Starting phenix.real_space_refine
on Thu Jul 24 01:45:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odb_70353/07_2025/9odb_70353.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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      22      5.16       5
     C    3048      2.51       5
     N     813      2.21       5
     O     979      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4862
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 727
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 7, 'TRANS': 91}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 879
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
    Chain: "L"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 821
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "B"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 879
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
    Chain: "C"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 821
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 707
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 6, 'TRANS': 89}
          Chain breaks: 1
    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: "D"
      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: 3.91, per 1000 atoms: 0.80
  Number of scatterers: 4862
  At special positions: 0
  Unit cell: (65.55, 73.6, 135.7, 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      22     16.00
     O     979      8.00
     N     813      7.00
     C    3048      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS D 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 257 " - pdb=" SG  CYS A 315 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS D 245 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H 104 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L 104 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B 104 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C 104 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 257 " - pdb=" SG  CYS D 315 " distance=2.04

  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 A 601 " - " ASN A 301 "
      " NAG D 601 " - " ASN D 301 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 569.3 milliseconds
  

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1154

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 13 sheets defined
      4.0% alpha, 36.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 320 through 323
    Processing helix  chain 'H' and resid 29 through 37
    Processing helix  chain 'B' and resid 69 through 72
    Processing helix  chain 'B' and resid 95 through 99
      removed outlier: 3.510A  pdb=" N   THR B  99 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 240
      removed outlier: 6.054A  pdb=" N   TYR A 294 " --> pdb=" O   GLY A 261 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER A 295 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 288 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 277
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 5.875A  pdb=" N   LEU H  19 " --> pdb=" O   LEU H  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 12 through 13
    Processing sheet with id=AA5, first strand: chain 'H' and resid 65 through 66
      removed outlier: 5.061A  pdb=" N   TRP H  41 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   TYR H  55 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   TRP H  39 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.667A  pdb=" N   SER L  79 " --> pdb=" O   THR L  88 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 5.124A  pdb=" N   CYS L 104 " --> pdb=" O   GLY L 119 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLY L 121 " --> pdb=" O   TYR L 102 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   TYR L 102 " --> pdb=" O   GLY L 121 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.675A  pdb=" N   ARG B  43 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   TYR B  52 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   PHE B  45 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   LEU B  50 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.741A  pdb=" N   MET C  11 " --> pdb=" O   GLU C 125 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   TRP C  41 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 19 through 23
    Processing sheet with id=AB3, first strand: chain 'D' and resid 236 through 240
    Processing sheet with id=AB4, first strand: chain 'D' and resid 276 through 277

    174 hydrogen bonds defined for protein.
    420 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: 1.42

