Starting phenix.real_space_refine
on Wed Sep 17 05:45:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnt_50610/09_2025/9fnt_50610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnt_50610/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnt_50610/09_2025/9fnt_50610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnt_50610/09_2025/9fnt_50610.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnt_50610/09_2025/9fnt_50610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnt_50610/09_2025/9fnt_50610.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1}
          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: 1.51, per 1000 atoms: 0.27
  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: 0.26
  Conformation dependent library (CDL) restraints added in 141.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 0.92

  Time building geometry restraints manager: 0.37 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:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     6.130
  Find NCS groups from input model:        0.090
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.530
-------------------------------------------------------------------------------
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 : 8.97
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG D 178 
 TYR   0.030   0.002   TYR F 166 
 PHE   0.033   0.002   PHE A 547 
 TRP   0.024   0.002   TRP E 114 
 HIS   0.006   0.001   HIS B 577 

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

*********************** 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  : 0.235 
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: 0.0523
  time to fit residues: 6.8811
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  : 0.212 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0000
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0370
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.2780

-------------------------------------------------------------------------------
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
** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.118638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.094194 restraints weight = 7844.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.097654 restraints weight = 3982.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.099975 restraints weight = 2597.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.101439 restraints weight = 1954.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.102528 restraints weight = 1622.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5669  Z= 0.107
  Angle     :  0.546   5.592   7750  Z= 0.297
  Chirality :  0.043   0.144    911
  Planarity :  0.004   0.047    968
  Dihedral  :  6.442  52.650    867
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  6.72 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.00 (0.30), residues: 324
  loop : -1.14 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 178 
 TYR   0.022   0.001   TYR D 166 
 PHE   0.016   0.002   PHE B 547 
 TRP   0.009   0.001   TRP B 472 
 HIS   0.003   0.001   HIS B 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 5661)
  covalent geometry    : angle       0.54047 ( 7732)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       1.82094 (   12)
  hydrogen bonds       : bond        0.04142 (  169)
  hydrogen bonds       : angle       5.76184 (  495)
  link_NAG-ASN         : bond        0.00067 (    2)
  link_NAG-ASN         : angle       1.26688 (    6)

*********************** 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
  82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.204 
Fit side-chains
REVERT: D  134 ASP cc_start: 0.8861 (m-30) cc_final: 0.8504 (m-30)
REVERT: D  218 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5874 (pt0)
REVERT: F  148 THR cc_start: 0.8989 (p) cc_final: 0.8560 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0709
  time to fit residues: 7.6559
Evaluate side-chains
  70 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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  218 GLN
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 11 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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
** 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 = 0.3129 r_free = 0.3129 target = 0.109675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.085648 restraints weight = 8068.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.088659 restraints weight = 4415.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.090628 restraints weight = 3026.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.092006 restraints weight = 2361.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.092888 restraints weight = 1991.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.100   5669  Z= 0.258
  Angle     :  0.674  10.333   7750  Z= 0.364
  Chirality :  0.046   0.169    911
  Planarity :  0.004   0.045    968
  Dihedral  :  6.062  54.221    847
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  7.90 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.80 (0.30), residues: 326
  loop : -1.42 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 178 
 TYR   0.025   0.002   TYR D 166 
 PHE   0.025   0.002   PHE A 547 
 TRP   0.011   0.002   TRP B 472 
 HIS   0.008   0.002   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 5661)
  covalent geometry    : angle       0.66044 ( 7732)
  SS BOND              : bond        0.00871 (    6)
  SS BOND              : angle       3.50840 (   12)
  hydrogen bonds       : bond        0.04772 (  169)
  hydrogen bonds       : angle       5.50577 (  495)
  link_NAG-ASN         : bond        0.00526 (    2)
  link_NAG-ASN         : angle       0.95978 (    6)

