Starting phenix.real_space_refine
on Thu Jun  5 06:45:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fns_50609/06_2025/9fns_50609.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
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      14      5.16       5
     C    3500      2.51       5
     N     923      2.21       5
     O    1105      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5542
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1074
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1080
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 738
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "E"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 930
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 746
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.07, per 1000 atoms: 0.73
  Number of scatterers: 5542
  At special positions: 0
  Unit cell: (104.92, 79.98, 85.14, 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      14     16.00
     O    1105      8.00
     N     923      7.00
     C    3500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 137 " - pdb=" SG  CYS D 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 137 " - pdb=" SG  CYS F 202 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1000 " - " ASN A 562 "
      " NAG B1000 " - " ASN B 562 "
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 697.9 milliseconds
  

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1330

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 19 sheets defined
      1.8% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 515 through 518
    Processing helix  chain 'C' and resid 28 through 31
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.012A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    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 508 through 510
      removed outlier: 3.570A  pdb=" N   VAL A 579 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   SER A 582 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   GLN A 568 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE A 569 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510
      removed outlier: 5.441A  pdb=" N   THR A 593 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 547 through 548
      removed outlier: 4.420A  pdb=" N   PHE A 547 " --> pdb=" O   GLY A 556 " (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 508 through 510
    Processing sheet with id=AA7, first strand: chain 'B' and resid 478 through 481
      removed outlier: 3.895A  pdb=" N   ILE B 581 " --> pdb=" O   TYR B 493 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 547 through 548
      removed outlier: 4.492A  pdb=" N   PHE B 547 " --> pdb=" O   GLY B 556 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6
      removed outlier: 4.006A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.725A  pdb=" N   THR C 115 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TYR C  94 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER C  33 " --> pdb=" O   VAL C  99 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.725A  pdb=" N   THR C 115 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TYR C  94 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   CYS C  96 " --> pdb=" O   TRP C 111 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   TRP C 111 " --> pdb=" O   CYS C  96 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ARG C  98 " --> pdb=" O   ASP C 109 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 126
    Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 138
    Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.988A  pdb=" N   VAL E  18 " --> pdb=" O   LEU E  83 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.571A  pdb=" N   THR E 118 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  94 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER E  33 " --> pdb=" O   VAL E  99 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ILE E  34 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   TRP E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.571A  pdb=" N   THR E 118 " --> pdb=" O   GLU E  10 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  94 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   TRP E 100 " --> pdb=" O   GLY E 108 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   GLY E 108 " --> pdb=" O   TRP E 100 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 126
      removed outlier: 6.492A  pdb=" N   LEU F 125 " --> pdb=" O   GLU F 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'F' and resid 133 through 138
    Processing sheet with id=AC1, first strand: chain 'F' and resid 159 through 162
      removed outlier: 6.943A  pdb=" N   TRP F 149 " --> pdb=" O   LEU F 161 " (cutoff:3.500A)

    186 hydrogen bonds defined for protein.
    459 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1060
        1.33 -     1.45: 1568
        1.45 -     1.57: 3026
        1.57 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 5674
  Sorted by residual:
  bond pdb=" CA  TYR A 584 "
       pdb=" C   TYR A 584 "
    ideal  model  delta    sigma   weight residual
    1.527  1.476  0.051 1.21e-02 6.83e+03 1.80e+01
  bond pdb=" N   VAL B 501 "
       pdb=" CA  VAL B 501 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 1.08e-02 8.57e+03 1.72e+01
  bond pdb=" N   ILE F 162 "
       pdb=" CA  ILE F 162 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.041 1.14e-02 7.69e+03 1.32e+01
  bond pdb=" N   VAL E  68 "
       pdb=" CA  VAL E  68 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.042 1.15e-02 7.56e+03 1.32e+01