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1534
        1.34 -     1.46: 1308
        1.46 -     1.59: 2101
        1.59 -     1.71: 0
        1.71 -     1.83: 28
  Bond restraints: 4971
  Sorted by residual:
  bond pdb=" CB  PHE L  42 "
       pdb=" CG  PHE L  42 "
    ideal  model  delta    sigma   weight residual
    1.502  1.431  0.071 2.30e-02 1.89e+03 9.57e+00
  bond pdb=" CD1 PHE L  42 "
       pdb=" CE1 PHE L  42 "
    ideal  model  delta    sigma   weight residual
    1.382  1.316  0.066 3.00e-02 1.11e+03 4.81e+00
  bond pdb=" CG  LEU C  89 "
       pdb=" CD1 LEU C  89 "
    ideal  model  delta    sigma   weight residual
    1.521  1.453  0.068 3.30e-02 9.18e+02 4.30e+00
  bond pdb=" CD1 TYR L 114 "
       pdb=" CE1 TYR L 114 "
    ideal  model  delta    sigma   weight residual
    1.382  1.322  0.060 3.00e-02 1.11e+03 4.05e+00
  bond pdb=" CB  PRO D 264 "
       pdb=" CG  PRO D 264 "
    ideal  model  delta    sigma   weight residual
    1.492  1.393  0.099 5.00e-02 4.00e+02 3.90e+00
  ... (remaining 4966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 6353
        2.38 -     4.77: 358
        4.77 -     7.15: 43
        7.15 -     9.53: 5
        9.53 -    11.92: 3
  Bond angle restraints: 6762
  Sorted by residual:
  angle pdb=" N   PRO A 264 "
        pdb=" CA  PRO A 264 "
        pdb=" C   PRO A 264 "
      ideal   model   delta    sigma   weight residual
     111.14  100.83   10.31 1.56e+00 4.11e-01 4.37e+01
  angle pdb=" N   SER A 263 "
        pdb=" CA  SER A 263 "
        pdb=" C   SER A 263 "
      ideal   model   delta    sigma   weight residual
     109.81  121.73  -11.92 2.21e+00 2.05e-01 2.91e+01
  angle pdb=" N   GLY H  47 "
        pdb=" CA  GLY H  47 "
        pdb=" C   GLY H  47 "
      ideal   model   delta    sigma   weight residual
     112.55  103.33    9.22 1.76e+00 3.23e-01 2.74e+01
  angle pdb=" N   ALA H 105 "
        pdb=" CA  ALA H 105 "
        pdb=" C   ALA H 105 "
      ideal   model   delta    sigma   weight residual
     114.12  120.51   -6.39 1.39e+00 5.18e-01 2.11e+01
  angle pdb=" N   PHE L  76 "
        pdb=" CA  PHE L  76 "
        pdb=" C   PHE L  76 "
      ideal   model   delta    sigma   weight residual
     108.48  116.68   -8.20 1.80e+00 3.09e-01 2.07e+01
  ... (remaining 6757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.61: 2813
       15.61 -    31.21: 99
       31.21 -    46.82: 31
       46.82 -    62.43: 18
       62.43 -    78.04: 7
  Dihedral angle restraints: 2968
    sinusoidal: 1153
      harmonic: 1815
  Sorted by residual:
  dihedral pdb=" CB  CYS A 245 "
           pdb=" SG  CYS A 245 "
           pdb=" SG  CYS D 333 "
           pdb=" CB  CYS D 333 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.10   51.90     1      1.00e+01 1.00e-02 3.68e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C 104 "
           pdb=" CB  CYS C 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.09   47.91     1      1.00e+01 1.00e-02 3.17e+01
  dihedral pdb=" CB  CYS A 333 "
           pdb=" SG  CYS A 333 "
           pdb=" SG  CYS D 245 "
           pdb=" CB  CYS D 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.46   47.46     1      1.00e+01 1.00e-02 3.11e+01
  ... (remaining 2965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 587
       0.068 -    0.135: 152
       0.135 -    0.202: 26
       0.202 -    0.270: 2
       0.270 -    0.337: 1
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" CA  SER A 263 "
            pdb=" N   SER A 263 "
            pdb=" C   SER A 263 "
            pdb=" CB  SER A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  ILE C  91 "
            pdb=" N   ILE C  91 "
            pdb=" C   ILE C  91 "
            pdb=" CB  ILE C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CA  TYR L 114 "
            pdb=" N   TYR L 114 "
            pdb=" C   TYR L 114 "
            pdb=" CB  TYR L 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 765 not shown)

  Planarity restraints: 856
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  40 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.05e+01
        pdb=" C   ASN B  40 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASN B  40 "    0.022 2.00e-02 2.50e+03
        pdb=" N   TRP B  41 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU L  53 "   -0.015 2.00e-02 2.50e+03   3.08e-02 9.47e+00
        pdb=" C   LEU L  53 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LEU L  53 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ILE L  54 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  41 "   -0.031 2.00e-02 2.50e+03   1.70e-02 7.20e+00
        pdb=" CG  TRP C  41 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  41 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  41 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  41 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  41 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  41 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  41 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  41 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 853 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 538
        2.75 -     3.28: 4564
        3.28 -     3.82: 7781
        3.82 -     4.36: 9523
        4.36 -     4.90: 16191
  Nonbonded interactions: 38597
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG C  67 "
            pdb=" OG1 THR C  77 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   ASP B 116 "
            pdb=" OG  SER C  52 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" NH2 ARG H  43 "
            pdb=" OE2 GLU H  51 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" O   ALA A 321 "
            pdb=" OG1 THR A 322 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" N   PHE D 262 "
            pdb=" OG1 THR D 293 "
     model   vdw
     2.452 3.120
  ... (remaining 38592 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 233 through 245 or resid 252 through 334 or resid 601))
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'L'
}