*********************** 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
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: D  182 SER cc_start: 0.8727 (t) cc_final: 0.8139 (p)
REVERT: D  218 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6224 (pt0)
REVERT: E  113 ASN cc_start: 0.8320 (m-40) cc_final: 0.8044 (m110)
  outliers start: 17
  outliers final: 13
  residues processed: 73
  average time/residue: 0.0525
  time to fit residues: 5.5120
Evaluate side-chains
  74 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  563 THR
Chi-restraints excluded: chain A residue  594 SER
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  563 THR
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 D residue  218 GLN
Chi-restraints excluded: chain E residue   25 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3192 r_free = 0.3192 target = 0.114010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.090124 restraints weight = 7846.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.093348 restraints weight = 4140.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.095441 restraints weight = 2771.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.096764 restraints weight = 2134.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.097693 restraints weight = 1799.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1938

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= 0.137
  Angle     :  0.553   9.906   7750  Z= 0.296
  Chirality :  0.042   0.174    911
  Planarity :  0.003   0.044    968
  Dihedral  :  5.528  57.796    847
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.75 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.91 (0.30), residues: 326
  loop : -1.35 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 178 
 TYR   0.013   0.001   TYR D 166 
 PHE   0.015   0.002   PHE A 547 
 TRP   0.007   0.001   TRP E  47 
 HIS   0.003   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5661)
  covalent geometry    : angle       0.54136 ( 7732)
  SS BOND              : bond        0.00773 (    6)
  SS BOND              : angle       2.84764 (   12)
  hydrogen bonds       : bond        0.03579 (  169)
  hydrogen bonds       : angle       5.01184 (  495)
  link_NAG-ASN         : bond        0.00106 (    2)
  link_NAG-ASN         : angle       0.85064 (    6)

*********************** 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
  78 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: B  497 THR cc_start: 0.8558 (p) cc_final: 0.8350 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0533
  time to fit residues: 5.5249
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  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain B residue  487 SER
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0370
   chunk 19 optimal weight:    0.0980
   chunk 55 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5460

-------------------------------------------------------------------------------
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 = 0.3224 r_free = 0.3224 target = 0.116664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.092631 restraints weight = 7993.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.095889 restraints weight = 4172.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.098012 restraints weight = 2774.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099484 restraints weight = 2137.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.100383 restraints weight = 1780.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067   5669  Z= 0.095
  Angle     :  0.499   8.942   7750  Z= 0.267
  Chirality :  0.041   0.182    911
  Planarity :  0.003   0.045    968
  Dihedral  :  4.847  57.545    842
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.09 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.98 (0.30), residues: 330
  loop : -1.19 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 178 
 TYR   0.009   0.001   TYR D 166 
 PHE   0.010   0.001   PHE A 547 
 TRP   0.006   0.001   TRP E  47 
 HIS   0.003   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5661)
  covalent geometry    : angle       0.48637 ( 7732)
  SS BOND              : bond        0.00781 (    6)
  SS BOND              : angle       2.81596 (   12)
  hydrogen bonds       : bond        0.02941 (  169)
  hydrogen bonds       : angle       4.76651 (  495)
  link_NAG-ASN         : bond        0.00034 (    2)
  link_NAG-ASN         : angle       0.89062 (    6)

*********************** 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
  68 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.232 
Fit side-chains
REVERT: D  134 ASP cc_start: 0.8843 (m-30) cc_final: 0.8570 (m-30)
REVERT: F  182 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8010 (p)
  outliers start: 10
  outliers final: 6
  residues processed: 64
  average time/residue: 0.0588
  time to fit residues: 5.1091
Evaluate side-chains
  63 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
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  182 SER
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 70 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.111137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.087316 restraints weight = 7891.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.090355 restraints weight = 4302.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.092412 restraints weight = 2941.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.093682 restraints weight = 2284.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.094535 restraints weight = 1939.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   5669  Z= 0.218
  Angle     :  0.606   9.445   7750  Z= 0.326
  Chirality :  0.044   0.153    911
  Planarity :  0.004   0.041    968
  Dihedral  :  5.332  59.641    842
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.30), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.96 (0.30), residues: 326
  loop : -1.49 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 141 
 TYR   0.020   0.002   TYR D 166 
 PHE   0.019   0.002   PHE A 547 
 TRP   0.010   0.001   TRP B 472 
 HIS   0.005   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 5661)
  covalent geometry    : angle       0.59142 ( 7732)
  SS BOND              : bond        0.00913 (    6)
  SS BOND              : angle       3.39538 (   12)
  hydrogen bonds       : bond        0.04060 (  169)
  hydrogen bonds       : angle       4.83753 (  495)
  link_NAG-ASN         : bond        0.00460 (    2)
  link_NAG-ASN         : angle       0.93415 (    6)

