Starting phenix.real_space_refine
on Tue Apr 29 12:05:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vkj_43319/04_2025/8vkj_43319.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      39      5.16       5
     C    5685      2.51       5
     N    1382      2.21       5
     O    1510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8622
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4254
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 548, 4243
          Classifications: {'peptide': 548}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 26, 'TRANS': 521}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 68
      Conformer: "B"
        Number of residues, atoms: 548, 4243
          Classifications: {'peptide': 548}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 26, 'TRANS': 521}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 68
          bond proxies already assigned to first conformer: 4350
    Chain: "B"
      Number of atoms: 4168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4168
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 26, 'TRANS': 514}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 138
          Unresolved non-hydrogen angles: 171
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 59
    Chain: "C"
      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: "A"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 79
          Unusual residues: {'ACO': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 93
          Unusual residues: {'ACO': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 269 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 269 " occ=0.50
  Time building chain proxies: 8.37, per 1000 atoms: 0.97
  Number of scatterers: 8622
  At special positions: 0
  Unit cell: (104.877, 81.3, 104.064, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     P       6     15.00
     O    1510      8.00
     N    1382      7.00
     C    5685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 162 "
      " NAG A 703 " - " ASN A  94 "
      " NAG B 701 " - " ASN B 162 "
      " NAG B 703 " - " ASN B  94 "
      " NAG B 704 " - " ASN B 142 "
      " NAG C   1 " - " ASN A 142 "
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      56.8% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 196 through 228
      removed outlier: 3.691A  pdb=" N   LEU A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASP A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 287
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 6.608A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
    Processing helix  chain 'A' and resid 308 through 331
    Processing helix  chain 'A' and resid 334 through 357
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 414 through 416
      No H-bonds generated for 'chain 'A' and resid 414 through 416'
    Processing helix  chain 'A' and resid 417 through 437
    Processing helix  chain 'A' and resid 453 through 458
      removed outlier: 3.652A  pdb=" N   LYS A 458 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 476 through 480
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 3.794A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 524
      removed outlier: 4.026A  pdb=" N   ASN A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.685A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 600 through 606
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
    Processing helix  chain 'B' and resid 191 through 196
    Processing helix  chain 'B' and resid 197 through 228
      removed outlier: 3.661A  pdb=" N   LEU B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASP B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 287
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 6.551A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
    Processing helix  chain 'B' and resid 308 through 331
    Processing helix  chain 'B' and resid 334 through 356
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.537A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 458
      removed outlier: 3.610A  pdb=" N   LYS B 458 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 476
    Processing helix  chain 'B' and resid 477 through 480
      removed outlier: 3.698A  pdb=" N   LEU B 480 " --> pdb=" O   ASP B 477 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 477 through 480'
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 4.178A  pdb=" N   VAL B 488 " --> pdb=" O   SER B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 524
      removed outlier: 4.234A  pdb=" N   ASN B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 551
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 658
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129
      removed outlier: 6.137A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   ASN A 169 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.814A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132
      removed outlier: 3.524A  pdb=" N   SER B 125 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL B 167 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 132
      removed outlier: 3.524A  pdb=" N   SER B 125 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL B 167 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.717A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   ASP B 143 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   GLU B 149 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1446 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1373
