Starting phenix.real_space_refine
on Wed Sep 17 05:14:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odb_70353/09_2025/9odb_70353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odb_70353/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odb_70353/09_2025/9odb_70353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odb_70353/09_2025/9odb_70353.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odb_70353/09_2025/9odb_70353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odb_70353/09_2025/9odb_70353.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.34
  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: 0.44
  Conformation dependent library (CDL) restraints added in 208.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.18
  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: 0.57

  Time building geometry restraints manager: 0.57 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 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:             1.820
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.570
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.160
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (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
 ARG   0.008   0.001   ARG D 318 
 TYR   0.034   0.006   TYR A 294 
 PHE   0.026   0.005   PHE C  76 
 TRP   0.031   0.008   TRP C  41 
 HIS   0.016   0.004   HIS L 105 

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

*********************** 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  : 0.204 
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: 0.8264 (t)
REVERT: A  296 LEU cc_start: 0.7644 (pp) cc_final: 0.7314 (pt)
REVERT: H   58 TYR cc_start: 0.8154 (p90) cc_final: 0.7918 (p90)
REVERT: L   13 THR cc_start: 0.7960 (m) cc_final: 0.7645 (m)
REVERT: L   42 PHE cc_start: 0.5018 (t80) cc_final: 0.3674 (t80)
REVERT: L   75 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7744 (ppt170)
REVERT: L  105 HIS cc_start: 0.4176 (m170) cc_final: 0.3665 (m170)
REVERT: L  122 THR cc_start: 0.8195 (m) cc_final: 0.7732 (p)
REVERT: L  123 LYS cc_start: 0.7766 (tttt) cc_final: 0.7564 (ptmt)
REVERT: B   55 TYR cc_start: 0.7105 (t80) cc_final: 0.6604 (t80)
REVERT: B   84 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8162 (mmpt)
REVERT: B   92 ASN cc_start: 0.8133 (m-40) cc_final: 0.7426 (m-40)
REVERT: C   11 MET cc_start: 0.6825 (mtm) cc_final: 0.6609 (mtp)
REVERT: C   38 ASN cc_start: 0.7671 (m-40) cc_final: 0.7370 (m110)
REVERT: C  105 HIS cc_start: 0.6963 (t-170) cc_final: 0.6652 (t-170)
REVERT: C  106 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6650 (mm-40)
REVERT: D  313 TYR cc_start: 0.8446 (m-80) cc_final: 0.7902 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.0853
  time to fit residues: 28.2686
Evaluate side-chains
  155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
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
** 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  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.094695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.080048 restraints weight = 14716.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.082880 restraints weight = 8513.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.084884 restraints weight = 5820.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.086288 restraints weight = 4381.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.087328 restraints weight = 3517.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   4981  Z= 0.219
  Angle     :  0.908   8.491   6784  Z= 0.477
  Chirality :  0.051   0.165    768
  Planarity :  0.006   0.068    854
  Dihedral  :  6.071  42.808    729
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.61 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.33), residues: 615
  helix:  0.79 (2.23), residues: 8
  sheet:  0.15 (0.29), residues: 300
  loop : -0.78 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  18 
 TYR   0.031   0.003   TYR B  88 
 PHE   0.023   0.003   PHE L  76 
 TRP   0.020   0.003   TRP B 118 
 HIS   0.008   0.002   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 4971)
  covalent geometry    : angle       0.90195 ( 6762)
  SS BOND              : bond        0.00564 (    8)
  SS BOND              : angle       1.29493 (   16)
  hydrogen bonds       : bond        0.05349 (  174)
  hydrogen bonds       : angle       7.50818 (  420)
  link_NAG-ASN         : bond        0.00654 (    2)
  link_NAG-ASN         : angle       3.19559 (    6)