  bond pdb=" CA  SER D 142 "
       pdb=" CB  SER D 142 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.046 1.35e-02 5.49e+03 1.18e+01
  ... (remaining 5669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 6960
        2.53 -     5.06: 631
        5.06 -     7.59: 115
        7.59 -    10.12: 37
       10.12 -    12.65: 12
  Bond angle restraints: 7755
  Sorted by residual:
  angle pdb=" N   TYR A 561 "
        pdb=" CA  TYR A 561 "
        pdb=" C   TYR A 561 "
      ideal   model   delta    sigma   weight residual
     111.36  102.09    9.27 1.09e+00 8.42e-01 7.23e+01
  angle pdb=" C   ALA D 157 "
        pdb=" N   PRO D 158 "
        pdb=" CA  PRO D 158 "
      ideal   model   delta    sigma   weight residual
     119.92  128.79   -8.87 1.07e+00 8.73e-01 6.87e+01
  angle pdb=" N   LYS A 534 "
        pdb=" CA  LYS A 534 "
        pdb=" CB  LYS A 534 "
      ideal   model   delta    sigma   weight residual
     110.77   98.12   12.65 1.57e+00 4.06e-01 6.49e+01
  angle pdb=" N   THR A 564 "
        pdb=" CA  THR A 564 "
        pdb=" C   THR A 564 "
      ideal   model   delta    sigma   weight residual
     110.68   99.99   10.69 1.39e+00 5.18e-01 5.92e+01
  angle pdb=" N   GLN B 482 "
        pdb=" CA  GLN B 482 "
        pdb=" CB  GLN B 482 "
      ideal   model   delta    sigma   weight residual
     110.88  121.31  -10.43 1.38e+00 5.25e-01 5.71e+01
  ... (remaining 7750 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.26: 3011
       23.26 -    46.51: 201
       46.51 -    69.77: 63
       69.77 -    93.02: 12
       93.02 -   116.28: 6
  Dihedral angle restraints: 3293
    sinusoidal: 1198
      harmonic: 2095
  Sorted by residual:
  dihedral pdb=" CD  ARG E  67 "
           pdb=" NE  ARG E  67 "
           pdb=" CZ  ARG E  67 "
           pdb=" NH1 ARG E  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.05  -78.05     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" CD  ARG B 512 "
           pdb=" NE  ARG B 512 "
           pdb=" CZ  ARG B 512 "
           pdb=" NH1 ARG B 512 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.23  -70.23     1      1.00e+01 1.00e-02 6.35e+01
  dihedral pdb=" N   GLN B 482 "
           pdb=" C   GLN B 482 "
           pdb=" CA  GLN B 482 "
           pdb=" CB  GLN B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.55  -17.75     0      2.50e+00 1.60e-01 5.04e+01
  ... (remaining 3290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 780
       0.135 -    0.269: 96
       0.269 -    0.404: 17
       0.404 -    0.538: 3
       0.538 -    0.673: 1
  Chirality restraints: 897
  Sorted by residual:
  chirality pdb=" CA  GLN B 482 "
            pdb=" N   GLN B 482 "
            pdb=" C   GLN B 482 "
            pdb=" CB  GLN B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" CA  SER A 533 "
            pdb=" N   SER A 533 "
            pdb=" C   SER A 533 "
            pdb=" CB  SER A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" CA  ALA A 504 "
            pdb=" N   ALA A 504 "
            pdb=" C   ALA A 504 "
            pdb=" CB  ALA A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.04    0.44 2.00e-01 2.50e+01 4.88e+00
  ... (remaining 894 not shown)

  Planarity restraints: 976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  67 "    1.086 9.50e-02 1.11e+02   4.86e-01 1.43e+02
        pdb=" NE  ARG E  67 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  67 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  67 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  67 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 512 "   -1.028 9.50e-02 1.11e+02   4.61e-01 1.28e+02
        pdb=" NE  ARG B 512 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 512 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 512 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 512 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 138 "    0.540 9.50e-02 1.11e+02   2.42e-01 3.58e+01
        pdb=" NE  ARG F 138 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 138 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 138 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 138 "    0.019 2.00e-02 2.50e+03
  ... (remaining 973 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 3
        2.19 -     2.86: 2167
        2.86 -     3.54: 6482
        3.54 -     4.22: 11633
        4.22 -     4.90: 20816
  Nonbonded interactions: 41101
  Sorted by model distance:
  nonbonded pdb=" O   SER C   7 "
            pdb=" CG2 THR C 115 "
     model   vdw
     1.508 3.460
  nonbonded pdb=" O   ASP B 515 "
            pdb=" OD1 ASP B 515 "
     model   vdw
     1.546 3.040
  nonbonded pdb=" OG1 THR A 476 "
            pdb=" OG1 THR A 497 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" CG  ARG B 466 "
            pdb=" OD2 ASP B 469 "
     model   vdw
     2.210 3.440
  nonbonded pdb=" O   PRO D 122 "
            pdb=" OG1 THR D 217 "
     model   vdw
     2.238 3.040
  ... (remaining 41096 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' and (resid 461 through 465 or (resid 466 through 467 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 468 through 603 or resid 1000) \ 
)
}
ncs_group {
  reference = (chain 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 2 through 9 or (resid 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 13 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 14 through 120))