        1.32 -     1.45: 2496
        1.45 -     1.57: 4929
        1.57 -     1.69: 10
        1.69 -     1.82: 53
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.522 -0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" N   PRO A 419 "
       pdb=" CD  PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.473  1.511 -0.038 1.40e-02 5.10e+03 7.48e+00
  bond pdb=" CB  PRO A 419 "
       pdb=" CG  PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.492  1.627 -0.135 5.00e-02 4.00e+02 7.27e+00
  bond pdb=" N   PRO A 419 "
       pdb=" CA  PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.469  1.435  0.033 1.28e-02 6.10e+03 6.81e+00
  bond pdb=" CG  PRO A 419 "
       pdb=" CD  PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.503  1.423  0.080 3.40e-02 8.65e+02 5.58e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.98: 12080
        3.98 -     7.95: 36
        7.95 -    11.93: 1
       11.93 -    15.91: 1
       15.91 -    19.89: 1
  Bond angle restraints: 12119
  Sorted by residual:
  angle pdb=" CA  PRO A 419 "
        pdb=" N   PRO A 419 "
        pdb=" CD  PRO A 419 "
      ideal   model   delta    sigma   weight residual
     112.00   92.11   19.89 1.40e+00 5.10e-01 2.02e+02
  angle pdb=" N   PRO A 419 "
        pdb=" CD  PRO A 419 "
        pdb=" CG  PRO A 419 "
      ideal   model   delta    sigma   weight residual
     103.20   95.41    7.79 1.50e+00 4.44e-01 2.70e+01
  angle pdb=" CA  LEU B 411 "
        pdb=" CB  LEU B 411 "
        pdb=" CG  LEU B 411 "
      ideal   model   delta    sigma   weight residual
     116.30  129.52  -13.22 3.50e+00 8.16e-02 1.43e+01
  angle pdb=" CA  PRO A 419 "
        pdb=" CB  PRO A 419 "
        pdb=" CG  PRO A 419 "
      ideal   model   delta    sigma   weight residual
     104.50   98.27    6.23 1.90e+00 2.77e-01 1.07e+01
  angle pdb=" CA  LYS A 529 "
        pdb=" CB  LYS A 529 "
        pdb=" CG  LYS A 529 "
      ideal   model   delta    sigma   weight residual
     114.10  120.42   -6.32 2.00e+00 2.50e-01 9.98e+00
  ... (remaining 12114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.38: 4775
       22.38 -    44.76: 372
       44.76 -    67.13: 72
       67.13 -    89.51: 12
       89.51 -   111.89: 1
  Dihedral angle restraints: 5232
    sinusoidal: 2080
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 462 "
           pdb=" CB  CYS A 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.28  -74.28     1      1.00e+01 1.00e-02 7.00e+01
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.30  -70.30     1      1.00e+01 1.00e-02 6.36e+01
  dihedral pdb=" CA  GLY A 597 "
           pdb=" C   GLY A 597 "
           pdb=" N   THR A 598 "
           pdb=" CA  THR A 598 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.57  -21.43     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 5229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 844
       0.033 -    0.066: 419
       0.066 -    0.098: 118
       0.098 -    0.131: 33
       0.131 -    0.164: 4
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  THR B 598 "
            pdb=" N   THR B 598 "
            pdb=" C   THR B 598 "
            pdb=" CB  THR B 598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.70e-01
  chirality pdb=" CG  LEU B  90 "
            pdb=" CB  LEU B  90 "
            pdb=" CD1 LEU B  90 "
            pdb=" CD2 LEU B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  PHE B 621 "
            pdb=" N   PHE B 621 "
            pdb=" C   PHE B 621 "
            pdb=" CB  PHE B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1415 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 418 "    0.114 5.00e-02 4.00e+02   1.55e-01 3.85e+01
        pdb=" N   PRO A 419 "   -0.267 5.00e-02 4.00e+02
        pdb=" CA  PRO A 419 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO A 419 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 123 "   -0.049 5.00e-02 4.00e+02   7.32e-02 8.58e+00
        pdb=" N   PRO B 124 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 269 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.24e+00
        pdb=" C   ARG B 269 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ARG B 269 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 270 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 757
        2.74 -     3.28: 8761
        3.28 -     3.82: 15571
        3.82 -     4.36: 18266
        4.36 -     4.90: 31725
  Nonbonded interactions: 75080
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 447 "
            pdb=" OD2 ASP B 455 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG1 THR A 304 "
            pdb=" OD2 ASP A 307 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ILE B 355 "
            pdb=" OH  TYR B 361 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP B 413 "
            pdb=" OH  TYR B 524 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   ILE A 355 "
            pdb=" OH  TYR A 361 "
     model   vdw
     2.254 3.040
  ... (remaining 75075 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 'A' and (resid 76 through 144 or (resid 145 through 146 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 147 or (resid 148 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 149 through 167 or (resid 1 \ 
68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 
