Starting phenix.real_space_refine
on Thu Jun  5 06:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnt_50610/06_2025/9fnt_50610.cif"
  }
  resolution = 3.5
  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=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3489      2.51       5
     N     927      2.21       5
     O    1099      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5535
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1095
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 138}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1095
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 138}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 914
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 759
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 918
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "F"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 726
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.33, per 1000 atoms: 0.78
  Number of scatterers: 5535
  At special positions: 0
  Unit cell: (92.02, 122.12, 79.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1099      8.00
     N     927      7.00
     C    3489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 102 " - pdb=" SG  CYS C 107 " distance=2.13
    Simple disulfide: pdb=" SG  CYS D 140 " - pdb=" SG  CYS D 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 102 " - pdb=" SG  CYS E 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 140 " - pdb=" SG  CYS F 205 " 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
    NAG-ASN
      " NAG A1000 " - " ASN A 562 "
      " NAG B1000 " - " ASN B 562 "
  Time building additional restraints: 1.24
  Conformation dependent library (CDL) restraints added in 653.8 milliseconds
  

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1338

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 19 sheets defined
      1.2% alpha, 44.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'D' and resid 196 through 200
      removed outlier: 4.271A  pdb=" N   PHE D 200 " --> pdb=" O   PRO D 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 64
      removed outlier: 3.600A  pdb=" N   LYS E  64 " --> pdb=" O   GLY E  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 61 through 64'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465
    Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 495
      removed outlier: 3.550A  pdb=" N   THR A 499 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 495
      removed outlier: 4.083A  pdb=" N   ALA A 477 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   THR A 593 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   SER A 594 " --> pdb=" O   TRP A 548 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   TRP A 548 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   SER A 596 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   SER A 546 " --> pdb=" O   SER A 596 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   VAL A 598 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS A 544 " --> pdb=" O   VAL A 598 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   VAL A 600 " --> pdb=" O   ARG A 542 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   PHE A 547 " --> pdb=" O   GLY A 556 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529
      removed outlier: 3.536A  pdb=" N   ILE A 571 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 464 through 465
    Processing sheet with id=AA6, first strand: chain 'B' and resid 492 through 495
      removed outlier: 3.755A  pdb=" N   THR B 499 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 495
      removed outlier: 3.892A  pdb=" N   ALA B 477 " --> pdb=" O   THR B 593 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   THR B 593 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   TRP B 548 " --> pdb=" O   SER B 596 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL B 598 " --> pdb=" O   SER B 546 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER B 546 " --> pdb=" O   VAL B 598 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   VAL B 600 " --> pdb=" O   LYS B 544 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LYS B 544 " --> pdb=" O   VAL B 600 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   PHE B 547 " --> pdb=" O   GLY B 556 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 528 through 529
      removed outlier: 3.610A  pdb=" N   ILE B 571 " --> pdb=" O   TYR B 537 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 570 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7
      removed outlier: 3.793A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.960A  pdb=" N   VAL C  33 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12
      removed outlier: 7.055A  pdb=" N   CYS C  95 " --> pdb=" O   TRP C 114 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   TRP C 114 " --> pdb=" O   CYS C  95 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   ASN C  97 " --> pdb=" O   ASP C 112 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASP C 112 " --> pdb=" O   ASN C  97 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY C 110 " --> pdb=" O   VAL C  99 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 130
      removed outlier: 3.624A  pdb=" N   ALA D 130 " --> pdb=" O   GLU D 223 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   TRP D 152 " --> pdb=" O   LEU D 164 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 136 through 141
      removed outlier: 3.527A  pdb=" N   THR D 187 " --> pdb=" O   SER D 184 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.665A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.280A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL E  33 " --> pdb=" O   VAL E  98 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASN E  97 " --> pdb=" O   ASN E 113 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ASN E 113 " --> pdb=" O   ASN E  97 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.280A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER E  49 " --> pdb=" O   TRP E  36 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL E  33 " --> pdb=" O   VAL E  98 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102
    Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 129
      removed outlier: 3.555A  pdb=" N   TYR F 203 " --> pdb=" O   THR F 220 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   TRP F 152 " --> pdb=" O   LEU F 164 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 136 through 141