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:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.670
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
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      :  0.007   0.099   4981  Z= 0.314
  Angle     :  1.208  11.918   6784  Z= 0.707
  Chirality :  0.063   0.337    768
  Planarity :  0.006   0.032    854
  Dihedral  : 10.692  78.036   1790
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.33), residues: 615
  helix: -0.58 (1.67), residues: 8
  sheet:  0.33 (0.29), residues: 287
  loop : -0.32 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.008   TRP C  41 
 HIS   0.016   0.004   HIS L 105 
 PHE   0.026   0.005   PHE C  76 
 TYR   0.034   0.006   TYR A 294 
 ARG   0.008   0.001   ARG D 318 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (    2)
  link_NAG-ASN         : angle       1.22276 (    6)
  hydrogen bonds       : bond        0.13746 (  174)
  hydrogen bonds       : angle       8.66300 (  420)
  SS BOND              : bond        0.00742 (    8)
  SS BOND              : angle       1.64640 (   16)
  covalent geometry    : bond        0.00694 ( 4971)
  covalent geometry    : angle       1.20725 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 VAL cc_start: 0.8654 (t) cc_final: 0.8258 (t)
REVERT: A  296 LEU cc_start: 0.7644 (pp) cc_final: 0.7321 (pt)
REVERT: H   58 TYR cc_start: 0.8154 (p90) cc_final: 0.7912 (p90)
REVERT: L   13 THR cc_start: 0.7960 (m) cc_final: 0.7642 (m)
REVERT: L   42 PHE cc_start: 0.5018 (t80) cc_final: 0.3660 (t80)
REVERT: L   75 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7748 (ppt170)
REVERT: L  105 HIS cc_start: 0.4176 (m170) cc_final: 0.3671 (m170)
REVERT: L  122 THR cc_start: 0.8195 (m) cc_final: 0.7746 (p)
REVERT: B   55 TYR cc_start: 0.7105 (t80) cc_final: 0.6665 (t80)
REVERT: B   84 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8161 (mmpt)
REVERT: B   92 ASN cc_start: 0.8133 (m-40) cc_final: 0.7431 (m-40)
REVERT: B  115 PHE cc_start: 0.8221 (m-80) cc_final: 0.6626 (m-80)
REVERT: C   11 MET cc_start: 0.6825 (mtm) cc_final: 0.6606 (mtp)
REVERT: C   38 ASN cc_start: 0.7671 (m-40) cc_final: 0.7076 (m110)
REVERT: C  106 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6784 (mm-40)
REVERT: D  313 TYR cc_start: 0.8446 (m-80) cc_final: 0.7896 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.1872
  time to fit residues: 61.7004
Evaluate side-chains
  158 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 ASN
H  92 ASN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  28 ASN
B   5 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.095977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.081573 restraints weight = 14474.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.084462 restraints weight = 8298.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.086442 restraints weight = 5591.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4981  Z= 0.195
  Angle     :  0.885   8.870   6784  Z= 0.467
  Chirality :  0.051   0.164    768
  Planarity :  0.006   0.066    854
  Dihedral  :  5.989  42.509    729
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 15.06 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.33), residues: 615
  helix:  1.03 (2.26), residues: 8
  sheet:  0.20 (0.29), residues: 303
  loop : -0.84 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP H 118 
 HIS   0.008   0.002   HIS A 319 
 PHE   0.024   0.003   PHE H 115 
 TYR   0.032   0.003   TYR B  88 
 ARG   0.007   0.001   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00653 (    2)
  link_NAG-ASN         : angle       3.04253 (    6)
  hydrogen bonds       : bond        0.05188 (  174)
  hydrogen bonds       : angle       7.32314 (  420)
  SS BOND              : bond        0.00362 (    8)
  SS BOND              : angle       1.29281 (   16)
  covalent geometry    : bond        0.00447 ( 4971)
  covalent geometry    : angle       0.88004 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7755 (mmm)
REVERT: L  107 TYR cc_start: 0.8558 (p90) cc_final: 0.8212 (p90)
REVERT: B    5 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7250 (mp10)
REVERT: B  115 PHE cc_start: 0.8225 (m-80) cc_final: 0.7802 (m-80)
REVERT: C    4 MET cc_start: 0.7558 (tpp) cc_final: 0.7198 (tpp)
REVERT: C   98 ASP cc_start: 0.7899 (t70) cc_final: 0.7667 (t70)
REVERT: D  328 ASP cc_start: 0.7662 (m-30) cc_final: 0.7347 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 189
  average time/residue: 0.1629
  time to fit residues: 38.9617
Evaluate side-chains
  154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0060
   chunk 22 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 ASN
B   5 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.096492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.081372 restraints weight = 14544.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.084209 restraints weight = 8513.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086156 restraints weight = 5849.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4981  Z= 0.170