 170 or resid 177 through 190 or (resid 191 through 193 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 194 through 199 or (resid 200 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 201 through 223 or (re \ 
sid 224 through 266 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 267 through 268 or resid 270 through 336 or (resid 337 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 338 through 400 or (resid 407 thr \ 
ough 409 and (name N or name CA or name C or name O or name CB )) or resid 410 t \ 
hrough 528 or (resid 529 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 530 through 555 or (resid 556 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 557 through 663 or resid 701 through 703))
  selection = (chain 'B' and (resid 76 through 116 or (resid 117 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 118 through 210 or (resid 211 through 266 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 267 through 268 \ 
 or resid 270 through 368 or (resid 369 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 370 through 400 or (resid 407 through 409 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 410 through 663 or resid 7 \ 
01 through 703))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.710
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.270
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
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   0.135   8874  Z= 0.196
  Angle     :  0.641  19.887  12152  Z= 0.333
  Chirality :  0.041   0.164   1418
  Planarity :  0.006   0.155   1466
  Dihedral  : 16.087 111.891   3194
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 11.56 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.26), residues: 1078
  helix:  2.04 (0.22), residues: 525
  sheet: -0.39 (0.49), residues: 126
  loop : -1.51 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 418 
 HIS   0.004   0.001   HIS A 614 
 PHE   0.014   0.001   PHE B 322 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00528 (    6)
  link_NAG-ASN         : angle       2.69712 (   18)
  link_BETA1-4         : bond        0.02316 (    1)
  link_BETA1-4         : angle       5.21611 (    3)
  hydrogen bonds       : bond        0.14337 (  499)
  hydrogen bonds       : angle       6.12165 ( 1446)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       1.24112 (   12)
  covalent geometry    : bond        0.00475 ( 8861)
  covalent geometry    : angle       0.62716 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.999 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 62
  average time/residue: 1.2974
  time to fit residues: 86.8827
Evaluate side-chains
  60 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
A 506 ASN
A 614 HIS
B  87 HIS
B 134 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.143893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113186 restraints weight = 20081.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.32
r_work: 0.3138 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8874  Z= 0.173
  Angle     :  0.593  10.327  12152  Z= 0.301
  Chirality :  0.042   0.160   1418
  Planarity :  0.004   0.078   1466
  Dihedral  :  9.961  77.612   1417
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.53 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1078
  helix:  2.08 (0.22), residues: 523
  sheet: -0.23 (0.50), residues: 122
  loop : -1.54 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.016   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00563 (    6)
  link_NAG-ASN         : angle       2.94662 (   18)
  link_BETA1-4         : bond        0.01424 (    1)
  link_BETA1-4         : angle       3.40670 (    3)
  hydrogen bonds       : bond        0.04125 (  499)
  hydrogen bonds       : angle       4.95642 ( 1446)
  SS BOND              : bond        0.00555 (    6)
  SS BOND              : angle       1.10658 (   12)
  covalent geometry    : bond        0.00409 ( 8861)
  covalent geometry    : angle       0.57912 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7666 (mmtt)
REVERT: A  180 ASP cc_start: 0.7424 (t0) cc_final: 0.6666 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 1.0262
  time to fit residues: 89.4897
Evaluate side-chains
  73 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 89 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0170
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
A 516 GLN
B 135 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.113322 restraints weight = 18506.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.13
r_work: 0.3152 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8874  Z= 0.167
  Angle     :  0.568   9.728  12152  Z= 0.288
  Chirality :  0.042   0.160   1418
  Planarity :  0.004   0.036   1466
  Dihedral  :  9.305  67.615   1416
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.78 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1078
  helix:  2.00 (0.22), residues: 537
  sheet: -0.39 (0.48), residues: 122
  loop : -1.52 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.015   0.001   PHE B 601 
 TYR   0.016   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00514 (    6)
  link_NAG-ASN         : angle       2.80321 (   18)
  link_BETA1-4         : bond        0.00862 (    1)
  link_BETA1-4         : angle       3.22519 (    3)
  hydrogen bonds       : bond        0.03869 (  499)