    194 hydrogen bonds defined for protein.
    495 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.49 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: 930
        1.32 -     1.45: 1656
        1.45 -     1.57: 3047
        1.57 -     1.69: 0
        1.69 -     1.82: 28
  Bond restraints: 5661
  Sorted by residual:
  bond pdb=" CA  SER F 208 "
       pdb=" CB  SER F 208 "
    ideal  model  delta    sigma   weight residual
    1.528  1.450  0.077 1.35e-02 5.49e+03 3.26e+01
  bond pdb=" CA  SER D 208 "
       pdb=" CB  SER D 208 "
    ideal  model  delta    sigma   weight residual
    1.528  1.453  0.075 1.34e-02 5.57e+03 3.15e+01
  bond pdb=" CA  SER C  50 "
       pdb=" CB  SER C  50 "
    ideal  model  delta    sigma   weight residual
    1.533  1.456  0.077 1.66e-02 3.63e+03 2.16e+01
  bond pdb=" CA  SER D 169 "
       pdb=" CB  SER D 169 "
    ideal  model  delta    sigma   weight residual
    1.536  1.484  0.053 1.46e-02 4.69e+03 1.30e+01
  bond pdb=" C   SER B 487 "
       pdb=" O   SER B 487 "
    ideal  model  delta    sigma   weight residual
    1.234  1.196  0.038 1.07e-02 8.73e+03 1.24e+01
  ... (remaining 5656 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 7242
        3.01 -     6.02: 410
        6.02 -     9.03: 67
        9.03 -    12.04: 12
       12.04 -    15.05: 1
  Bond angle restraints: 7732
  Sorted by residual:
  angle pdb=" CA  PHE B 547 "
        pdb=" CB  PHE B 547 "
        pdb=" CG  PHE B 547 "
      ideal   model   delta    sigma   weight residual
     113.80  122.40   -8.60 1.00e+00 1.00e+00 7.39e+01
  angle pdb=" CA  PHE A 547 "
        pdb=" CB  PHE A 547 "
        pdb=" CG  PHE A 547 "
      ideal   model   delta    sigma   weight residual
     113.80  121.77   -7.97 1.00e+00 1.00e+00 6.35e+01
  angle pdb=" N   SER A 587 "
        pdb=" CA  SER A 587 "
        pdb=" C   SER A 587 "
      ideal   model   delta    sigma   weight residual
     113.55  103.64    9.91 1.26e+00 6.30e-01 6.18e+01
  angle pdb=" CA  PHE F 216 "
        pdb=" CB  PHE F 216 "
        pdb=" CG  PHE F 216 "
      ideal   model   delta    sigma   weight residual
     113.80  121.57   -7.77 1.00e+00 1.00e+00 6.04e+01
  angle pdb=" C   SER A 487 "
        pdb=" CA  SER A 487 "
        pdb=" CB  SER A 487 "
      ideal   model   delta    sigma   weight residual
     111.22   96.17   15.05 2.02e+00 2.45e-01 5.55e+01
  ... (remaining 7727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3004
       17.95 -    35.89: 221
       35.89 -    53.84: 54
       53.84 -    71.78: 10
       71.78 -    89.73: 3
  Dihedral angle restraints: 3292
    sinusoidal: 1185
      harmonic: 2107
  Sorted by residual:
  dihedral pdb=" C   SER A 487 "
           pdb=" N   SER A 487 "
           pdb=" CA  SER A 487 "
           pdb=" CB  SER A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.33  -20.27     0      2.50e+00 1.60e-01 6.57e+01
  dihedral pdb=" C   THR A 489 "
           pdb=" N   THR A 489 "
           pdb=" CA  THR A 489 "
           pdb=" CB  THR A 489 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -136.48   14.48     0      2.50e+00 1.60e-01 3.36e+01
  dihedral pdb=" C   THR B 489 "
           pdb=" N   THR B 489 "
           pdb=" CA  THR B 489 "
           pdb=" CB  THR B 489 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.63   12.63     0      2.50e+00 1.60e-01 2.55e+01
  ... (remaining 3289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 781
       0.107 -    0.214: 85
       0.214 -    0.321: 38
       0.321 -    0.428: 3
       0.428 -    0.535: 4
  Chirality restraints: 911
  Sorted by residual:
  chirality pdb=" CA  SER E  55 "
            pdb=" N   SER E  55 "
            pdb=" C   SER E  55 "
            pdb=" CB  SER E  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.54 2.00e-01 2.50e+01 7.16e+00
  chirality pdb=" CA  THR A 489 "
            pdb=" N   THR A 489 "
            pdb=" C   THR A 489 "
            pdb=" CB  THR A 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.01    0.52 2.00e-01 2.50e+01 6.64e+00
  chirality pdb=" CA  THR B 489 "
            pdb=" N   THR B 489 "
            pdb=" C   THR B 489 "
            pdb=" CB  THR B 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.04    0.49 2.00e-01 2.50e+01 5.97e+00
  ... (remaining 908 not shown)