  Angle     :  0.820   8.969   6784  Z= 0.429
  Chirality :  0.049   0.170    768
  Planarity :  0.006   0.054    854
  Dihedral  :  5.730  40.460    729
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 18.33 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.33), residues: 615
  helix:  0.02 (1.89), residues: 8
  sheet:  0.04 (0.30), residues: 289
  loop : -0.86 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP H  39 
 HIS   0.005   0.002   HIS A 319 
 PHE   0.016   0.002   PHE C  87 
 TYR   0.028   0.002   TYR B  88 
 ARG   0.006   0.001   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       1.90076 (    6)
  hydrogen bonds       : bond        0.04802 (  174)
  hydrogen bonds       : angle       6.96665 (  420)
  SS BOND              : bond        0.00449 (    8)
  SS BOND              : angle       1.50151 (   16)
  covalent geometry    : bond        0.00383 ( 4971)
  covalent geometry    : angle       0.81570 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 VAL cc_start: 0.8697 (t) cc_final: 0.7260 (t)
REVERT: H   89 LEU cc_start: 0.6255 (tp) cc_final: 0.5879 (tt)
REVERT: L  107 TYR cc_start: 0.8502 (p90) cc_final: 0.8234 (p90)
REVERT: B    5 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7221 (mp-120)
REVERT: B  103 TYR cc_start: 0.8630 (m-80) cc_final: 0.8420 (m-80)
REVERT: C   98 ASP cc_start: 0.7997 (t70) cc_final: 0.7547 (t70)
REVERT: C  105 HIS cc_start: 0.7058 (t-170) cc_final: 0.6778 (t-170)
REVERT: C  106 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7095 (tm-30)
REVERT: D  313 TYR cc_start: 0.7956 (m-80) cc_final: 0.7652 (m-80)
REVERT: D  328 ASP cc_start: 0.7854 (m-30) cc_final: 0.7329 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1497
  time to fit residues: 32.3604
Evaluate side-chains
  156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain D residue  240 LEU
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0270
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0770
   chunk 44 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:   30.0000
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
A 241 HIS
H  92 ASN
B   3 GLN
B   5 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.096787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.081428 restraints weight = 14736.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.084322 restraints weight = 8683.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.086365 restraints weight = 5966.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4981  Z= 0.159
  Angle     :  0.784   8.518   6784  Z= 0.413
  Chirality :  0.049   0.166    768
  Planarity :  0.006   0.053    854
  Dihedral  :  5.674  40.265    729
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 21.60 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -0.95 (0.33), residues: 615
  helix: -0.93 (1.55), residues: 8
  sheet: -0.07 (0.30), residues: 291
  loop : -1.14 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP H  39 
 HIS   0.005   0.002   HIS A 319 
 PHE   0.039   0.003   PHE B 115 
 TYR   0.026   0.002   TYR B  88 
 ARG   0.005   0.001   ARG C  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    2)
  link_NAG-ASN         : angle       1.58475 (    6)
  hydrogen bonds       : bond        0.04497 (  174)
  hydrogen bonds       : angle       6.97861 (  420)
  SS BOND              : bond        0.00463 (    8)
  SS BOND              : angle       1.19304 (   16)
  covalent geometry    : bond        0.00365 ( 4971)
  covalent geometry    : angle       0.78220 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 TRP cc_start: 0.6262 (t60) cc_final: 0.5511 (t60)
REVERT: H   58 TYR cc_start: 0.7734 (p90) cc_final: 0.7339 (p90)
REVERT: L    4 MET cc_start: 0.7949 (mmm) cc_final: 0.7709 (mmm)
REVERT: L   18 ARG cc_start: 0.6843 (ttp80) cc_final: 0.6473 (ttp80)
REVERT: B    5 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7304 (mp-120)
REVERT: B  103 TYR cc_start: 0.8592 (m-80) cc_final: 0.8360 (m-80)
REVERT: B  115 PHE cc_start: 0.8211 (m-80) cc_final: 0.7701 (m-80)
REVERT: C   18 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7648 (mmm-85)
REVERT: C   98 ASP cc_start: 0.8015 (t70) cc_final: 0.7511 (t70)
REVERT: C  106 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7095 (tm-30)
REVERT: D  272 LEU cc_start: 0.9271 (mp) cc_final: 0.9045 (mt)
REVERT: D  328 ASP cc_start: 0.7899 (m-30) cc_final: 0.7411 (m-30)
  outliers start: 30
  outliers final: 21
  residues processed: 156
  average time/residue: 0.1678
  time to fit residues: 33.0680
Evaluate side-chains
  146 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   71 VAL
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  274 ASP
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0470
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.9480