  hydrogen bonds       : angle       4.77497 ( 1446)
  SS BOND              : bond        0.00513 (    6)
  SS BOND              : angle       1.02078 (   12)
  covalent geometry    : bond        0.00399 ( 8861)
  covalent geometry    : angle       0.55485 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  135 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7808 (p90)
REVERT: A  337 ARG cc_start: 0.7785 (tmt170) cc_final: 0.7459 (ttt-90)
REVERT: B  199 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7575 (mm)
REVERT: B  411 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7716 (tt)
  outliers start: 20
  outliers final: 9
  residues processed: 78
  average time/residue: 0.9097
  time to fit residues: 77.8928
Evaluate side-chains
  75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
B 135 HIS
B 140 GLN
B 479 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.115941 restraints weight = 17441.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.13
r_work: 0.3184 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082   8874  Z= 0.244
  Angle     :  0.631  10.109  12152  Z= 0.318
  Chirality :  0.044   0.178   1418
  Planarity :  0.004   0.054   1466
  Dihedral  :  9.335  59.706   1416
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.13 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1078
  helix:  1.84 (0.22), residues: 531
  sheet: -0.57 (0.47), residues: 123
  loop : -1.59 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 647 
 HIS   0.007   0.001   HIS B 614 
 PHE   0.016   0.002   PHE A 322 
 TYR   0.019   0.002   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00536 (    6)
  link_NAG-ASN         : angle       2.95696 (   18)
  link_BETA1-4         : bond        0.00850 (    1)
  link_BETA1-4         : angle       2.76340 (    3)
  hydrogen bonds       : bond        0.04026 (  499)
  hydrogen bonds       : angle       4.92451 ( 1446)
  SS BOND              : bond        0.00706 (    6)
  SS BOND              : angle       1.33343 (   12)
  covalent geometry    : bond        0.00593 ( 8861)
  covalent geometry    : angle       0.61893 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7854 (mmtt)
REVERT: A  180 ASP cc_start: 0.7450 (t0) cc_final: 0.6656 (p0)
REVERT: A  337 ARG cc_start: 0.7820 (tmt170) cc_final: 0.7454 (ttt-90)
REVERT: B  199 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7615 (mm)
REVERT: B  411 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7764 (tt)
  outliers start: 24
  outliers final: 11
  residues processed: 83
  average time/residue: 0.9263
  time to fit residues: 84.7328
Evaluate side-chains
  76 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 95 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119663 restraints weight = 14403.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.99
r_work: 0.3236 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8874  Z= 0.169
  Angle     :  0.570   9.704  12152  Z= 0.289
  Chirality :  0.042   0.159   1418
  Planarity :  0.004   0.052   1466
  Dihedral  :  8.960  59.212   1416
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.50 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1078
  helix:  1.96 (0.22), residues: 531
  sheet: -0.56 (0.47), residues: 123
  loop : -1.57 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.015   0.001   PHE B 601 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00532 (    6)
  link_NAG-ASN         : angle       2.81296 (   18)
  link_BETA1-4         : bond        0.00787 (    1)
  link_BETA1-4         : angle       2.48519 (    3)
  hydrogen bonds       : bond        0.03748 (  499)
  hydrogen bonds       : angle       4.73845 ( 1446)
  SS BOND              : bond        0.00558 (    6)
  SS BOND              : angle       1.10208 (   12)
  covalent geometry    : bond        0.00404 ( 8861)
  covalent geometry    : angle       0.55772 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 3.262 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7752 (mmtt)
REVERT: A  180 ASP cc_start: 0.7406 (t0) cc_final: 0.6620 (p0)
REVERT: A  337 ARG cc_start: 0.7706 (tmt170) cc_final: 0.7342 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8018 (mttp)
REVERT: A  477 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7787 (m-30)
REVERT: A  605 MET cc_start: 0.8599 (mmm) cc_final: 0.8286 (mpp)
REVERT: B  199 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7573 (mm)
REVERT: B  411 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7717 (tt)
  outliers start: 22
  outliers final: 13
  residues processed: 79
  average time/residue: 1.1789
  time to fit residues: 104.5341
Evaluate side-chains
  80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 614 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 = 0.3696 r_free = 0.3696 target = 0.147041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.118295 restraints weight = 19512.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.30
r_work: 0.3210 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8874  Z= 0.168
  Angle     :  0.567   9.606  12152  Z= 0.287
  Chirality :  0.042   0.162   1418
  Planarity :  0.004   0.049   1466
  Dihedral  :  8.637  59.243   1416
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.37 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.07 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 1078
  helix:  2.00 (0.22), residues: 531
  sheet: -0.55 (0.46), residues: 123