  Planarity restraints: 970
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 546 "    0.021 2.00e-02 2.50e+03   4.15e-02 1.72e+01
        pdb=" C   SER B 546 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   SER B 546 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PHE B 547 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C 100 "   -0.020 2.00e-02 2.50e+03   3.92e-02 1.53e+01
        pdb=" C   HIS C 100 "    0.068 2.00e-02 2.50e+03
        pdb=" O   HIS C 100 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ARG C 101 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 109 "   -0.338 9.50e-02 1.11e+02   1.52e-01 1.41e+01
        pdb=" NE  ARG C 109 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 109 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 109 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 109 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 967 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 19
        2.43 -     3.04: 3236
        3.04 -     3.66: 7200
        3.66 -     4.28: 10642
        4.28 -     4.90: 19547
  Nonbonded interactions: 40644
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 550 "
            pdb=" OG  SER B 551 "
     model   vdw
     1.806 3.040
  nonbonded pdb=" CD2 LEU F 150 "
            pdb=" CD1 PHE F 188 "
     model   vdw
     1.980 3.760
  nonbonded pdb=" O   GLN A 482 "
            pdb=" O   GLY A 486 "
     model   vdw
     1.998 3.040
  nonbonded pdb=" N   GLU E   6 "
            pdb=" OE1 GLU E   6 "
     model   vdw
     2.075 3.120
  nonbonded pdb=" O   ASN B 573 "
            pdb=" ND2 ASN B 573 "
     model   vdw
     2.076 3.120
  ... (remaining 40639 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'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 14 through 124))
  selection = (chain 'E' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 44 through 45 or (resid 46 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 47 through 124))
}
ncs_group {
  reference = (chain 'D' and (resid 126 through 134 or (resid 135 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 136 through 158 or (resid 159 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 160 through 177 or (resid  \ 
178 and (name N or name CA or name C or name O or name CB )) or resid 179 throug \ 
h 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 197 or (resid 198 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 199 through 220 or (resid 221 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 222 through 224))
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.260
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.950
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
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      :  0.008   0.095   5669  Z= 0.550
  Angle     :  1.491  17.902   7750  Z= 1.000
  Chirality :  0.088   0.535    911
  Planarity :  0.009   0.152    968
  Dihedral  : 13.311  89.725   1936
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.35 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  :  3.53 %
    Favored  : 92.77 %
  Cbeta Deviations :  1.35 %
  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: -0.87 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.59 (0.30), residues: 316
  loop : -1.63 (0.27), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 114 
 HIS   0.006   0.001   HIS B 577 
 PHE   0.033   0.002   PHE A 547 
 TYR   0.030   0.002   TYR F 166 
 ARG   0.007   0.001   ARG D 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01700 (    2)
  link_NAG-ASN         : angle       3.26596 (    6)
  hydrogen bonds       : bond        0.27944 (  169)
  hydrogen bonds       : angle       8.61871 (  495)
  SS BOND              : bond        0.03892 (    6)
  SS BOND              : angle       6.04962 (   12)
  covalent geometry    : bond        0.00782 ( 5661)
  covalent geometry    : angle       1.47030 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  150 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (tm)
REVERT: E  113 ASN cc_start: 0.8308 (m-40) cc_final: 0.8039 (m110)
REVERT: F  148 THR cc_start: 0.9156 (p) cc_final: 0.8672 (t)
REVERT: F  207 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8484 (pp30)
REVERT: F  218 GLN cc_start: 0.5626 (OUTLIER) cc_final: 0.4929 (pp30)
  outliers start: 22
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1450
  time to fit residues: 18.8558
Evaluate side-chains
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  547 PHE
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  166 TYR
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  218 GLN
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  207 GLN
Chi-restraints excluded: chain F residue  212 LEU
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0470
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0020
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.4888