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

Flipped N/Q/H residues before XYZ refinement:
H  92 ASN
B   5 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.094709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.079729 restraints weight = 14699.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.082411 restraints weight = 8795.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.084324 restraints weight = 6129.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.6239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4981  Z= 0.171
  Angle     :  0.799   9.502   6784  Z= 0.411
  Chirality :  0.048   0.165    768
  Planarity :  0.005   0.057    854
  Dihedral  :  5.574  39.946    729
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.23 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -1.10 (0.33), residues: 615
  helix: -0.67 (1.66), residues: 8
  sheet: -0.13 (0.30), residues: 292
  loop : -1.30 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP H  39 
 HIS   0.004   0.002   HIS C 105 
 PHE   0.023   0.003   PHE L  76 
 TYR   0.021   0.002   TYR L  68 
 ARG   0.004   0.000   ARG D 318 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    2)
  link_NAG-ASN         : angle       1.38238 (    6)
  hydrogen bonds       : bond        0.04411 (  174)
  hydrogen bonds       : angle       6.86945 (  420)
  SS BOND              : bond        0.00468 (    8)
  SS BOND              : angle       1.15114 (   16)
  covalent geometry    : bond        0.00400 ( 4971)
  covalent geometry    : angle       0.79728 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 TRP cc_start: 0.6603 (t60) cc_final: 0.5551 (t60)
REVERT: L    4 MET cc_start: 0.8045 (mmm) cc_final: 0.7812 (mmm)
REVERT: B  103 TYR cc_start: 0.8562 (m-80) cc_final: 0.8339 (m-80)
REVERT: B  115 PHE cc_start: 0.8234 (m-80) cc_final: 0.7933 (m-80)
REVERT: C   98 ASP cc_start: 0.8099 (t70) cc_final: 0.7565 (t70)
REVERT: C  106 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7115 (tp-100)
REVERT: D  327 GLU cc_start: 0.8015 (pm20) cc_final: 0.7764 (pm20)
REVERT: D  328 ASP cc_start: 0.7872 (m-30) cc_final: 0.7494 (m-30)
  outliers start: 26
  outliers final: 21
  residues processed: 140
  average time/residue: 0.1759
  time to fit residues: 30.9261
Evaluate side-chains
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue   88 TYR
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   71 VAL
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0020
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0870
   overall best weight:    0.4766