  selection = (chain 'E' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 20 through 120))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'F' and (resid 122 through 217 or (resid 218 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 219 or (resid 220 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 221))
}

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:             1.600
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.870
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
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      :  0.009   0.060   5680  Z= 0.632
  Angle     :  1.648  13.174   7769  Z= 1.096
  Chirality :  0.100   0.673    897
  Planarity :  0.024   0.486    974
  Dihedral  : 18.272 116.280   1951
  Min Nonbonded Distance : 1.508

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.52 %
    Favored  : 97.34 %
  Rotamer:
    Outliers : 11.00 %
    Allowed  : 11.00 %
    Favored  : 78.00 %
  Cbeta Deviations :  2.71 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.29), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.99 (0.27), residues: 335
  loop : -1.70 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 100 
 HIS   0.006   0.001   HIS A 602 
 PHE   0.021   0.002   PHE B 547 
 TYR   0.025   0.002   TYR A 557 
 ARG   0.004   0.000   ARG F 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01127 (    2)
  link_NAG-ASN         : angle       6.08992 (    6)
  hydrogen bonds       : bond        0.28678 (  173)
  hydrogen bonds       : angle       9.83644 (  459)
  SS BOND              : bond        0.01948 (    4)
  SS BOND              : angle       1.46575 (    8)
  covalent geometry    : bond        0.00875 ( 5674)
  covalent geometry    : angle       1.64024 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 106
  time to evaluate  : 0.640 
Fit side-chains
REVERT: B  487 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9045 (p)
REVERT: B  490 ASN cc_start: 0.8137 (m-40) cc_final: 0.7754 (t0)
REVERT: C   78 THR cc_start: 0.8480 (p) cc_final: 0.8203 (p)
REVERT: E   65 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8099 (tp-100)
REVERT: E   78 THR cc_start: 0.8487 (p) cc_final: 0.8247 (p)
REVERT: F  204 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8798 (tm-30)
  outliers start: 65
  outliers final: 31
  residues processed: 153
  average time/residue: 0.2018
  time to fit residues: 38.9391
Evaluate side-chains
  135 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  488 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  557 TYR
Chi-restraints excluded: chain B residue  560 ASN
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain C residue   67 ARG
Chi-restraints excluded: chain C residue  107 ARG
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  107 ARG
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  145 THR
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  166 SER
Chi-restraints excluded: chain F residue  168 LEU
Chi-restraints excluded: chain F residue  202 CYS
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 602 HIS
C  62 GLN
C 113 GLN
E 106 ASN
F 204 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.124764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099667 restraints weight = 8178.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.103256 restraints weight = 4163.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105642 restraints weight = 2778.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5680  Z= 0.123
  Angle     :  0.590   8.948   7769  Z= 0.308
  Chirality :  0.045   0.236    897
  Planarity :  0.005   0.055    974
  Dihedral  :  8.912  83.423    890
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.82 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 12.52 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.45 (0.27), residues: 347
  loop : -1.31 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 100 
 HIS   0.004   0.001   HIS D 163 
 PHE   0.017   0.002   PHE B 500 
 TYR   0.014   0.001   TYR E  54 
 ARG   0.005   0.001   ARG E  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00052 (    2)
  link_NAG-ASN         : angle       1.37922 (    6)
  hydrogen bonds       : bond        0.03834 (  173)
  hydrogen bonds       : angle       6.54620 (  459)
  SS BOND              : bond        0.00669 (    4)
  SS BOND              : angle       0.89895 (    8)
  covalent geometry    : bond        0.00272 ( 5674)
  covalent geometry    : angle       0.58883 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 0.590 
Fit side-chains
REVERT: B  487 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9062 (p)
REVERT: C   78 THR cc_start: 0.8255 (p) cc_final: 0.7938 (p)
REVERT: E   19 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8014 (ttm-80)
REVERT: E   78 THR cc_start: 0.8229 (p) cc_final: 0.7981 (p)
REVERT: F  204 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8809 (tm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1885
  time to fit residues: 29.0159
Evaluate side-chains
  107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain B residue  482 GLN
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  587 SER
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0770
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
C  62 GLN
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.119489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.094121 restraints weight = 8366.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.097637 restraints weight = 4189.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.099960 restraints weight = 2804.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5680  Z= 0.158
