : -2.22 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 566 
 HIS   0.007   0.001   HIS A 555 
 PHE   0.031   0.002   PHE A  72 
 TYR   0.020   0.001   TYR A  50 
 ARG   0.002   0.000   ARG A 514 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01276 (    4)
  link_NAG-ASN         : angle       6.02562 (   12)
  link_BETA1-4         : bond        0.00235 (    1)
  link_BETA1-4         : angle       1.67386 (    3)
  hydrogen bonds       : bond        0.03370 (  173)
  hydrogen bonds       : angle       5.63906 (  468)
  link_BETA1-6         : bond        0.01358 (    1)
  link_BETA1-6         : angle       2.91732 (    3)
  SS BOND              : bond        0.00609 (    6)
  SS BOND              : angle       1.23031 (   12)
  covalent geometry    : bond        0.00291 ( 6635)
  covalent geometry    : angle       0.73510 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 1.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.6870 (mm) cc_final: 0.6283 (pt)
REVERT: A  171 GLU cc_start: 0.9175 (pp20) cc_final: 0.8802 (pm20)
REVERT: A  203 TRP cc_start: 0.6620 (t-100) cc_final: 0.4887 (m-10)
REVERT: A  252 TYR cc_start: 0.3677 (OUTLIER) cc_final: 0.3324 (p90)
REVERT: A  279 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.4997 (m-10)
REVERT: A  376 MET cc_start: 0.8806 (tpt) cc_final: 0.7971 (ptt)
REVERT: A  381 TYR cc_start: 0.5813 (OUTLIER) cc_final: 0.4098 (p90)
REVERT: A  462 MET cc_start: 0.7340 (ppp) cc_final: 0.7115 (ppp)
REVERT: A  579 MET cc_start: 0.6941 (ppp) cc_final: 0.5491 (tpp)
REVERT: B  410 ILE cc_start: 0.8165 (mm) cc_final: 0.7844 (mm)
REVERT: B  528 LYS cc_start: 0.3310 (OUTLIER) cc_final: 0.1641 (tttm)
  outliers start: 30
  outliers final: 24
  residues processed: 97
  average time/residue: 0.2609
  time to fit residues: 34.8689
Evaluate side-chains
  102 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    0.0040
   chunk 5 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0040
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0870
   chunk 55 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0770
   overall best weight:    0.1940

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.146272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.127037 restraints weight = 40643.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.128993 restraints weight = 32332.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.130175 restraints weight = 27196.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5343
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6647  Z= 0.122
  Angle     :  0.756  17.500   9042  Z= 0.361
  Chirality :  0.047   0.493    946
  Planarity :  0.005   0.064   1164
  Dihedral  :  7.335  60.290    980
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 28.84 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.31), residues: 775
  helix: -0.72 (0.35), residues: 244
  sheet:  2.19 (0.97), residues: 27
  loop : -2.15 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 566 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.033   0.001   PHE A  72 
 TYR   0.014   0.001   TYR A  50 
 ARG   0.014   0.001   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01291 (    4)
  link_NAG-ASN         : angle       6.12207 (   12)
  link_BETA1-4         : bond        0.00672 (    1)
  link_BETA1-4         : angle       1.62810 (    3)
  hydrogen bonds       : bond        0.03235 (  173)
  hydrogen bonds       : angle       5.52575 (  468)
  link_BETA1-6         : bond        0.01266 (    1)
  link_BETA1-6         : angle       2.95303 (    3)
  SS BOND              : bond        0.00360 (    6)
  SS BOND              : angle       1.17164 (   12)
  covalent geometry    : bond        0.00260 ( 6635)
  covalent geometry    : angle       0.72014 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.6884 (mm) cc_final: 0.6325 (pt)
REVERT: A  123 MET cc_start: -0.1229 (tpt) cc_final: -0.1569 (tpt)
REVERT: A  171 GLU cc_start: 0.9235 (pp20) cc_final: 0.8891 (pm20)
REVERT: A  203 TRP cc_start: 0.6687 (t-100) cc_final: 0.4887 (m-10)
REVERT: A  252 TYR cc_start: 0.3670 (OUTLIER) cc_final: 0.3364 (p90)
REVERT: A  279 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4947 (m-10)
REVERT: A  332 MET cc_start: 0.7277 (pmm) cc_final: 0.5792 (tpp)
REVERT: A  376 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7988 (ptt)
REVERT: A  381 TYR cc_start: 0.5776 (OUTLIER) cc_final: 0.4060 (p90)
REVERT: A  462 MET cc_start: 0.7329 (ppp) cc_final: 0.7118 (ppp)
REVERT: A  579 MET cc_start: 0.6907 (ppp) cc_final: 0.5389 (tpp)
REVERT: B  410 ILE cc_start: 0.8182 (mm) cc_final: 0.7873 (mm)
REVERT: B  528 LYS cc_start: 0.3136 (OUTLIER) cc_final: 0.1473 (tttm)
  outliers start: 26
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1919
  time to fit residues: 23.9039
Evaluate side-chains
  96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0070
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A  79 HIS
