Starting phenix.real_space_refine
on Mon May 12 02:37:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vkj_43319/05_2025/8vkj_43319.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vkj_43319/05_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_43319/05_2025/8vkj_43319.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vkj_43319/05_2025/8vkj_43319.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vkj_43319/05_2025/8vkj_43319.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vkj_43319/05_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-5687/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: 8.88, per 1000 atoms: 1.03
  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.6 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: 0.92
  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: 2.55

  Time building geometry restraints manager: 2.68 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:             7.060
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.840
  Find NCS groups from input model:        0.390
  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:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.630
-------------------------------------------------------------------------------
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  : 0.879 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 62
  average time/residue: 1.2054
  time to fit residues: 80.5591
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  : 0.884 
-------------------------------------------------------------------------------
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 = 48)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113187 restraints weight = 20081.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.30
r_work: 0.3139 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
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 = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
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  : 0.900 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7629 (mmtt)
REVERT: A  180 ASP cc_start: 0.7433 (t0) cc_final: 0.6641 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 0.9753
  time to fit residues: 84.8642
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  : 0.855 
-------------------------------------------------------------------------------
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:    0.9990
   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:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.143636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113159 restraints weight = 18511.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.13
r_work: 0.3148 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.0841

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= 0.170
  Angle     :  0.570   9.734  12152  Z= 0.290
  Chirality :  0.042   0.160   1418
  Planarity :  0.004   0.036   1466
  Dihedral  :  9.304  67.013   1416
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 11.67 %
    Favored  : 85.81 %
  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:  0.60 (0.26), residues: 1078
  helix:  2.03 (0.22), residues: 531
  sheet: -0.39 (0.48), residues: 122
  loop : -1.54 (0.28), residues: 425

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 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00513 (    6)
  link_NAG-ASN         : angle       2.80706 (   18)
  link_BETA1-4         : bond        0.00854 (    1)
  link_BETA1-4         : angle       3.19570 (    3)
  hydrogen bonds       : bond        0.03856 (  499)
  hydrogen bonds       : angle       4.78261 ( 1446)
  SS BOND              : bond        0.00513 (    6)
  SS BOND              : angle       1.03359 (   12)
  covalent geometry    : bond        0.00405 ( 8861)
  covalent geometry    : angle       0.55737 (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
  91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7640 (mmtt)
REVERT: A  135 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7806 (p90)
REVERT: A  337 ARG cc_start: 0.7794 (tmt170) cc_final: 0.7476 (ttt-90)
REVERT: B  151 CYS cc_start: 0.7628 (p) cc_final: 0.7423 (p)
REVERT: B  199 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7572 (mm)
REVERT: B  411 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7715 (tt)
  outliers start: 22
  outliers final: 9
  residues processed: 82
  average time/residue: 0.8998
  time to fit residues: 80.7130
Evaluate side-chains
  78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
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:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 140 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.116865 restraints weight = 17416.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.19
r_work: 0.3199 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   8874  Z= 0.215
  Angle     :  0.608  10.024  12152  Z= 0.307
  Chirality :  0.043   0.172   1418
  Planarity :  0.004   0.039   1466
  Dihedral  :  9.237  59.882   1416
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.36 %
    Favored  : 85.01 %
  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:  0.47 (0.26), residues: 1078
  helix:  1.92 (0.22), residues: 531
  sheet: -0.53 (0.47), residues: 123
  loop : -1.58 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.006   0.001   HIS B 614 
 PHE   0.015   0.002   PHE A 601 
 TYR   0.018   0.002   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    6)
  link_NAG-ASN         : angle       2.91575 (   18)
  link_BETA1-4         : bond        0.00830 (    1)
  link_BETA1-4         : angle       2.74881 (    3)
  hydrogen bonds       : bond        0.03915 (  499)
  hydrogen bonds       : angle       4.84276 ( 1446)
  SS BOND              : bond        0.00619 (    6)
  SS BOND              : angle       1.17686 (   12)
  covalent geometry    : bond        0.00520 ( 8861)
  covalent geometry    : angle       0.59564 (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
  88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7778 (mmtt)
REVERT: A  135 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7831 (p90)
REVERT: A  180 ASP cc_start: 0.7418 (t0) cc_final: 0.6612 (p0)
REVERT: A  337 ARG cc_start: 0.7792 (tmt170) cc_final: 0.7395 (ttt-90)
REVERT: B  151 CYS cc_start: 0.7683 (p) cc_final: 0.7479 (p)
REVERT: B  199 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7588 (mm)
REVERT: B  411 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7764 (tt)
  outliers start: 23
  outliers final: 11
  residues processed: 80
  average time/residue: 0.8881
  time to fit residues: 77.9498
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  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LYS
Chi-restraints excluded: chain A residue  135 HIS
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:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0010
   chunk 7 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0670
   chunk 102 optimal weight:    0.4980
   overall best weight:    0.3724