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

Flipped N/Q/H residues before XYZ refinement:
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.096129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.080903 restraints weight = 14919.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.083644 restraints weight = 8838.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.085602 restraints weight = 6146.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.6485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4981  Z= 0.146
  Angle     :  0.787   9.304   6784  Z= 0.402
  Chirality :  0.048   0.173    768
  Planarity :  0.005   0.055    854
  Dihedral  :  5.412  37.875    729
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.77 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -1.11 (0.33), residues: 615
  helix: -0.75 (1.64), residues: 8
  sheet: -0.05 (0.30), residues: 291
  loop : -1.40 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  39 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.022   0.003   PHE B 115 
 TYR   0.018   0.002   TYR L  68 
 ARG   0.003   0.001   ARG C  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    2)
  link_NAG-ASN         : angle       1.24591 (    6)
  hydrogen bonds       : bond        0.04148 (  174)
  hydrogen bonds       : angle       6.81611 (  420)
  SS BOND              : bond        0.00553 (    8)
  SS BOND              : angle       1.19420 (   16)
  covalent geometry    : bond        0.00339 ( 4971)
  covalent geometry    : angle       0.78541 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.8732 (mt) cc_final: 0.8513 (mt)
REVERT: H   53 MET cc_start: 0.7872 (ptm) cc_final: 0.6549 (ppp)
REVERT: L    4 MET cc_start: 0.8042 (mmm) cc_final: 0.7824 (mmm)
REVERT: L  101 GLU cc_start: 0.6397 (pm20) cc_final: 0.5974 (pm20)
REVERT: B  103 TYR cc_start: 0.8493 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  107 ASP cc_start: 0.8082 (t0) cc_final: 0.7564 (t0)
REVERT: B  115 PHE cc_start: 0.8173 (m-80) cc_final: 0.7525 (m-80)
REVERT: C    4 MET cc_start: 0.7157 (tpp) cc_final: 0.6519 (tpp)
REVERT: C   18 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7823 (mmm-85)
REVERT: C   97 GLU cc_start: 0.8369 (mp0) cc_final: 0.8152 (mp0)
REVERT: C   98 ASP cc_start: 0.8152 (t70) cc_final: 0.7649 (t70)
REVERT: C  106 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: D  272 LEU cc_start: 0.9119 (mt) cc_final: 0.8781 (mt)
REVERT: D  327 GLU cc_start: 0.7991 (pm20) cc_final: 0.7694 (pm20)
REVERT: D  328 ASP cc_start: 0.7895 (m-30) cc_final: 0.7439 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 143
  average time/residue: 0.1579
  time to fit residues: 28.9697
Evaluate side-chains
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue   92 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    0.0170
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0970
   chunk 36 optimal weight:    0.0670
   chunk 37 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
H  92 ASN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.097482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.082570 restraints weight = 14793.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.085342 restraints weight = 8713.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.087329 restraints weight = 6015.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.6766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4981  Z= 0.141
  Angle     :  0.780   9.398   6784  Z= 0.397
  Chirality :  0.048   0.182    768
  Planarity :  0.005   0.059    854
  Dihedral  :  5.230  36.915    729
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.59 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -1.05 (0.33), residues: 615
  helix: -0.63 (1.71), residues: 8
  sheet: -0.05 (0.30), residues: 300
  loop : -1.35 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H  39 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.024   0.002   PHE L  42 
 TYR   0.018   0.002   TYR A 294 
 ARG   0.007   0.001   ARG C  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    2)
  link_NAG-ASN         : angle       1.18995 (    6)
  hydrogen bonds       : bond        0.03998 (  174)
  hydrogen bonds       : angle       6.76107 (  420)
  SS BOND              : bond        0.00553 (    8)
  SS BOND              : angle       1.23682 (   16)
  covalent geometry    : bond        0.00328 ( 4971)
  covalent geometry    : angle       0.77858 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   51 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7829 (mm-30)
REVERT: L   11 MET cc_start: 0.7425 (ppp) cc_final: 0.7044 (ppp)
REVERT: L   21 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.6961 (t)
REVERT: B  103 TYR cc_start: 0.8508 (m-80) cc_final: 0.8268 (m-80)
REVERT: B  115 PHE cc_start: 0.8322 (m-80) cc_final: 0.7796 (m-80)
REVERT: C    4 MET cc_start: 0.7211 (tpp) cc_final: 0.6604 (tpp)
REVERT: C   18 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7990 (mmm-85)
REVERT: C   97 GLU cc_start: 0.8329 (mp0) cc_final: 0.8100 (mp0)
REVERT: C   98 ASP cc_start: 0.8151 (t70) cc_final: 0.7607 (t70)
REVERT: C  106 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: D  272 LEU cc_start: 0.9104 (mt) cc_final: 0.8584 (mt)
REVERT: D  327 GLU cc_start: 0.7978 (pm20) cc_final: 0.7588 (pm20)
REVERT: D  328 ASP cc_start: 0.7938 (m-30) cc_final: 0.7445 (m-30)
  outliers start: 20
  outliers final: 16
  residues processed: 143
  average time/residue: 0.1679
  time to fit residues: 30.9765
Evaluate side-chains
  138 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.096160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.081384 restraints weight = 14954.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.084120 restraints weight = 8740.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.086071 restraints weight = 6039.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.6939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4981  Z= 0.163
  Angle     :  0.800  10.344   6784  Z= 0.408
  Chirality :  0.048   0.180    768
  Planarity :  0.005   0.058    854
  Dihedral  :  5.298  37.462    729
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 24.50 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -0.98 (0.33), residues: 615
  helix: -0.41 (1.77), residues: 8
  sheet:  0.05 (0.30), residues: 294
  loop : -1.35 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP H  39 
 HIS   0.004   0.002   HIS A 319 
 PHE   0.051   0.003   PHE L  42 
 TYR   0.018   0.002   TYR A 294 
 ARG   0.009   0.001   ARG C  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    2)
  link_NAG-ASN         : angle       1.18584 (    6)
  hydrogen bonds       : bond        0.04108 (  174)
  hydrogen bonds       : angle       6.78292 (  420)
  SS BOND              : bond        0.00498 (    8)
  SS BOND              : angle       1.15686 (   16)
  covalent geometry    : bond        0.00386 ( 4971)
  covalent geometry    : angle       0.79867 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   53 MET cc_start: 0.7862 (ptm) cc_final: 0.6578 (ppp)
REVERT: B  107 ASP cc_start: 0.7991 (t70) cc_final: 0.7237 (t0)
REVERT: B  115 PHE cc_start: 0.8316 (m-80) cc_final: 0.7833 (m-80)
REVERT: C    4 MET cc_start: 0.7252 (tpp) cc_final: 0.6627 (tpp)
REVERT: C   67 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7877 (mtt90)
REVERT: C   97 GLU cc_start: 0.8351 (mp0) cc_final: 0.8116 (mp0)
REVERT: C   98 ASP cc_start: 0.8202 (t70) cc_final: 0.7662 (t70)
REVERT: D  272 LEU cc_start: 0.9212 (mt) cc_final: 0.8998 (mt)
REVERT: D  306 ASP cc_start: 0.8054 (t0) cc_final: 0.7709 (t0)
REVERT: D  313 TYR cc_start: 0.7734 (m-80) cc_final: 0.7516 (m-80)
REVERT: D  327 GLU cc_start: 0.8040 (pm20) cc_final: 0.7690 (pm20)
REVERT: D  328 ASP cc_start: 0.7957 (m-30) cc_final: 0.7466 (m-30)
  outliers start: 21
  outliers final: 17
  residues processed: 140
  average time/residue: 0.1610
  time to fit residues: 28.8045
Evaluate side-chains
  136 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Chi-restraints excluded: chain D residue  323 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0770
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0370
   chunk 3 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.3016