  Angle     :  0.589   8.170   7769  Z= 0.311
  Chirality :  0.045   0.147    897
  Planarity :  0.004   0.049    974
  Dihedral  :  7.634  88.848    853
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 12.52 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.32 (0.27), residues: 362
  loop : -1.34 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 100 
 HIS   0.009   0.002   HIS D 163 
 PHE   0.016   0.002   PHE B 500 
 TYR   0.017   0.002   TYR E  54 
 ARG   0.002   0.000   ARG C  84 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00452 (    2)
  link_NAG-ASN         : angle       0.75399 (    6)
  hydrogen bonds       : bond        0.04180 (  173)
  hydrogen bonds       : angle       5.97931 (  459)
  SS BOND              : bond        0.00816 (    4)
  SS BOND              : angle       1.27660 (    8)
  covalent geometry    : bond        0.00369 ( 5674)
  covalent geometry    : angle       0.58777 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.611 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8507 (tttt) cc_final: 0.8098 (ttpt)
REVERT: E   78 THR cc_start: 0.8406 (p) cc_final: 0.8138 (p)
  outliers start: 31
  outliers final: 26
  residues processed: 105
  average time/residue: 0.1991
  time to fit residues: 27.0575
Evaluate side-chains
  100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  563 THR
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  162 ILE
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0570
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    1.0504

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
E  65 GLN
F 163 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.120474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.095007 restraints weight = 8445.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.098520 restraints weight = 4215.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.100775 restraints weight = 2818.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5680  Z= 0.126
  Angle     :  0.522   8.595   7769  Z= 0.277
  Chirality :  0.043   0.151    897
  Planarity :  0.004   0.045    974
  Dihedral  :  6.723  89.043    850
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 15.40 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.22 (0.26), residues: 365
  loop : -1.34 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 100 
 HIS   0.008   0.002   HIS F 163 
 PHE   0.014   0.001   PHE B 547 
 TYR   0.015   0.001   TYR E  54 
 ARG   0.004   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    2)
  link_NAG-ASN         : angle       0.62777 (    6)
  hydrogen bonds       : bond        0.03395 (  173)
  hydrogen bonds       : angle       5.67454 (  459)
  SS BOND              : bond        0.00616 (    4)
  SS BOND              : angle       1.02197 (    8)
  covalent geometry    : bond        0.00292 ( 5674)
  covalent geometry    : angle       0.52108 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.552 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8503 (tttt) cc_final: 0.8061 (ttpt)
REVERT: E   78 THR cc_start: 0.8354 (p) cc_final: 0.8073 (p)
REVERT: F  204 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8802 (tm-30)
  outliers start: 26
  outliers final: 23
  residues processed: 102
  average time/residue: 0.1965
  time to fit residues: 25.8653
Evaluate side-chains
  98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  163 HIS
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN
D 204 GLN
E  65 GLN
F 163 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.120788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.095555 restraints weight = 8349.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.098993 restraints weight = 4235.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.101259 restraints weight = 2854.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5680  Z= 0.112
  Angle     :  0.508   8.462   7769  Z= 0.267
  Chirality :  0.043   0.141    897
  Planarity :  0.004   0.043    974
  Dihedral  :  6.385  88.999    846
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 16.58 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.30), residues: 715
  helix:  None (None), residues: 0
  sheet: -0.05 (0.27), residues: 365
  loop : -1.34 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.011   0.002   HIS F 163 
 PHE   0.013   0.001   PHE B 547 
 TYR   0.013   0.001   TYR E  54 
 ARG   0.004   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00181 (    2)
  link_NAG-ASN         : angle       0.67563 (    6)
  hydrogen bonds       : bond        0.03188 (  173)
  hydrogen bonds       : angle       5.52086 (  459)
  SS BOND              : bond        0.00616 (    4)
  SS BOND              : angle       0.97790 (    8)
  covalent geometry    : bond        0.00258 ( 5674)
  covalent geometry    : angle       0.50675 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.602 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8473 (tttt) cc_final: 0.7998 (ttpt)
REVERT: E   78 THR cc_start: 0.8281 (p) cc_final: 0.7973 (p)
REVERT: F  204 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8787 (tm-30)
  outliers start: 32
  outliers final: 25
  residues processed: 99
  average time/residue: 0.1905
  time to fit residues: 24.2652
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0570
   chunk 21 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
F 163 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.122201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.096937 restraints weight = 8340.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.100435 restraints weight = 4156.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.102727 restraints weight = 2779.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5680  Z= 0.094