*********************** 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
  197 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.196 
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: H   39 TRP cc_start: 0.5957 (t60) cc_final: 0.5574 (t60)
REVERT: L    4 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7775 (mmm)
REVERT: L  107 TYR cc_start: 0.8605 (p90) cc_final: 0.8266 (p90)
REVERT: B    5 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7332 (mp10)
REVERT: B   53 MET cc_start: 0.6628 (mtm) cc_final: 0.6342 (mtm)
REVERT: B   56 ILE cc_start: 0.8550 (tt) cc_final: 0.8184 (tt)
REVERT: B   71 LEU cc_start: 0.8332 (mt) cc_final: 0.7685 (mt)
REVERT: B  118 TRP cc_start: 0.8258 (m-10) cc_final: 0.8022 (m100)
REVERT: C    4 MET cc_start: 0.7636 (tpp) cc_final: 0.7306 (tpp)
REVERT: D  311 LYS cc_start: 0.7992 (tttt) cc_final: 0.7695 (ttmm)
REVERT: D  328 ASP cc_start: 0.7693 (m-30) cc_final: 0.7367 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 184
  average time/residue: 0.0729
  time to fit residues: 17.1649
Evaluate side-chains
  149 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 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    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   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 54 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0970
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 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 = 0.3724 r_free = 0.3724 target = 0.095901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.081187 restraints weight = 14714.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084066 restraints weight = 8529.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086001 restraints weight = 5799.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.087383 restraints weight = 4376.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.088382 restraints weight = 3531.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4981  Z= 0.170
  Angle     :  0.834   9.148   6784  Z= 0.433
  Chirality :  0.049   0.175    768
  Planarity :  0.006   0.057    854
  Dihedral  :  5.892  40.531    729
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 19.96 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.33), residues: 615
  helix:  0.02 (1.89), residues: 8
  sheet:  0.02 (0.29), residues: 300
  loop : -0.94 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  43 
 TYR   0.028   0.003   TYR B  88 
 PHE   0.016   0.003   PHE L  42 
 TRP   0.016   0.002   TRP B 118 
 HIS   0.009   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4971)
  covalent geometry    : angle       0.83112 ( 6762)
  SS BOND              : bond        0.00608 (    8)
  SS BOND              : angle       1.30917 (   16)
  hydrogen bonds       : bond        0.04897 (  174)
  hydrogen bonds       : angle       7.24200 (  420)
  link_NAG-ASN         : bond        0.00397 (    2)
  link_NAG-ASN         : angle       1.90713 (    6)

*********************** 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
  174 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 VAL cc_start: 0.8676 (t) cc_final: 0.7524 (t)
REVERT: L   19 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.7023 (m)
REVERT: L  107 TYR cc_start: 0.8481 (p90) cc_final: 0.8252 (p90)
REVERT: B  103 TYR cc_start: 0.8775 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  115 PHE cc_start: 0.8357 (m-10) cc_final: 0.8022 (m-80)
REVERT: C  101 GLU cc_start: 0.6579 (tp30) cc_final: 0.6266 (tm-30)
REVERT: C  103 PHE cc_start: 0.7472 (m-80) cc_final: 0.6818 (m-80)
REVERT: D  313 TYR cc_start: 0.7988 (m-80) cc_final: 0.7665 (m-80)
REVERT: D  327 GLU cc_start: 0.8261 (pm20) cc_final: 0.8005 (pm20)
REVERT: D  328 ASP cc_start: 0.7886 (m-30) cc_final: 0.7305 (m-30)
  outliers start: 26
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0746
  time to fit residues: 15.1389
Evaluate side-chains
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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   19 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   89 LEU
Chi-restraints excluded: chain D residue  240 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0470
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:   30.0000
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.095973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.080962 restraints weight = 14611.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.083756 restraints weight = 8647.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.085702 restraints weight = 5962.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.087078 restraints weight = 4519.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.088010 restraints weight = 3664.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.5974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4981  Z= 0.159
  Angle     :  0.780  10.109   6784  Z= 0.408
  Chirality :  0.048   0.161    768
  Planarity :  0.006   0.055    854
  Dihedral  :  5.783  40.606    729
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 21.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.33), residues: 615
  helix: -0.48 (1.68), residues: 8
  sheet: -0.17 (0.28), residues: 315
  loop : -1.17 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  18 
 TYR   0.023   0.002   TYR B  52 
 PHE   0.022   0.003   PHE L  76 
 TRP   0.053   0.003   TRP H  39 
 HIS   0.006   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4971)
  covalent geometry    : angle       0.77794 ( 6762)
  SS BOND              : bond        0.00501 (    8)
  SS BOND              : angle       1.07920 (   16)
  hydrogen bonds       : bond        0.04562 (  174)
  hydrogen bonds       : angle       7.18168 (  420)
  link_NAG-ASN         : bond        0.00235 (    2)
  link_NAG-ASN         : angle       1.51012 (    6)