*********************** 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
  75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: F  150 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8451 (mp)
REVERT: F  182 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8043 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 68
  average time/residue: 0.0601
  time to fit residues: 5.7107
Evaluate side-chains
  72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  573 ASN
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  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 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  182 SER
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 16 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.113871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.089997 restraints weight = 7906.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.093114 restraints weight = 4245.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.095217 restraints weight = 2875.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.096539 restraints weight = 2215.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.097570 restraints weight = 1875.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   5669  Z= 0.113
  Angle     :  0.515   8.521   7750  Z= 0.278
  Chirality :  0.041   0.146    911
  Planarity :  0.003   0.042    968
  Dihedral  :  4.983  56.002    842
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.60 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.91 (0.30), residues: 330
  loop : -1.31 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 141 
 TYR   0.011   0.001   TYR D 166 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.007   0.001   TRP E  47 
 HIS   0.002   0.001   HIS C  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5661)
  covalent geometry    : angle       0.50415 ( 7732)
  SS BOND              : bond        0.00725 (    6)
  SS BOND              : angle       2.69612 (   12)
  hydrogen bonds       : bond        0.03200 (  169)
  hydrogen bonds       : angle       4.65466 (  495)
  link_NAG-ASN         : bond        0.00068 (    2)
  link_NAG-ASN         : angle       0.84825 (    6)

*********************** 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
  77 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8890 (t70) cc_final: 0.8646 (t0)
REVERT: F  150 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8365 (mp)
REVERT: F  182 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.7947 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 72
  average time/residue: 0.0673
  time to fit residues: 6.4838
Evaluate side-chains
  72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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  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  150 LEU
Chi-restraints excluded: chain F residue  171 LEU
Chi-restraints excluded: chain F residue  182 SER
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 56 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.112783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.089014 restraints weight = 7833.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.092076 restraints weight = 4242.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.094176 restraints weight = 2890.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.095464 restraints weight = 2234.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.096313 restraints weight = 1890.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
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      :  0.004   0.064   5669  Z= 0.150
  Angle     :  0.538   8.302   7750  Z= 0.291
  Chirality :  0.042   0.150    911
  Planarity :  0.003   0.040    968
  Dihedral  :  5.003  55.043    842
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.97 (0.30), residues: 328
  loop : -1.45 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 141 
 TYR   0.015   0.001   TYR D 166 
 PHE   0.015   0.002   PHE A 547 
 TRP   0.007   0.001   TRP B 472 
 HIS   0.003   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5661)
  covalent geometry    : angle       0.52670 ( 7732)
  SS BOND              : bond        0.00740 (    6)
  SS BOND              : angle       2.79237 (   12)
  hydrogen bonds       : bond        0.03448 (  169)
  hydrogen bonds       : angle       4.61871 (  495)
  link_NAG-ASN         : bond        0.00227 (    2)
  link_NAG-ASN         : angle       0.88737 (    6)