A 220 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.141278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.122529 restraints weight = 41502.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.124407 restraints weight = 33497.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.125425 restraints weight = 27937.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5510
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6647  Z= 0.148
  Angle     :  0.788  17.238   9042  Z= 0.382
  Chirality :  0.048   0.512    946
  Planarity :  0.006   0.068   1164
  Dihedral  :  6.749  54.017    980
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.96 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.31), residues: 775
  helix: -0.80 (0.35), residues: 249
  sheet:  2.15 (0.95), residues: 27
  loop : -2.19 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 566 
 HIS   0.014   0.002   HIS A  79 
 PHE   0.020   0.002   PHE A 452 
 TYR   0.017   0.002   TYR A  50 
 ARG   0.005   0.001   ARG A 273 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01283 (    4)
  link_NAG-ASN         : angle       6.43470 (   12)
  link_BETA1-4         : bond        0.00359 (    1)
  link_BETA1-4         : angle       1.92424 (    3)
  hydrogen bonds       : bond        0.03674 (  173)
  hydrogen bonds       : angle       5.79298 (  468)
  link_BETA1-6         : bond        0.01408 (    1)
  link_BETA1-6         : angle       2.72556 (    3)
  SS BOND              : bond        0.00303 (    6)
  SS BOND              : angle       1.11538 (   12)
  covalent geometry    : bond        0.00320 ( 6635)
  covalent geometry    : angle       0.75019 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 74
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.6980 (mm) cc_final: 0.6406 (pt)
REVERT: A  171 GLU cc_start: 0.9213 (pp20) cc_final: 0.8869 (pm20)
REVERT: A  252 TYR cc_start: 0.4275 (OUTLIER) cc_final: 0.3454 (p90)
REVERT: A  279 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.4865 (m-10)
REVERT: A  332 MET cc_start: 0.7202 (pmm) cc_final: 0.5489 (tpp)
REVERT: A  376 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8000 (ptt)
REVERT: A  381 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.3794 (p90)
REVERT: A  464 PHE cc_start: 0.2481 (OUTLIER) cc_final: -0.1030 (t80)
REVERT: A  497 TYR cc_start: 0.7154 (t80) cc_final: 0.6888 (t80)
REVERT: A  514 ARG cc_start: 0.1526 (OUTLIER) cc_final: 0.1310 (mtm180)
REVERT: A  579 MET cc_start: 0.7155 (ppp) cc_final: 0.6737 (ppp)
  outliers start: 32
  outliers final: 23
  residues processed: 97
  average time/residue: 0.2735
  time to fit residues: 35.3843
Evaluate side-chains
  95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 HIS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0170
   chunk 34 optimal weight:    0.0020
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5026

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

Flipped N/Q/H residues before XYZ refinement:
A  79 HIS
** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.141860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.122782 restraints weight = 41883.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.124429 restraints weight = 33567.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.125440 restraints weight = 28402.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6647  Z= 0.131
  Angle     :  0.761  17.332   9042  Z= 0.370
  Chirality :  0.048   0.499    946
  Planarity :  0.005   0.066   1164
  Dihedral  :  6.575  53.653    980
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 29.14 %
    Favored  : 66.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.30), residues: 775
  helix: -0.86 (0.34), residues: 249
  sheet:  2.22 (0.98), residues: 27
  loop : -2.15 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 566 
 HIS   0.033   0.002   HIS A  79 
 PHE   0.023   0.002   PHE B 377 
 TYR   0.015   0.002   TYR A 613 
 ARG   0.008   0.001   ARG A 113 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01251 (    4)
  link_NAG-ASN         : angle       6.35335 (   12)
  link_BETA1-4         : bond        0.00717 (    1)
  link_BETA1-4         : angle       1.37582 (    3)
  hydrogen bonds       : bond        0.03527 (  173)
  hydrogen bonds       : angle       5.72748 (  468)
  link_BETA1-6         : bond        0.01262 (    1)
  link_BETA1-6         : angle       2.75716 (    3)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       0.92781 (   12)
  covalent geometry    : bond        0.00285 ( 6635)
  covalent geometry    : angle       0.72354 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.9230 (pp20) cc_final: 0.8908 (pm20)
REVERT: A  252 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3544 (p90)
REVERT: A  279 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.4733 (m-10)
REVERT: A  332 MET cc_start: 0.7331 (pmm) cc_final: 0.5803 (tpp)
REVERT: A  376 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7986 (ptt)
REVERT: A  381 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.3585 (p90)
REVERT: A  382 ASP cc_start: 0.9220 (t0) cc_final: 0.8810 (t0)
REVERT: A  464 PHE cc_start: 0.2226 (OUTLIER) cc_final: -0.1167 (t80)
REVERT: A  514 ARG cc_start: 0.1471 (OUTLIER) cc_final: 0.1256 (mtm180)