*********************** 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
  166 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  262 PHE cc_start: 0.7411 (p90) cc_final: 0.7127 (p90)
REVERT: H    3 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8100 (mp10)
REVERT: H   58 TYR cc_start: 0.7549 (p90) cc_final: 0.7181 (p90)
REVERT: L    4 MET cc_start: 0.7886 (mmm) cc_final: 0.7657 (mmm)
REVERT: B    5 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7211 (mp-120)
REVERT: B  115 PHE cc_start: 0.8487 (m-10) cc_final: 0.8254 (m-80)
REVERT: C   18 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7667 (mmm-85)
REVERT: C  101 GLU cc_start: 0.6742 (tp30) cc_final: 0.6460 (tm-30)
REVERT: C  103 PHE cc_start: 0.7533 (m-80) cc_final: 0.6653 (m-80)
REVERT: D  327 GLU cc_start: 0.8194 (pm20) cc_final: 0.7896 (pm20)
REVERT: D  328 ASP cc_start: 0.7928 (m-30) cc_final: 0.7443 (m-30)
  outliers start: 29
  outliers final: 21
  residues processed: 149
  average time/residue: 0.0702
  time to fit residues: 13.6930
Evaluate side-chains
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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    4 LEU
Chi-restraints excluded: chain H residue   78 ILE
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   21 LEU
Chi-restraints excluded: chain B residue   72 LYS
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.091461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.076516 restraints weight = 14994.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.079096 restraints weight = 9098.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.080934 restraints weight = 6374.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.082236 restraints weight = 4933.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.083187 restraints weight = 4051.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.6408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   4981  Z= 0.225
  Angle     :  0.813   9.212   6784  Z= 0.427
  Chirality :  0.049   0.183    768
  Planarity :  0.006   0.058    854
  Dihedral  :  5.926  40.965    729
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 20.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 22.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.34), residues: 615
  helix: -0.56 (1.67), residues: 8
  sheet: -0.18 (0.29), residues: 305
  loop : -1.40 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  18 
 TYR   0.026   0.003   TYR L  68 
 PHE   0.018   0.003   PHE B 115 
 TRP   0.059   0.004   TRP H  39 
 HIS   0.004   0.002   HIS L 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 4971)
  covalent geometry    : angle       0.81133 ( 6762)
  SS BOND              : bond        0.00396 (    8)
  SS BOND              : angle       1.04634 (   16)
  hydrogen bonds       : bond        0.04585 (  174)
  hydrogen bonds       : angle       7.31721 (  420)
  link_NAG-ASN         : bond        0.00195 (    2)
  link_NAG-ASN         : angle       1.31203 (    6)

*********************** 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
  156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.8001 (mmm) cc_final: 0.7779 (mmm)
REVERT: B  103 TYR cc_start: 0.8719 (m-80) cc_final: 0.8484 (m-10)
REVERT: C    4 MET cc_start: 0.7412 (tpp) cc_final: 0.6611 (tpp)
REVERT: C  101 GLU cc_start: 0.6901 (tp30) cc_final: 0.6418 (tm-30)
REVERT: C  103 PHE cc_start: 0.7774 (m-80) cc_final: 0.6906 (m-80)
REVERT: D  327 GLU cc_start: 0.8206 (pm20) cc_final: 0.7844 (pm20)
REVERT: D  328 ASP cc_start: 0.7783 (m-30) cc_final: 0.7394 (m-30)
  outliers start: 34
  outliers final: 27
  residues processed: 138
  average time/residue: 0.0728
  time to fit residues: 13.0543
Evaluate side-chains
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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    4 LEU
Chi-restraints excluded: chain H residue   78 ILE
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   19 VAL
Chi-restraints excluded: chain L residue   90 THR
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   72 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0570
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 105 HIS ** 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 = 0.3701 r_free = 0.3701 target = 0.094348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.079500 restraints weight = 15098.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.082237 restraints weight = 8933.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.084131 restraints weight = 6193.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.085349 restraints weight = 4718.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.086379 restraints weight = 3884.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.6709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4981  Z= 0.159
  Angle     :  0.802   9.694   6784  Z= 0.413
  Chirality :  0.049   0.209    768
  Planarity :  0.005   0.055    854
  Dihedral  :  5.730  38.637    729
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 23.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.33), residues: 615
  helix: -0.66 (1.66), residues: 8
  sheet: -0.14 (0.29), residues: 304
  loop : -1.61 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  67 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.032   0.003   PHE B 115 
 TRP   0.037   0.002   TRP H  39 
 HIS   0.004   0.002   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4971)
  covalent geometry    : angle       0.80047 ( 6762)
  SS BOND              : bond        0.00514 (    8)
  SS BOND              : angle       1.09484 (   16)
  hydrogen bonds       : bond        0.04293 (  174)
  hydrogen bonds       : angle       7.09781 (  420)
  link_NAG-ASN         : bond        0.00182 (    2)
  link_NAG-ASN         : angle       1.18520 (    6)