*********************** 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
  75 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8881 (t70) cc_final: 0.8633 (t0)
REVERT: F  150 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: F  182 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.7955 (p)
  outliers start: 15
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0753
  time to fit residues: 7.0797
Evaluate side-chains
  70 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
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  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  171 LEU
Chi-restraints excluded: chain F residue  182 SER
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 36 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3179 r_free = 0.3179 target = 0.113278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.089476 restraints weight = 7893.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.092508 restraints weight = 4235.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.094602 restraints weight = 2886.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.095874 restraints weight = 2234.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.096862 restraints weight = 1891.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5669  Z= 0.135
  Angle     :  0.523   8.213   7750  Z= 0.283
  Chirality :  0.042   0.147    911
  Planarity :  0.003   0.041    968
  Dihedral  :  4.866  51.208    842
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  0.98 (0.30), residues: 326
  loop : -1.41 (0.28), residues: 397

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5661)
  covalent geometry    : angle       0.51140 ( 7732)
  SS BOND              : bond        0.00667 (    6)
  SS BOND              : angle       2.72667 (   12)
  hydrogen bonds       : bond        0.03270 (  169)
  hydrogen bonds       : angle       4.56691 (  495)
  link_NAG-ASN         : bond        0.00160 (    2)
  link_NAG-ASN         : angle       0.88018 (    6)

*********************** 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
  77 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: F  150 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: F  182 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.7918 (p)
  outliers start: 16
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0729
  time to fit residues: 7.0642
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  : 0.203 
-------------------------------------------------------------------------------
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 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  182 SER
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 64 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3181 r_free = 0.3181 target = 0.113440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.089608 restraints weight = 7936.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.092696 restraints weight = 4244.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.094762 restraints weight = 2879.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.096055 restraints weight = 2231.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.097034 restraints weight = 1885.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5669  Z= 0.133
  Angle     :  0.531   8.304   7750  Z= 0.286
  Chirality :  0.041   0.149    911
  Planarity :  0.003   0.041    968
  Dihedral  :  4.765  47.396    842
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.61 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.02 (0.30), residues: 328
  loop : -1.42 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 141 
 TYR   0.013   0.001   TYR D 166 
 PHE   0.013   0.001   PHE A 547 
 TRP   0.006   0.001   TRP E  47 
 HIS   0.002   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5661)
  covalent geometry    : angle       0.51676 ( 7732)
  SS BOND              : bond        0.00757 (    6)
  SS BOND              : angle       3.05848 (   12)
  hydrogen bonds       : bond        0.03253 (  169)
  hydrogen bonds       : angle       4.59540 (  495)
  link_NAG-ASN         : bond        0.00156 (    2)
  link_NAG-ASN         : angle       0.87996 (    6)

********************** 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
  76 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8893 (t70) cc_final: 0.8676 (t0)
REVERT: F  150 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: F  182 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.7870 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0709
  time to fit residues: 6.8242
Evaluate side-chains
  72 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  182 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 66 optimal weight:    0.0010
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9388

-------------------------------------------------------------------------------
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 = 0.3173 r_free = 0.3173 target = 0.113070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.089170 restraints weight = 7907.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.092255 restraints weight = 4238.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.094305 restraints weight = 2874.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.095751 restraints weight = 2226.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.096635 restraints weight = 1860.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   5669  Z= 0.123
  Angle     :  0.523   8.391   7750  Z= 0.282
  Chirality :  0.041   0.148    911
  Planarity :  0.003   0.041    968
  Dihedral  :  4.378  44.897    839
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.11 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.31), residues: 723
  helix:  None (None), residues: 0
  sheet:  1.01 (0.30), residues: 326
  loop : -1.39 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 141 
 TYR   0.012   0.001   TYR D 166 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.006   0.001   TRP E  47 
 HIS   0.002   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5661)
  covalent geometry    : angle       0.50898 ( 7732)
  SS BOND              : bond        0.00775 (    6)
  SS BOND              : angle       3.03141 (   12)
  hydrogen bonds       : bond        0.03170 (  169)
  hydrogen bonds       : angle       4.57685 (  495)
  link_NAG-ASN         : bond        0.00116 (    2)
  link_NAG-ASN         : angle       0.87166 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1027.72 seconds
wall clock time: 18 minutes 21.23 seconds (1101.23 seconds total)