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.145585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116728 restraints weight = 14747.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.16
r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8874  Z= 0.127
  Angle     :  0.536   9.312  12152  Z= 0.272
  Chirality :  0.041   0.152   1418
  Planarity :  0.003   0.031   1466
  Dihedral  :  8.677  59.146   1416
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.81 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.04 %
    Favored  : 84.44 %
  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:  0.70 (0.26), residues: 1078
  helix:  2.09 (0.22), residues: 537
  sheet: -0.45 (0.47), residues: 122
  loop : -1.49 (0.28), residues: 419

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   0.015   0.001   PHE A 601 
 TYR   0.016   0.001   TYR B 570 
 ARG   0.006   0.000   ARG A 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00535 (    6)
  link_NAG-ASN         : angle       2.66021 (   18)
  link_BETA1-4         : bond        0.00732 (    1)
  link_BETA1-4         : angle       2.46179 (    3)
  hydrogen bonds       : bond        0.03530 (  499)
  hydrogen bonds       : angle       4.56336 ( 1446)
  SS BOND              : bond        0.00366 (    6)
  SS BOND              : angle       0.74637 (   12)
  covalent geometry    : bond        0.00293 ( 8861)
  covalent geometry    : angle       0.52456 (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
  91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  135 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7891 (p90)
REVERT: A  180 ASP cc_start: 0.7306 (t0) cc_final: 0.6518 (p0)
REVERT: A  337 ARG cc_start: 0.7666 (tmt170) cc_final: 0.7293 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7967 (mttp)
REVERT: A  477 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: B  151 CYS cc_start: 0.7576 (p) cc_final: 0.7365 (p)
REVERT: B  199 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7517 (mm)
REVERT: B  411 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7600 (tt)
  outliers start: 22
  outliers final: 12
  residues processed: 84
  average time/residue: 0.9055
  time to fit residues: 83.4825
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 HIS
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:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 97 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.143450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.113101 restraints weight = 19466.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.22
r_work: 0.3138 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8874  Z= 0.174
  Angle     :  0.568   9.484  12152  Z= 0.287
  Chirality :  0.042   0.165   1418
  Planarity :  0.003   0.037   1466
  Dihedral  :  8.516  58.139   1416
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.19 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 13.84 %
    Favored  : 83.64 %
  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:  0.64 (0.26), residues: 1078
  helix:  2.05 (0.22), residues: 537
  sheet: -0.45 (0.47), residues: 122
  loop : -1.53 (0.28), residues: 419

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   0.019   0.001   PHE A 601 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00514 (    6)
  link_NAG-ASN         : angle       2.72025 (   18)
  link_BETA1-4         : bond        0.00738 (    1)
  link_BETA1-4         : angle       2.21214 (    3)
  hydrogen bonds       : bond        0.03664 (  499)
  hydrogen bonds       : angle       4.63836 ( 1446)
  SS BOND              : bond        0.00535 (    6)
  SS BOND              : angle       1.04665 (   12)
  covalent geometry    : bond        0.00418 ( 8861)
  covalent geometry    : angle       0.55697 (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
  88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  135 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7965 (p90)
REVERT: A  180 ASP cc_start: 0.7410 (t0) cc_final: 0.6576 (p0)
REVERT: A  337 ARG cc_start: 0.7721 (tmt170) cc_final: 0.7298 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (mttp)
REVERT: A  477 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7767 (m-30)
REVERT: A  481 TYR cc_start: 0.8807 (t80) cc_final: 0.8596 (t80)
REVERT: B  151 CYS cc_start: 0.7686 (p) cc_final: 0.7477 (p)
REVERT: B  199 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7506 (mm)
REVERT: B  411 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7645 (tt)
  outliers start: 22
  outliers final: 11
  residues processed: 80
  average time/residue: 0.8830
  time to fit residues: 77.5314
Evaluate side-chains
  80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  135 HIS
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  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:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 39 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 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 = 0.3643 r_free = 0.3643 target = 0.144067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115756 restraints weight = 14031.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.13
r_work: 0.3163 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1099