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

Flipped N/Q/H residues before XYZ refinement:
** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.098703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.084208 restraints weight = 14712.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.087054 restraints weight = 8572.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.089012 restraints weight = 5873.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.7231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4981  Z= 0.144
  Angle     :  0.803  10.879   6784  Z= 0.406
  Chirality :  0.048   0.188    768
  Planarity :  0.005   0.057    854
  Dihedral  :  5.265  35.857    729
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.68 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -1.14 (0.33), residues: 615
  helix: -1.40 (1.36), residues: 8
  sheet: -0.05 (0.29), residues: 303
  loop : -1.46 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  39 
 HIS   0.004   0.002   HIS C 105 
 PHE   0.016   0.002   PHE B 115 
 TYR   0.019   0.001   TYR A 294 
 ARG   0.009   0.001   ARG C  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    2)
  link_NAG-ASN         : angle       1.17035 (    6)
  hydrogen bonds       : bond        0.03930 (  174)
  hydrogen bonds       : angle       6.89817 (  420)
  SS BOND              : bond        0.00540 (    8)
  SS BOND              : angle       1.20474 (   16)
  covalent geometry    : bond        0.00331 ( 4971)
  covalent geometry    : angle       0.80099 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   89 LEU cc_start: 0.6448 (mt) cc_final: 0.5894 (mt)
REVERT: C    4 MET cc_start: 0.7254 (tpp) cc_final: 0.6708 (tpp)
REVERT: C   67 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7732 (mtt90)
REVERT: C   97 GLU cc_start: 0.8298 (mp0) cc_final: 0.8088 (mp0)
REVERT: C   98 ASP cc_start: 0.8230 (t70) cc_final: 0.7666 (t70)
REVERT: D  272 LEU cc_start: 0.8968 (mt) cc_final: 0.8766 (mt)
REVERT: D  306 ASP cc_start: 0.8029 (t0) cc_final: 0.7716 (t0)
REVERT: D  327 GLU cc_start: 0.7995 (pm20) cc_final: 0.7697 (pm20)
REVERT: D  328 ASP cc_start: 0.7958 (m-30) cc_final: 0.7444 (m-30)
REVERT: D  331 LYS cc_start: 0.8203 (tptp) cc_final: 0.7982 (tppt)
  outliers start: 18
  outliers final: 17
  residues processed: 139
  average time/residue: 0.1631
  time to fit residues: 29.0189
Evaluate side-chains
  135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue   92 ASN
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 ASN
** C 106 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.096407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.081717 restraints weight = 15077.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.084479 restraints weight = 8929.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.086448 restraints weight = 6194.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.7346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4981  Z= 0.173
  Angle     :  0.835   9.904   6784  Z= 0.431
  Chirality :  0.049   0.182    768
  Planarity :  0.006   0.060    854
  Dihedral  :  5.353  36.571    729
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 25.23 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -1.14 (0.33), residues: 615
  helix: -0.58 (1.69), residues: 7
  sheet: -0.11 (0.30), residues: 294
  loop : -1.39 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP H  39 
 HIS   0.006   0.002   HIS L 105 
 PHE   0.024   0.003   PHE B 115 
 TYR   0.019   0.002   TYR A 294 
 ARG   0.009   0.001   ARG C  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    2)
  link_NAG-ASN         : angle       1.21734 (    6)
  hydrogen bonds       : bond        0.04060 (  174)
  hydrogen bonds       : angle       6.98776 (  420)
  SS BOND              : bond        0.00452 (    8)
  SS BOND              : angle       1.08424 (   16)
  covalent geometry    : bond        0.00409 ( 4971)
  covalent geometry    : angle       0.83356 ( 6762)