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

Flipped N/Q/H residues before XYZ refinement:
A 530 GLN
A 573 ASN
B 530 GLN
B 573 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.117929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.093547 restraints weight = 7838.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.096996 restraints weight = 3982.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099358 restraints weight = 2597.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   5669  Z= 0.116
  Angle     :  0.543   5.213   7750  Z= 0.296
  Chirality :  0.043   0.144    911
  Planarity :  0.004   0.049    968
  Dihedral  :  6.372  54.221    867
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.89 %
    Favored  : 91.26 %
  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: -0.27 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.92 (0.30), residues: 324
  loop : -1.18 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 472 
 HIS   0.003   0.001   HIS B 603 
 PHE   0.015   0.002   PHE B 547 
 TYR   0.021   0.001   TYR D 166 
 ARG   0.006   0.000   ARG D 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00094 (    2)
  link_NAG-ASN         : angle       1.09056 (    6)
  hydrogen bonds       : bond        0.04042 (  169)
  hydrogen bonds       : angle       5.63925 (  495)
  SS BOND              : bond        0.00481 (    6)
  SS BOND              : angle       1.55082 (   12)
  covalent geometry    : bond        0.00238 ( 5661)
  covalent geometry    : angle       0.53964 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.598 
Fit side-chains
REVERT: D  134 ASP cc_start: 0.8880 (m-30) cc_final: 0.8501 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1663
  time to fit residues: 17.1433
Evaluate side-chains
  67 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 65 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0000
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.5382