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= 0.163
  Angle     :  0.560   9.496  12152  Z= 0.283
  Chirality :  0.041   0.162   1418
  Planarity :  0.003   0.032   1466
  Dihedral  :  8.347  55.441   1416
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.63 %
  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:  0.64 (0.26), residues: 1078
  helix:  2.08 (0.22), residues: 531
  sheet: -0.48 (0.47), residues: 123
  loop : -1.52 (0.28), residues: 424

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 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00516 (    6)
  link_NAG-ASN         : angle       2.72722 (   18)
  link_BETA1-4         : bond        0.00743 (    1)
  link_BETA1-4         : angle       2.10419 (    3)
  hydrogen bonds       : bond        0.03630 (  499)
  hydrogen bonds       : angle       4.60317 ( 1446)
  SS BOND              : bond        0.00481 (    6)
  SS BOND              : angle       0.93967 (   12)
  covalent geometry    : bond        0.00392 ( 8861)
  covalent geometry    : angle       0.54859 (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
  88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  135 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7920 (p90)
REVERT: A  180 ASP cc_start: 0.7386 (t0) cc_final: 0.6535 (p0)
REVERT: A  337 ARG cc_start: 0.7630 (tmt170) cc_final: 0.7213 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7988 (mttp)
REVERT: A  477 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7717 (m-30)
REVERT: A  481 TYR cc_start: 0.8781 (t80) cc_final: 0.8548 (t80)
REVERT: B  151 CYS cc_start: 0.7587 (p) cc_final: 0.7376 (p)
REVERT: B  199 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7501 (mm)
REVERT: B  411 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7605 (tt)
  outliers start: 22
  outliers final: 14
  residues processed: 81
  average time/residue: 0.8457
  time to fit residues: 75.7709
Evaluate side-chains
  83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  135 HIS
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  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:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.113531 restraints weight = 18642.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.35
r_work: 0.3133 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8874  Z= 0.177
  Angle     :  0.573   9.546  12152  Z= 0.290
  Chirality :  0.042   0.164   1418
  Planarity :  0.003   0.037   1466
  Dihedral  :  8.284  55.292   1416
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.28 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.42 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.26), residues: 1078
  helix:  2.01 (0.22), residues: 537
  sheet: -0.51 (0.47), residues: 123
  loop : -1.53 (0.28), residues: 418

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   0.017   0.001   PHE A 601 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.006   0.000   ARG A 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00515 (    6)
  link_NAG-ASN         : angle       2.75168 (   18)
  link_BETA1-4         : bond        0.00720 (    1)
  link_BETA1-4         : angle       1.98036 (    3)
  hydrogen bonds       : bond        0.03724 (  499)
  hydrogen bonds       : angle       4.63083 ( 1446)
  SS BOND              : bond        0.00532 (    6)
  SS BOND              : angle       1.05199 (   12)
  covalent geometry    : bond        0.00425 ( 8861)
  covalent geometry    : angle       0.56166 (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: 21
    poor density    : 64
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7660 (mmtt)
REVERT: A  135 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7942 (p90)
REVERT: A  180 ASP cc_start: 0.7403 (t0) cc_final: 0.6571 (p0)
REVERT: A  337 ARG cc_start: 0.7682 (tmt170) cc_final: 0.7244 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8024 (mttp)
REVERT: A  477 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7828 (m-30)
REVERT: A  481 TYR cc_start: 0.8825 (t80) cc_final: 0.8569 (t80)
REVERT: B  199 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7450 (mm)
REVERT: B  411 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7621 (tt)
  outliers start: 21
  outliers final: 14
  residues processed: 78
  average time/residue: 0.9130
  time to fit residues: 78.1529
Evaluate side-chains
  83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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  135 HIS
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  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:    0.9980
   chunk 29 optimal weight:    0.0570
   chunk 89 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0270
   chunk 44 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.4556

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.145269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.114821 restraints weight = 18496.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.52
r_work: 0.3144 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8874  Z= 0.140
  Angle     :  0.551   9.329  12152  Z= 0.278
  Chirality :  0.041   0.155   1418
  Planarity :  0.004   0.053   1466
  Dihedral  :  7.969  55.355   1416
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.63 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.65 %
    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:  0.71 (0.26), residues: 1078
  helix:  2.10 (0.22), residues: 537
  sheet: -0.42 (0.47), residues: 121
  loop : -1.50 (0.28), residues: 420