*********************** 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
  149 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.7296 (mp10) cc_final: 0.7021 (mp10)
REVERT: L    4 MET cc_start: 0.7949 (mmm) cc_final: 0.7679 (mmm)
REVERT: C   18 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7788 (mmm-85)
REVERT: C   89 LEU cc_start: 0.8613 (mt) cc_final: 0.8401 (mt)
REVERT: C   97 GLU cc_start: 0.8291 (mp0) cc_final: 0.8044 (mp0)
REVERT: C  101 GLU cc_start: 0.6924 (tp30) cc_final: 0.6450 (tm-30)
REVERT: C  103 PHE cc_start: 0.7791 (m-80) cc_final: 0.7082 (m-80)
REVERT: D  327 GLU cc_start: 0.8081 (pm20) cc_final: 0.7710 (pm20)
REVERT: D  328 ASP cc_start: 0.7867 (m-30) cc_final: 0.7449 (m-30)
  outliers start: 24
  outliers final: 23
  residues processed: 134
  average time/residue: 0.0780
  time to fit residues: 13.1667
Evaluate side-chains
  137 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  280 LEU
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   78 ILE
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 B residue   21 LEU
Chi-restraints excluded: chain B residue   72 LYS
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  107 TYR
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 42 optimal weight:    8.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 34 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H  85 ASN
H  92 ASN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 105 HIS ** 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 = 0.3700 r_free = 0.3700 target = 0.094369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.079744 restraints weight = 14906.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.082417 restraints weight = 8844.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.084272 restraints weight = 6139.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.085596 restraints weight = 4674.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.086560 restraints weight = 3803.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.6876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4981  Z= 0.159
  Angle     :  0.804  10.814   6784  Z= 0.415
  Chirality :  0.050   0.273    768
  Planarity :  0.005   0.059    854
  Dihedral  :  5.679  38.420    729
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 22.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.34), residues: 615
  helix: -0.39 (1.75), residues: 8
  sheet: -0.02 (0.30), residues: 299
  loop : -1.56 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  18 
 TYR   0.021   0.002   TYR B  88 
 PHE   0.053   0.003   PHE B 115 
 TRP   0.029   0.002   TRP H  39 
 HIS   0.004   0.002   HIS A 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4971)
  covalent geometry    : angle       0.80246 ( 6762)
  SS BOND              : bond        0.00450 (    8)
  SS BOND              : angle       1.07452 (   16)
  hydrogen bonds       : bond        0.04134 (  174)
  hydrogen bonds       : angle       6.97959 (  420)
  link_NAG-ASN         : bond        0.00180 (    2)
  link_NAG-ASN         : angle       1.20979 (    6)

*********************** 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
  155 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   41 TRP cc_start: 0.7716 (m100) cc_final: 0.5958 (m100)
REVERT: L    4 MET cc_start: 0.7996 (mmm) cc_final: 0.7625 (mmm)
REVERT: B   76 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8570 (mt)
REVERT: C    4 MET cc_start: 0.7332 (tpp) cc_final: 0.6604 (tpp)
REVERT: C   97 GLU cc_start: 0.8262 (mp0) cc_final: 0.8032 (mp0)
REVERT: C  101 GLU cc_start: 0.6944 (tp30) cc_final: 0.6446 (tm-30)
REVERT: C  103 PHE cc_start: 0.7854 (m-80) cc_final: 0.7079 (m-80)
REVERT: D  272 LEU cc_start: 0.9163 (mt) cc_final: 0.8804 (mt)
REVERT: D  327 GLU cc_start: 0.8077 (pm20) cc_final: 0.7700 (pm20)
REVERT: D  328 ASP cc_start: 0.7889 (m-30) cc_final: 0.7473 (m-30)
REVERT: D  331 LYS cc_start: 0.8258 (tptp) cc_final: 0.7942 (tppt)
  outliers start: 28
  outliers final: 24
  residues processed: 139
  average time/residue: 0.0700
  time to fit residues: 12.5355
Evaluate side-chains
  140 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
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  280 LEU
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   78 ILE
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   21 VAL
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   72 LYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  85 ASN
H  92 ASN
** 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 = 0.3705 r_free = 0.3705 target = 0.094528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.079620 restraints weight = 15287.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.082408 restraints weight = 8963.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.084333 restraints weight = 6159.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.085686 restraints weight = 4656.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.086666 restraints weight = 3763.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.7093