  Angle     :  0.486   8.172   7769  Z= 0.254
  Chirality :  0.042   0.144    897
  Planarity :  0.004   0.042    974
  Dihedral  :  6.200  88.255    846
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 16.75 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.03 (0.27), residues: 369
  loop : -1.23 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.011   0.002   HIS F 163 
 PHE   0.011   0.001   PHE B 547 
 TYR   0.012   0.001   TYR E  54 
 ARG   0.005   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00082 (    2)
  link_NAG-ASN         : angle       0.73148 (    6)
  hydrogen bonds       : bond        0.02913 (  173)
  hydrogen bonds       : angle       5.36439 (  459)
  SS BOND              : bond        0.00538 (    4)
  SS BOND              : angle       0.85265 (    8)
  covalent geometry    : bond        0.00214 ( 5674)
  covalent geometry    : angle       0.48515 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.616 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8484 (tttt) cc_final: 0.8014 (ttpt)
REVERT: E   78 THR cc_start: 0.8238 (p) cc_final: 0.7911 (p)
REVERT: F  204 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8795 (tm-30)
  outliers start: 31
  outliers final: 28
  residues processed: 98
  average time/residue: 0.1760
  time to fit residues: 22.4084
Evaluate side-chains
  101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain E residue  109 ASP
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  163 HIS
Chi-restraints excluded: chain F residue  204 GLN
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
F 144 ASN
F 163 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.123390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.098309 restraints weight = 8307.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.101777 restraints weight = 4215.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104058 restraints weight = 2831.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5680  Z= 0.084
  Angle     :  0.471   8.174   7769  Z= 0.246
  Chirality :  0.042   0.140    897
  Planarity :  0.004   0.041    974
  Dihedral  :  6.079  88.354    846
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.10 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 17.09 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.25 (0.27), residues: 365
  loop : -1.29 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 100 
 HIS   0.015   0.002   HIS F 163 
 PHE   0.010   0.001   PHE B 547 
 TYR   0.011   0.001   TYR E  54 
 ARG   0.005   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    2)
  link_NAG-ASN         : angle       0.77675 (    6)
  hydrogen bonds       : bond        0.02726 (  173)
  hydrogen bonds       : angle       5.22086 (  459)
  SS BOND              : bond        0.00502 (    4)
  SS BOND              : angle       0.79967 (    8)
  covalent geometry    : bond        0.00187 ( 5674)
  covalent geometry    : angle       0.47034 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.610 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8502 (tttt) cc_final: 0.8027 (ttpt)
REVERT: E   78 THR cc_start: 0.8222 (p) cc_final: 0.7880 (p)
  outliers start: 30
  outliers final: 27
  residues processed: 101
  average time/residue: 0.1820
  time to fit residues: 23.8415
Evaluate side-chains
  99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
F 144 ASN
F 163 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.121978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.096644 restraints weight = 8330.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.100165 restraints weight = 4168.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.102302 restraints weight = 2784.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5680  Z= 0.104
  Angle     :  0.490   8.077   7769  Z= 0.257
  Chirality :  0.042   0.141    897
  Planarity :  0.004   0.041    974
  Dihedral  :  4.537  38.896    839
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.38 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.44 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.23 (0.27), residues: 369
  loop : -1.26 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 100 
 HIS   0.010   0.002   HIS F 163 
 PHE   0.012   0.001   PHE B 547 
 TYR   0.011   0.001   TYR E  54 
 ARG   0.004   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       0.75410 (    6)
  hydrogen bonds       : bond        0.02914 (  173)
  hydrogen bonds       : angle       5.22445 (  459)
  SS BOND              : bond        0.00549 (    4)
  SS BOND              : angle       0.97353 (    8)
  covalent geometry    : bond        0.00240 ( 5674)
  covalent geometry    : angle       0.48856 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.581 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8499 (tttt) cc_final: 0.8025 (ttpt)
REVERT: E   78 THR cc_start: 0.8252 (p) cc_final: 0.7915 (p)
  outliers start: 26
  outliers final: 25
  residues processed: 92
  average time/residue: 0.1855
  time to fit residues: 22.0593
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  101 THR
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 530 GLN
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.118280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.093091 restraints weight = 8426.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096457 restraints weight = 4221.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.098689 restraints weight = 2838.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5680  Z= 0.166