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   0.015   0.001   PHE B 601 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.002   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (    6)
  link_NAG-ASN         : angle       2.66287 (   18)
  link_BETA1-4         : bond        0.00746 (    1)
  link_BETA1-4         : angle       1.91254 (    3)
  hydrogen bonds       : bond        0.03552 (  499)
  hydrogen bonds       : angle       4.51936 ( 1446)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       1.04335 (   12)
  covalent geometry    : bond        0.00332 ( 8861)
  covalent geometry    : angle       0.53988 (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
  87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7628 (mmtt)
REVERT: A  135 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7980 (p90)
REVERT: A  180 ASP cc_start: 0.7430 (t0) cc_final: 0.6571 (p0)
REVERT: A  337 ARG cc_start: 0.7687 (tmt170) cc_final: 0.7264 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8018 (mttp)
REVERT: A  477 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7797 (m-30)
REVERT: B  199 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7405 (mm)
REVERT: B  411 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7592 (tt)
  outliers start: 21
  outliers final: 13
  residues processed: 82
  average time/residue: 1.0199
  time to fit residues: 91.0223
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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  135 HIS
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  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:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 99 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0570
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6300

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.144197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113499 restraints weight = 21434.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.36
r_work: 0.3137 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
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 = 0.29   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 = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8874  Z= 0.166
  Angle     :  0.568   9.377  12152  Z= 0.289
  Chirality :  0.041   0.162   1418
  Planarity :  0.004   0.054   1466
  Dihedral  :  7.974  54.897   1416
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.19 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.76 %
    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:  0.67 (0.26), residues: 1078
  helix:  2.05 (0.22), residues: 537
  sheet: -0.36 (0.47), residues: 121
  loop : -1.51 (0.28), residues: 420

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   0.018   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        0.00503 (    6)
  link_NAG-ASN         : angle       2.68847 (   18)
  link_BETA1-4         : bond        0.00676 (    1)
  link_BETA1-4         : angle       1.75584 (    3)
  hydrogen bonds       : bond        0.03676 (  499)
  hydrogen bonds       : angle       4.57724 ( 1446)
  SS BOND              : bond        0.00491 (    6)
  SS BOND              : angle       1.13661 (   12)
  covalent geometry    : bond        0.00396 ( 8861)
  covalent geometry    : angle       0.55771 (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
  84 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7676 (mmtt)
REVERT: A  135 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7992 (p90)
REVERT: A  180 ASP cc_start: 0.7395 (t0) cc_final: 0.6597 (p0)
REVERT: A  337 ARG cc_start: 0.7719 (tmt170) cc_final: 0.7294 (ttt-90)
REVERT: A  370 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8042 (mttp)
REVERT: A  477 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7798 (m-30)
REVERT: A  527 ARG cc_start: 0.5911 (ptt-90) cc_final: 0.5584 (pmt170)
REVERT: A  605 MET cc_start: 0.8544 (mtp) cc_final: 0.8305 (mpp)
REVERT: B  199 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7480 (mm)
REVERT: B  411 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7629 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 78
  average time/residue: 0.9305
  time to fit residues: 79.3991
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  135 HIS
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  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:    0.2980
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 93 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.144109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.113824 restraints weight = 17334.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.20
r_work: 0.3153 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    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 = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1187

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= 0.157
  Angle     :  0.562   9.342  12152  Z= 0.286
  Chirality :  0.041   0.161   1418
  Planarity :  0.004   0.054   1466
  Dihedral  :  7.947  54.717   1416
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.19 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.76 %
    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:  0.65 (0.26), residues: 1078
  helix:  2.10 (0.22), residues: 531
  sheet: -0.32 (0.47), residues: 121
  loop : -1.58 (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   0.017   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        0.00501 (    6)
  link_NAG-ASN         : angle       2.67494 (   18)
  link_BETA1-4         : bond        0.00644 (    1)
  link_BETA1-4         : angle       1.67339 (    3)
  hydrogen bonds       : bond        0.03650 (  499)
  hydrogen bonds       : angle       4.56139 ( 1446)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       1.10178 (   12)
  covalent geometry    : bond        0.00376 ( 8861)
  covalent geometry    : angle       0.55196 (12119)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5828.49 seconds
wall clock time: 101 minutes 33.44 seconds (6093.44 seconds total)