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= 0.162
  Angle     :  0.820   9.378   6784  Z= 0.429
  Chirality :  0.050   0.240    768
  Planarity :  0.006   0.057    854
  Dihedral  :  5.703  37.869    729
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.41 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.34), residues: 615
  helix: -0.49 (1.71), residues: 8
  sheet: -0.16 (0.29), residues: 304
  loop : -1.58 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  67 
 TYR   0.023   0.002   TYR B  88 
 PHE   0.021   0.003   PHE B 115 
 TRP   0.026   0.002   TRP H  39 
 HIS   0.012   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4971)
  covalent geometry    : angle       0.81825 ( 6762)
  SS BOND              : bond        0.00570 (    8)
  SS BOND              : angle       1.15244 (   16)
  hydrogen bonds       : bond        0.04103 (  174)
  hydrogen bonds       : angle       7.08298 (  420)
  link_NAG-ASN         : bond        0.00154 (    2)
  link_NAG-ASN         : angle       1.20121 (    6)

*********************** 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
  150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 TRP cc_start: 0.6454 (t60) cc_final: 0.6231 (t60)
REVERT: C   18 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7845 (mmm-85)
REVERT: C   67 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7880 (mtt90)
REVERT: C   97 GLU cc_start: 0.8219 (mp0) cc_final: 0.7963 (mp0)
REVERT: C  101 GLU cc_start: 0.6913 (tp30) cc_final: 0.6586 (tm-30)
REVERT: C  105 HIS cc_start: 0.7361 (t-170) cc_final: 0.7158 (t-170)
REVERT: D  272 LEU cc_start: 0.9120 (mt) cc_final: 0.8730 (mt)
REVERT: D  327 GLU cc_start: 0.8120 (pm20) cc_final: 0.7737 (pm20)
REVERT: D  328 ASP cc_start: 0.7935 (m-30) cc_final: 0.7455 (m-30)
REVERT: D  331 LYS cc_start: 0.8221 (tptp) cc_final: 0.7946 (tppt)
  outliers start: 26
  outliers final: 25
  residues processed: 134
  average time/residue: 0.0793
  time to fit residues: 13.5738
Evaluate side-chains
  135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  280 LEU
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   78 ILE
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   53 LEU
Chi-restraints excluded: chain L residue   94 VAL
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   72 LYS
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  107 TYR
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 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0020
   chunk 21 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0070
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4606

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

Flipped N/Q/H residues before XYZ refinement:
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.097058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.082095 restraints weight = 15087.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.084834 restraints weight = 9008.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.086781 restraints weight = 6255.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.088198 restraints weight = 4754.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.089109 restraints weight = 3832.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.7360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4981  Z= 0.153
  Angle     :  0.805  10.039   6784  Z= 0.422
  Chirality :  0.050   0.201    768
  Planarity :  0.005   0.058    854
  Dihedral  :  5.638  36.665    729
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.41 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.33), residues: 615
  helix: -0.26 (1.94), residues: 7
  sheet: -0.12 (0.30), residues: 296
  loop : -1.55 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  67 
 TYR   0.021   0.002   TYR B  88 
 PHE   0.019   0.003   PHE B 115 
 TRP   0.021   0.002   TRP H  39 
 HIS   0.009   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4971)
  covalent geometry    : angle       0.80333 ( 6762)
  SS BOND              : bond        0.00580 (    8)
  SS BOND              : angle       1.16080 (   16)
  hydrogen bonds       : bond        0.04106 (  174)
  hydrogen bonds       : angle       7.10583 (  420)
  link_NAG-ASN         : bond        0.00186 (    2)
  link_NAG-ASN         : angle       1.21648 (    6)