  loop : -1.55 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 601 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       2.77214 (   18)
  link_BETA1-4         : bond        0.00785 (    1)
  link_BETA1-4         : angle       2.24981 (    3)
  hydrogen bonds       : bond        0.03700 (  499)
  hydrogen bonds       : angle       4.67335 ( 1446)
  SS BOND              : bond        0.00550 (    6)
  SS BOND              : angle       1.12782 (   12)
  covalent geometry    : bond        0.00401 ( 8861)
  covalent geometry    : angle       0.55492 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7624 (mmtt)
REVERT: A  180 ASP cc_start: 0.7411 (t0) cc_final: 0.6525 (p0)
REVERT: A  337 ARG cc_start: 0.7659 (tmt170) cc_final: 0.7231 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8012 (mttp)
REVERT: A  477 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7692 (m-30)
REVERT: A  481 TYR cc_start: 0.8787 (t80) cc_final: 0.8552 (t80)
REVERT: A  605 MET cc_start: 0.8523 (mmm) cc_final: 0.8218 (mpp)
REVERT: B  199 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7374 (mm)
REVERT: B  411 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7585 (tt)
  outliers start: 22
  outliers final: 12
  residues processed: 79
  average time/residue: 0.9000
  time to fit residues: 78.1477
Evaluate side-chains
  80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 88 optimal weight:    0.1980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.144166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.115367 restraints weight = 14573.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.29
r_work: 0.3153 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8874  Z= 0.151
  Angle     :  0.552   9.537  12152  Z= 0.280
  Chirality :  0.041   0.158   1418
  Planarity :  0.004   0.046   1466
  Dihedral  :  8.317  55.541   1416
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.84 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1078
  helix:  2.07 (0.22), residues: 531
  sheet: -0.48 (0.47), residues: 121
  loop : -1.54 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00519 (    6)
  link_NAG-ASN         : angle       2.73252 (   18)
  link_BETA1-4         : bond        0.00777 (    1)
  link_BETA1-4         : angle       2.12395 (    3)
  hydrogen bonds       : bond        0.03604 (  499)
  hydrogen bonds       : angle       4.59940 ( 1446)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.01397 (   12)
  covalent geometry    : bond        0.00359 ( 8861)
  covalent geometry    : angle       0.54048 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (mmtt)
REVERT: A  180 ASP cc_start: 0.7399 (t0) cc_final: 0.6559 (p0)
REVERT: A  337 ARG cc_start: 0.7695 (tmt170) cc_final: 0.7283 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8014 (mttp)
REVERT: A  477 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7809 (m-30)
REVERT: A  481 TYR cc_start: 0.8823 (t80) cc_final: 0.8578 (t80)
REVERT: B  199 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (mm)
REVERT: B  411 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7633 (tt)
  outliers start: 25
  outliers final: 13
  residues processed: 84
  average time/residue: 0.7979
  time to fit residues: 74.2036
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0770
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 97 optimal weight:    0.3980
   chunk 67 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
A 614 HIS
B 297 HIS
B 461 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.146043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.115890 restraints weight = 18579.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.46
r_work: 0.3176 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8874  Z= 0.125
  Angle     :  0.535   9.190  12152  Z= 0.270
  Chirality :  0.040   0.151   1418
  Planarity :  0.003   0.046   1466
  Dihedral  :  7.867  55.639   1416
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.99 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1078
  helix:  2.16 (0.22), residues: 537
  sheet: -0.32 (0.47), residues: 115
  loop : -1.54 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 647 
 HIS   0.004   0.001   HIS B 614 
 PHE   0.018   0.001   PHE A 601 
 TYR   0.016   0.001   TYR B 570 
 ARG   0.002   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00519 (    6)
  link_NAG-ASN         : angle       2.61089 (   18)
  link_BETA1-4         : bond        0.00745 (    1)
  link_BETA1-4         : angle       2.00174 (    3)
  hydrogen bonds       : bond        0.03455 (  499)
  hydrogen bonds       : angle       4.46862 ( 1446)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       0.95140 (   12)
  covalent geometry    : bond        0.00291 ( 8861)
  covalent geometry    : angle       0.52436 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7697 (mmtt)
REVERT: A  180 ASP cc_start: 0.7431 (t0) cc_final: 0.6610 (p0)
REVERT: A  337 ARG cc_start: 0.7738 (tmt170) cc_final: 0.7339 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8050 (mttp)
REVERT: A  477 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7831 (m-30)
REVERT: B  199 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7500 (mm)
  outliers start: 17
  outliers final: 10
  residues processed: 81
  average time/residue: 0.8820
  time to fit residues: 78.6807
Evaluate side-chains
  79 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0020