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

Flipped N/Q/H residues before XYZ refinement:
B 530 GLN
B 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.118362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.094026 restraints weight = 7894.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.097441 restraints weight = 4031.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.099797 restraints weight = 2635.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.097   5669  Z= 0.104
  Angle     :  0.516  10.283   7750  Z= 0.277
  Chirality :  0.041   0.140    911
  Planarity :  0.003   0.047    968
  Dihedral  :  5.050  57.318    844
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  8.40 %
    Favored  : 90.25 %
  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: -0.08 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.07 (0.30), residues: 324
  loop : -1.07 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 472 
 HIS   0.002   0.001   HIS A 603 
 PHE   0.014   0.001   PHE A 547 
 TYR   0.012   0.001   TYR D 166 
 ARG   0.005   0.000   ARG D 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00028 (    2)
  link_NAG-ASN         : angle       1.00707 (    6)
  hydrogen bonds       : bond        0.03316 (  169)
  hydrogen bonds       : angle       5.17424 (  495)
  SS BOND              : bond        0.00925 (    6)
  SS BOND              : angle       3.08726 (   12)
  covalent geometry    : bond        0.00247 ( 5661)
  covalent geometry    : angle       0.50098 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.664 
Fit side-chains
REVERT: D  134 ASP cc_start: 0.8859 (m-30) cc_final: 0.8496 (m-30)
REVERT: D  213 MET cc_start: 0.8400 (mmm) cc_final: 0.8185 (tpp)
  outliers start: 8
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1538
  time to fit residues: 13.5867
Evaluate side-chains
  67 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0870
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 530 GLN
B 573 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.116076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.091888 restraints weight = 8060.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.095178 restraints weight = 4218.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.097445 restraints weight = 2799.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   5669  Z= 0.117
  Angle     :  0.520  10.145   7750  Z= 0.278
  Chirality :  0.041   0.162    911
  Planarity :  0.003   0.044    968
  Dihedral  :  4.894  58.559    842
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  8.57 %
    Favored  : 89.08 %
  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: -0.09 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.07 (0.30), residues: 326
  loop : -1.09 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 472 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.015   0.001   PHE A 547 
 TYR   0.013   0.001   TYR D 166 
 ARG   0.003   0.000   ARG D 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       0.90266 (    6)
  hydrogen bonds       : bond        0.03256 (  169)
  hydrogen bonds       : angle       4.88869 (  495)
  SS BOND              : bond        0.00914 (    6)
  SS BOND              : angle       3.08578 (   12)
  covalent geometry    : bond        0.00284 ( 5661)
  covalent geometry    : angle       0.50571 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  481 ASP cc_start: 0.8916 (t70) cc_final: 0.8691 (t0)
REVERT: D  134 ASP cc_start: 0.8852 (m-30) cc_final: 0.8497 (m-30)
REVERT: E  118 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8428 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1435
  time to fit residues: 14.4594
Evaluate side-chains
  66 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 58 optimal weight:    0.0270
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 56 optimal weight:    0.3980
   chunk 49 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.4642

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 530 GLN
B 573 ASN
** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.112775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.089088 restraints weight = 7870.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.092096 restraints weight = 4289.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.094151 restraints weight = 2931.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   5669  Z= 0.169
  Angle     :  0.571   9.546   7750  Z= 0.306
  Chirality :  0.043   0.204    911
  Planarity :  0.003   0.041    968
  Dihedral  :  5.100  57.396    842
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.92 %
    Favored  : 87.73 %
  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: -0.18 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.10 (0.30), residues: 326
  loop : -1.26 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.006   0.001   HIS E 100 
 PHE   0.019   0.002   PHE A 547 
 TYR   0.017   0.002   TYR D 166 
 ARG   0.002   0.000   ARG D 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00279 (    2)
  link_NAG-ASN         : angle       0.85972 (    6)
  hydrogen bonds       : bond        0.03724 (  169)
  hydrogen bonds       : angle       4.93325 (  495)
  SS BOND              : bond        0.00884 (    6)
  SS BOND              : angle       3.41989 (   12)
  covalent geometry    : bond        0.00413 ( 5661)
  covalent geometry    : angle       0.55519 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
REVERT: E  118 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8433 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 69
  average time/residue: 0.1470
  time to fit residues: 14.3411
Evaluate side-chains
  67 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0670
   chunk 64 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.5522