  Angle     :  0.549   7.840   7769  Z= 0.292
  Chirality :  0.044   0.147    897
  Planarity :  0.004   0.040    974
  Dihedral  :  4.795  37.738    838
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.36 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 18.10 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.18 (0.27), residues: 369
  loop : -1.38 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 100 
 HIS   0.004   0.001   HIS D 163 
 PHE   0.016   0.002   PHE B 547 
 TYR   0.014   0.002   TYR B 537 
 ARG   0.005   0.000   ARG D 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       0.73469 (    6)
  hydrogen bonds       : bond        0.03611 (  173)
  hydrogen bonds       : angle       5.50016 (  459)
  SS BOND              : bond        0.00725 (    4)
  SS BOND              : angle       1.27117 (    8)
  covalent geometry    : bond        0.00397 ( 5674)
  covalent geometry    : angle       0.54734 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.551 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8535 (tttt) cc_final: 0.8049 (ttpt)
REVERT: E   78 THR cc_start: 0.8412 (p) cc_final: 0.8073 (p)
  outliers start: 28
  outliers final: 24
  residues processed: 95
  average time/residue: 0.1831
  time to fit residues: 22.4861
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain B residue  579 VAL
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  168 LEU
Chi-restraints excluded: chain F residue  213 PHE
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.117813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.092666 restraints weight = 8408.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.096015 restraints weight = 4227.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.098182 restraints weight = 2848.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5680  Z= 0.169
  Angle     :  0.557   7.924   7769  Z= 0.296
  Chirality :  0.044   0.153    897
  Planarity :  0.004   0.040    974
  Dihedral  :  4.877  36.239    838
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.92 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 19.29 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.37 (0.27), residues: 367
  loop : -1.65 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 100 
 HIS   0.004   0.001   HIS D 163 
 PHE   0.016   0.002   PHE B 547 
 TYR   0.015   0.002   TYR B 537 
 ARG   0.006   0.001   ARG F 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00292 (    2)
  link_NAG-ASN         : angle       0.75277 (    6)
  hydrogen bonds       : bond        0.03620 (  173)
  hydrogen bonds       : angle       5.61110 (  459)
  SS BOND              : bond        0.00717 (    4)
  SS BOND              : angle       1.21367 (    8)
  covalent geometry    : bond        0.00402 ( 5674)
  covalent geometry    : angle       0.55560 ( 7755)

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

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

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1430 Ramachandran restraints generated.
    715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.550 
Fit side-chains
REVERT: D  159 LYS cc_start: 0.8531 (tttt) cc_final: 0.8049 (ttpt)
REVERT: D  175 ARG cc_start: 0.7360 (ptt-90) cc_final: 0.6996 (ptt-90)
REVERT: E   78 THR cc_start: 0.8432 (p) cc_final: 0.8093 (p)
  outliers start: 24
  outliers final: 22
  residues processed: 91
  average time/residue: 0.1894
  time to fit residues: 22.1875
Evaluate side-chains
  94 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  560 ASN
Chi-restraints excluded: chain A residue  593 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  168 LEU
Chi-restraints excluded: chain D residue  204 GLN
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain F residue  140 SER
Chi-restraints excluded: chain F residue  217 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0470
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.123626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.098405 restraints weight = 8364.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.101911 restraints weight = 4252.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104189 restraints weight = 2852.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5680  Z= 0.081
  Angle     :  0.476   8.042   7769  Z= 0.250
  Chirality :  0.042   0.149    897
  Planarity :  0.004   0.041    974
  Dihedral  :  4.280  31.397    838
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.80 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.97 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.31), residues: 715
  helix:  None (None), residues: 0
  sheet:  0.55 (0.28), residues: 351
  loop : -1.41 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 100 
 HIS   0.007   0.001   HIS F 163 
 PHE   0.011   0.001   PHE F 213 
 TYR   0.010   0.001   TYR E  54 
 ARG   0.007   0.000   ARG F 175 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    2)
  link_NAG-ASN         : angle       0.79918 (    6)
  hydrogen bonds       : bond        0.02549 (  173)
  hydrogen bonds       : angle       5.15058 (  459)
  SS BOND              : bond        0.00399 (    4)
  SS BOND              : angle       0.52993 (    8)
  covalent geometry    : bond        0.00175 ( 5674)
  covalent geometry    : angle       0.47534 ( 7755)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2139.12 seconds
wall clock time: 37 minutes 55.67 seconds (2275.67 seconds total)