   chunk 44 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0370
   chunk 102 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.8072

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.142700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.112773 restraints weight = 18577.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.18
r_work: 0.3128 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   8874  Z= 0.195
  Angle     :  0.596   9.514  12152  Z= 0.300
  Chirality :  0.043   0.170   1418
  Planarity :  0.004   0.049   1466
  Dihedral  :  8.138  54.639   1416
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.99 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1078
  helix:  2.00 (0.22), residues: 531
  sheet: -0.40 (0.47), residues: 121
  loop : -1.56 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.018   0.002   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00505 (    6)
  link_NAG-ASN         : angle       2.74435 (   18)
  link_BETA1-4         : bond        0.00687 (    1)
  link_BETA1-4         : angle       1.76507 (    3)
  hydrogen bonds       : bond        0.03763 (  499)
  hydrogen bonds       : angle       4.65817 ( 1446)
  SS BOND              : bond        0.00588 (    6)
  SS BOND              : angle       1.26785 (   12)
  covalent geometry    : bond        0.00471 ( 8861)
  covalent geometry    : angle       0.58502 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7673 (mmtt)
REVERT: A  180 ASP cc_start: 0.7426 (t0) cc_final: 0.6583 (p0)
REVERT: A  337 ARG cc_start: 0.7734 (tmt170) cc_final: 0.7431 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8028 (mttp)
REVERT: A  477 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7767 (m-30)
REVERT: B  199 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7509 (mm)
  outliers start: 20
  outliers final: 11
  residues processed: 79
  average time/residue: 0.9760
  time to fit residues: 84.9045
Evaluate side-chains
  79 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.143185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.112649 restraints weight = 21003.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.25
r_work: 0.3128 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8874  Z= 0.180
  Angle     :  0.581   9.547  12152  Z= 0.294
  Chirality :  0.042   0.164   1418
  Planarity :  0.004   0.048   1466
  Dihedral  :  8.155  54.611   1416
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.37 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.10 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1078
  helix:  2.06 (0.22), residues: 525
  sheet: -0.40 (0.47), residues: 121
  loop : -1.52 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE B 601 
 TYR   0.018   0.002   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00503 (    6)
  link_NAG-ASN         : angle       2.76206 (   18)
  link_BETA1-4         : bond        0.00674 (    1)
  link_BETA1-4         : angle       1.72028 (    3)
  hydrogen bonds       : bond        0.03716 (  499)
  hydrogen bonds       : angle       4.64529 ( 1446)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.09904 (   12)
  covalent geometry    : bond        0.00434 ( 8861)
  covalent geometry    : angle       0.56996 (12119)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (mmtt)
REVERT: A  180 ASP cc_start: 0.7458 (t0) cc_final: 0.6605 (p0)
REVERT: A  337 ARG cc_start: 0.7725 (tmt170) cc_final: 0.7419 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8032 (mttp)
REVERT: A  477 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7778 (m-30)
REVERT: B  199 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7475 (mm)
  outliers start: 17
  outliers final: 11
  residues processed: 74
  average time/residue: 0.9192
  time to fit residues: 74.6053
Evaluate side-chains
  78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  370 LYS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 93 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0670
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
B 461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.115582 restraints weight = 16467.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.11
r_work: 0.3153 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8874  Z= 0.147
  Angle     :  0.559   9.359  12152  Z= 0.283
  Chirality :  0.041   0.157   1418
  Planarity :  0.004   0.047   1466
  Dihedral  :  7.952  54.772   1416
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.33 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.26), residues: 1078
  helix:  2.18 (0.22), residues: 525
  sheet: -0.36 (0.47), residues: 121
  loop : -1.56 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 647 
 HIS   0.004   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 601 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00506 (    6)
  link_NAG-ASN         : angle       2.67805 (   18)
  link_BETA1-4         : bond        0.00656 (    1)
  link_BETA1-4         : angle       1.68376 (    3)
  hydrogen bonds       : bond        0.03627 (  499)
  hydrogen bonds       : angle       4.56390 ( 1446)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       1.01738 (   12)
  covalent geometry    : bond        0.00348 ( 8861)
  covalent geometry    : angle       0.54874 (12119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6367.27 seconds
wall clock time: 110 minutes 59.97 seconds (6659.97 seconds total)