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN
** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.111698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.088006 restraints weight = 7823.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.091058 restraints weight = 4200.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.093054 restraints weight = 2846.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   5669  Z= 0.175
  Angle     :  0.572   9.481   7750  Z= 0.307
  Chirality :  0.043   0.221    911
  Planarity :  0.003   0.039    968
  Dihedral  :  5.166  58.463    842
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 10.59 %
    Favored  : 86.89 %
  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: -0.30 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.06 (0.30), residues: 326
  loop : -1.38 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.005   0.001   HIS C 100 
 PHE   0.018   0.002   PHE A 547 
 TYR   0.017   0.001   TYR D 166 
 ARG   0.003   0.000   ARG D 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    2)
  link_NAG-ASN         : angle       0.86735 (    6)
  hydrogen bonds       : bond        0.03702 (  169)
  hydrogen bonds       : angle       4.85598 (  495)
  SS BOND              : bond        0.00851 (    6)
  SS BOND              : angle       3.22542 (   12)
  covalent geometry    : bond        0.00430 ( 5661)
  covalent geometry    : angle       0.55792 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: E  118 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8406 (m)
REVERT: F  182 SER cc_start: 0.8634 (t) cc_final: 0.8064 (p)
  outliers start: 15
  outliers final: 12
  residues processed: 67
  average time/residue: 0.1523
  time to fit residues: 14.5971
Evaluate side-chains
  68 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN
** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.113785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.090152 restraints weight = 7793.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.093232 restraints weight = 4188.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.095186 restraints weight = 2849.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   5669  Z= 0.137
  Angle     :  0.534   9.196   7750  Z= 0.287
  Chirality :  0.042   0.147    911
  Planarity :  0.003   0.040    968
  Dihedral  :  5.067  59.441    842
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.09 %
    Favored  : 85.88 %
  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: -0.27 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.07 (0.29), residues: 328
  loop : -1.36 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  47 
 HIS   0.003   0.001   HIS C 100 
 PHE   0.015   0.002   PHE A 547 
 TYR   0.014   0.001   TYR D 166 
 ARG   0.002   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00156 (    2)
  link_NAG-ASN         : angle       0.86270 (    6)
  hydrogen bonds       : bond        0.03374 (  169)
  hydrogen bonds       : angle       4.72734 (  495)
  SS BOND              : bond        0.00811 (    6)
  SS BOND              : angle       2.94551 (   12)
  covalent geometry    : bond        0.00333 ( 5661)
  covalent geometry    : angle       0.52083 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: F  150 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8470 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 70
  average time/residue: 0.1423
  time to fit residues: 13.9762
Evaluate side-chains
  72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0980
   chunk 35 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.114092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.090580 restraints weight = 7715.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.093552 restraints weight = 4218.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.095469 restraints weight = 2901.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   5669  Z= 0.130
  Angle     :  0.527   8.932   7750  Z= 0.284
  Chirality :  0.042   0.146    911
  Planarity :  0.003   0.039    968
  Dihedral  :  4.967  57.392    842
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.60 %
    Favored  : 85.38 %
  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: -0.27 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.07 (0.29), residues: 328
  loop : -1.35 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 603 
 PHE   0.014   0.001   PHE A 547 
 TYR   0.014   0.001   TYR D 166 
 ARG   0.002   0.000   ARG F 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    2)
  link_NAG-ASN         : angle       0.86074 (    6)
  hydrogen bonds       : bond        0.03279 (  169)
  hydrogen bonds       : angle       4.64029 (  495)
  SS BOND              : bond        0.00792 (    6)
  SS BOND              : angle       2.84880 (   12)
  covalent geometry    : bond        0.00314 ( 5661)
  covalent geometry    : angle       0.51535 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8891 (t70) cc_final: 0.8684 (t0)
REVERT: B  553 THR cc_start: 0.8732 (p) cc_final: 0.8332 (t)
REVERT: F  150 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8472 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 71
  average time/residue: 0.1398
  time to fit residues: 13.9696
Evaluate side-chains
  74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain A residue  594 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0570
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.114582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.091013 restraints weight = 7804.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.094075 restraints weight = 4234.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.096045 restraints weight = 2878.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5669  Z= 0.122
  Angle     :  0.512   8.495   7750  Z= 0.276
  Chirality :  0.041   0.146    911
  Planarity :  0.003   0.040    968
  Dihedral  :  4.781  52.519    842
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.27 %
    Favored  : 85.04 %
  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: -0.25 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.08 (0.30), residues: 326
  loop : -1.33 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  47 
 HIS   0.002   0.001   HIS A 603 
 PHE   0.013   0.001   PHE A 547 
 TYR   0.013   0.001   TYR D 166 
 ARG   0.003   0.000   ARG D 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00114 (    2)
  link_NAG-ASN         : angle       0.88308 (    6)
  hydrogen bonds       : bond        0.03139 (  169)
  hydrogen bonds       : angle       4.53748 (  495)
  SS BOND              : bond        0.00746 (    6)
  SS BOND              : angle       2.77488 (   12)
  covalent geometry    : bond        0.00293 ( 5661)
  covalent geometry    : angle       0.49977 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: B  553 THR cc_start: 0.8734 (p) cc_final: 0.8361 (t)
REVERT: F  150 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1417
  time to fit residues: 13.9197
Evaluate side-chains
  70 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  594 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  107 CYS
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 38 optimal weight:    0.1980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.110270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.086750 restraints weight = 7945.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.089490 restraints weight = 4475.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.091536 restraints weight = 3149.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   5669  Z= 0.200
  Angle     :  0.601   9.012   7750  Z= 0.321
  Chirality :  0.043   0.154    911
  Planarity :  0.004   0.038    968
  Dihedral  :  5.065  53.886    842
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.44 %
    Favored  : 84.71 %
  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: -0.42 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.95 (0.30), residues: 330
  loop : -1.46 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.019   0.002   PHE A 547 
 TYR   0.020   0.002   TYR D 166 
 ARG   0.003   0.000   ARG D 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00373 (    2)
  link_NAG-ASN         : angle       0.96168 (    6)
  hydrogen bonds       : bond        0.03751 (  169)
  hydrogen bonds       : angle       4.68681 (  495)
  SS BOND              : bond        0.00827 (    6)
  SS BOND              : angle       3.38973 (   12)
  covalent geometry    : bond        0.00491 ( 5661)
  covalent geometry    : angle       0.58624 ( 7732)