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

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

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1230 Ramachandran restraints generated.
    615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7756 (t)
REVERT: H   53 MET cc_start: 0.7847 (ptm) cc_final: 0.6585 (ppp)
REVERT: H   58 TYR cc_start: 0.8126 (p90) cc_final: 0.7913 (p90)
REVERT: L   89 LEU cc_start: 0.6467 (mt) cc_final: 0.6014 (mt)
REVERT: C    4 MET cc_start: 0.7325 (tpp) cc_final: 0.7012 (tpp)
REVERT: C   97 GLU cc_start: 0.8322 (mp0) cc_final: 0.8111 (mp0)
REVERT: C   98 ASP cc_start: 0.8274 (t70) cc_final: 0.7726 (t70)
REVERT: D  327 GLU cc_start: 0.8122 (pm20) cc_final: 0.7792 (pm20)
REVERT: D  328 ASP cc_start: 0.7977 (m-30) cc_final: 0.7467 (m-30)
  outliers start: 19
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1518
  time to fit residues: 25.8036
Evaluate side-chains
  133 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  259 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain C residue   55 TYR
Chi-restraints excluded: chain C residue   77 THR
Chi-restraints excluded: chain C residue   93 ASN
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  276 VAL
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  305 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 106 GLN ** 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 = 0.3751 r_free = 0.3751 target = 0.096253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.081571 restraints weight = 14990.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.084301 restraints weight = 8920.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.086246 restraints weight = 6208.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.7352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.103   4981  Z= 0.273
  Angle     :  1.273  59.197   6784  Z= 0.756
  Chirality :  0.050   0.262    768
  Planarity :  0.006   0.059    854
  Dihedral  :  5.465  36.535    729
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 22.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.50 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.41 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.17 %

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: -1.15 (0.33), residues: 615
  helix: -0.94 (1.71), residues: 7
  sheet: -0.12 (0.30), residues: 294
  loop : -1.39 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP H  39 
 HIS   0.005   0.002   HIS L 105 
 PHE   0.031   0.003   PHE B 115 
 TYR   0.028   0.002   TYR C  66 
 ARG   0.009   0.001   ARG H 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    2)
  link_NAG-ASN         : angle       1.21686 (    6)
  hydrogen bonds       : bond        0.04071 (  174)
  hydrogen bonds       : angle       6.98843 (  420)
  SS BOND              : bond        0.00439 (    8)
  SS BOND              : angle       1.08479 (   16)
  covalent geometry    : bond        0.00564 ( 4971)
  covalent geometry    : angle       1.27341 ( 6762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2108.90 seconds
wall clock time: 37 minutes 47.84 seconds (2267.84 seconds total)