REVERT: A  579 MET cc_start: 0.7214 (ppp) cc_final: 0.6750 (ppp)
  outliers start: 30
  outliers final: 24
  residues processed: 87
  average time/residue: 0.3000
  time to fit residues: 36.2305
Evaluate side-chains
  95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 65
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0370
   chunk 23 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0020
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.2666

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.143573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.124445 restraints weight = 41264.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.126326 restraints weight = 33058.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.127440 restraints weight = 27881.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5431
moved from start:          0.5155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6647  Z= 0.124
  Angle     :  0.762  17.039   9042  Z= 0.370
  Chirality :  0.048   0.480    946
  Planarity :  0.005   0.064   1164
  Dihedral  :  6.386  52.979    980
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.72 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.31), residues: 775
  helix: -0.79 (0.34), residues: 251
  sheet:  2.41 (0.98), residues: 27
  loop : -2.13 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 566 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.018   0.002   PHE A 452 
 TYR   0.015   0.001   TYR A 613 
 ARG   0.004   0.001   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01216 (    4)
  link_NAG-ASN         : angle       6.02554 (   12)
  link_BETA1-4         : bond        0.00629 (    1)
  link_BETA1-4         : angle       0.78531 (    3)
  hydrogen bonds       : bond        0.03464 (  173)
  hydrogen bonds       : angle       5.65419 (  468)
  link_BETA1-6         : bond        0.01259 (    1)
  link_BETA1-6         : angle       2.71337 (    3)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       0.80691 (   12)
  covalent geometry    : bond        0.00266 ( 6635)
  covalent geometry    : angle       0.72799 ( 9012)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7096 (mm) cc_final: 0.6473 (pt)
REVERT: A  171 GLU cc_start: 0.9177 (pp20) cc_final: 0.8844 (pm20)
REVERT: A  252 TYR cc_start: 0.4181 (OUTLIER) cc_final: 0.3639 (p90)
REVERT: A  279 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.4778 (m-10)
REVERT: A  332 MET cc_start: 0.7325 (pmm) cc_final: 0.5928 (tpp)
REVERT: A  376 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7857 (ptp)
REVERT: A  381 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.3490 (p90)
REVERT: A  382 ASP cc_start: 0.9134 (t0) cc_final: 0.8736 (t0)
REVERT: A  464 PHE cc_start: 0.1971 (OUTLIER) cc_final: -0.1515 (t80)
REVERT: A  579 MET cc_start: 0.7205 (ppp) cc_final: 0.6708 (ppp)
  outliers start: 28
  outliers final: 23
  residues processed: 91
  average time/residue: 0.2531
  time to fit residues: 31.3684
Evaluate side-chains
  94 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  308 PHE
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0980
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0670
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  79 HIS
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.141609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.122549 restraints weight = 42156.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.124261 restraints weight = 34228.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.125351 restraints weight = 28409.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5567
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6647  Z= 0.134
  Angle     :  0.779  16.772   9042  Z= 0.381
  Chirality :  0.048   0.500    946
  Planarity :  0.005   0.066   1164
  Dihedral  :  6.458  53.334    980
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.06 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 28.99 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.30), residues: 775
  helix: -0.67 (0.35), residues: 238
  sheet:  2.46 (0.96), residues: 27
  loop : -2.20 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 566 
 HIS   0.020   0.002   HIS A  79 
 PHE   0.019   0.002   PHE A 452 
 TYR   0.016   0.002   TYR A 202 
 ARG   0.005   0.001   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01231 (    4)
  link_NAG-ASN         : angle       5.93918 (   12)
  link_BETA1-4         : bond        0.00563 (    1)
  link_BETA1-4         : angle       0.77210 (    3)
  hydrogen bonds       : bond        0.03790 (  173)
  hydrogen bonds       : angle       5.81187 (  468)
  link_BETA1-6         : bond        0.01223 (    1)
  link_BETA1-6         : angle       2.59987 (    3)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       0.81901 (   12)
  covalent geometry    : bond        0.00292 ( 6635)
  covalent geometry    : angle       0.74730 ( 9012)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3853.21 seconds
wall clock time: 71 minutes 19.47 seconds (4279.47 seconds total)