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

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

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1446 Ramachandran restraints generated.
    723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: F  150 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8553 (mp)
  outliers start: 17
  outliers final: 13
  residues processed: 69
  average time/residue: 0.1524
  time to fit residues: 14.6566
Evaluate side-chains
  72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  563 THR
Chi-restraints excluded: chain A residue  594 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  573 ASN
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue  150 LEU
Chi-restraints excluded: chain D residue  175 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  150 LEU
Chi-restraints excluded: chain F residue  175 VAL
Chi-restraints excluded: chain F residue  218 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 34 optimal weight:    0.1980
   chunk 67 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
B 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.115486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.091941 restraints weight = 7833.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.095037 restraints weight = 4214.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.096977 restraints weight = 2866.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   5669  Z= 0.098
  Angle     :  0.501   8.453   7750  Z= 0.270
  Chirality :  0.040   0.142    911
  Planarity :  0.003   0.040    968
  Dihedral  :  4.612  45.637    842
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.28 %
    Favored  : 84.87 %
  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: -0.22 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.04 (0.30), residues: 330
  loop : -1.27 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  47 
 HIS   0.002   0.001   HIS A 603 
 PHE   0.009   0.001   PHE A 500 
 TYR   0.008   0.001   TYR D 166 
 ARG   0.003   0.000   ARG D 141 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00009 (    2)
  link_NAG-ASN         : angle       0.87522 (    6)
  hydrogen bonds       : bond        0.02821 (  169)
  hydrogen bonds       : angle       4.56627 (  495)
  SS BOND              : bond        0.00770 (    6)
  SS BOND              : angle       2.96042 (   12)
  covalent geometry    : bond        0.00223 ( 5661)
  covalent geometry    : angle       0.48718 ( 7732)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2163.07 seconds
wall clock time: 38 minutes 10.63 seconds (2290.63 seconds total)