*********************** 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
  148 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 TRP cc_start: 0.6276 (t60) cc_final: 0.5791 (t60)
REVERT: H   51 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7847 (mm-30)
REVERT: H   78 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7395 (mt)
REVERT: L    4 MET cc_start: 0.8354 (mmm) cc_final: 0.7932 (mmm)
REVERT: C    4 MET cc_start: 0.7369 (tpp) cc_final: 0.6726 (tpp)
REVERT: C   97 GLU cc_start: 0.8202 (mp0) cc_final: 0.7944 (mp0)
REVERT: C  101 GLU cc_start: 0.6933 (tp30) cc_final: 0.6580 (tm-30)
REVERT: D  272 LEU cc_start: 0.9117 (mt) cc_final: 0.8802 (mt)
REVERT: D  306 ASP cc_start: 0.7890 (t0) cc_final: 0.7530 (t0)
REVERT: D  327 GLU cc_start: 0.8160 (pm20) cc_final: 0.7735 (pm20)
REVERT: D  328 ASP cc_start: 0.8012 (m-30) cc_final: 0.7485 (m-30)
  outliers start: 23
  outliers final: 20
  residues processed: 133
  average time/residue: 0.0701
  time to fit residues: 12.1788
Evaluate side-chains
  135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue   78 ILE
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   94 VAL
Chi-restraints excluded: chain B residue   72 LYS
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  107 TYR
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 36 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H  92 ASN
** 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 = 0.3747 r_free = 0.3747 target = 0.096806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.081798 restraints weight = 15292.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.084535 restraints weight = 9050.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.086475 restraints weight = 6296.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.087823 restraints weight = 4800.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.088694 restraints weight = 3901.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.7505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4981  Z= 0.162
  Angle     :  0.829  10.441   6784  Z= 0.432
  Chirality :  0.050   0.197    768
  Planarity :  0.005   0.060    854
  Dihedral  :  5.637  36.592    729
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.33), residues: 615
  helix: -0.37 (1.79), residues: 7
  sheet: -0.09 (0.30), residues: 295
  loop : -1.60 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  67 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.018   0.003   PHE B 115 
 TRP   0.021   0.003   TRP H  39 
 HIS   0.007   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4971)
  covalent geometry    : angle       0.82693 ( 6762)
  SS BOND              : bond        0.00676 (    8)
  SS BOND              : angle       1.31594 (   16)
  hydrogen bonds       : bond        0.04117 (  174)
  hydrogen bonds       : angle       7.17711 (  420)
  link_NAG-ASN         : bond        0.00181 (    2)
  link_NAG-ASN         : angle       1.23675 (    6)

********************** 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
  139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 TRP cc_start: 0.6351 (t60) cc_final: 0.6088 (t60)
REVERT: H   51 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7836 (mm-30)
REVERT: L    4 MET cc_start: 0.8466 (mmm) cc_final: 0.8051 (mmm)
REVERT: C    4 MET cc_start: 0.7442 (tpp) cc_final: 0.6815 (tpp)
REVERT: C   97 GLU cc_start: 0.8161 (mp0) cc_final: 0.7894 (mp0)
REVERT: D  327 GLU cc_start: 0.8097 (pm20) cc_final: 0.7687 (pm20)
REVERT: D  328 ASP cc_start: 0.7979 (m-30) cc_final: 0.7441 (m-30)
  outliers start: 23
  outliers final: 19
  residues processed: 125
  average time/residue: 0.0596
  time to fit residues: 9.7141
Evaluate side-chains
  124 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain H residue   78 ILE
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   94 VAL
Chi-restraints excluded: chain B residue   87 TYR
Chi-restraints excluded: chain B residue  115 PHE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0060
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0770
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.4354

-------------------------------------------------------------------------------
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**
** 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 = 0.097713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.082717 restraints weight = 15375.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.085508 restraints weight = 9083.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.087409 restraints weight = 6293.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.088806 restraints weight = 4798.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.089693 restraints weight = 3889.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.7679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4981  Z= 0.154
  Angle     :  0.840  10.766   6784  Z= 0.437
  Chirality :  0.049   0.185    768
  Planarity :  0.005   0.057    854
  Dihedral  :  5.472  36.410    729
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.34), residues: 615
  helix: -0.27 (1.85), residues: 7
  sheet: -0.06 (0.30), residues: 291
  loop : -1.58 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  67 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.016   0.002   PHE B 115 
 TRP   0.017   0.002   TRP H  39 
 HIS   0.006   0.002   HIS C 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4971)
  covalent geometry    : angle       0.83869 ( 6762)
  SS BOND              : bond        0.00662 (    8)
  SS BOND              : angle       1.30825 (   16)
  hydrogen bonds       : bond        0.04092 (  174)
  hydrogen bonds       : angle       7.08758 (  420)
  link_NAG-ASN         : bond        0.00206 (    2)
  link_NAG-ASN         : angle       1.19481 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1016.35 seconds
wall clock time: 18 minutes 20.25 seconds (1100.25 seconds total)