Starting phenix.real_space_refine
on Fri Aug 22 16:42:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y3y_10676/08_2025/6y3y_10676.map"
  }
  resolution = 3.39
  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=   0.006
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      26      5.16       5
     C    3778      2.51       5
     N     886      2.21       5
     O    1164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5854
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2707
          Classifications: {'peptide': 332}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316}
    Chain: "C"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    B, G, H, I, J
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" C1  NAG A 406 " occ=0.81
      ... (12 atoms not shown)
      pdb=" O7  NAG A 406 " occ=0.81
    residue:
      pdb=" C1  NAG A 407 " occ=0.44
      ... (12 atoms not shown)
      pdb=" O7  NAG A 407 " occ=0.44
    residue:
      pdb=" C1  NAG B 406 " occ=0.81
      ... (12 atoms not shown)
      pdb=" O7  NAG B 406 " occ=0.81
    residue:
      pdb=" C1  NAG B 407 " occ=0.44
      ... (12 atoms not shown)
      pdb=" O7  NAG B 407 " occ=0.44
  Time building chain proxies: 2.19, per 1000 atoms: 0.37
  Number of scatterers: 5854
  At special positions: 0
  Unit cell: (105.455, 73.255, 88.55, 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      26     16.00
     O    1164      8.00
     N     886      7.00
     C    3778      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 154 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 317 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  38 " - pdb=" SG  CYS B  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 154 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 188 " - pdb=" SG  CYS B 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 277 " - pdb=" SG  CYS B 282 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 317 " - pdb=" SG  CYS B 341 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA D   3 " - " MAN D   4 "
      " BMA G   3 " - " MAN G   4 "
      " BMA H   3 " - " MAN H   4 "
    ALPHA1-6
      " BMA D   3 " - " MAN D   5 "
      " BMA H   3 " - " MAN H   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 405 " - " ASN A 110 "
      " NAG A 406 " - " ASN A 145 "
      " NAG A 407 " - " ASN A 193 "
      " NAG B 405 " - " ASN B 110 "
      " NAG B 406 " - " ASN B 145 "
      " NAG B 407 " - " ASN B 193 "
      " NAG C   1 " - " ASN A  83 "
      " NAG D   1 " - " ASN A 286 "
      " NAG E   1 " - " ASN A 314 "
      " NAG F   1 " - " ASN A 328 "
      " NAG G   1 " - " ASN B  83 "
      " NAG H   1 " - " ASN B 286 "
      " NAG I   1 " - " ASN B 314 "
      " NAG J   1 " - " ASN B 328 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 219.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1260

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      17.2% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 37
      removed outlier: 3.738A  pdb=" N   ASP A  37 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 3.518A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 78
    Processing helix  chain 'A' and resid 113 through 132
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 301 through 309
    Processing helix  chain 'A' and resid 310 through 313
      removed outlier: 3.689A  pdb=" N   TYR A 313 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 310 through 313'
    Processing helix  chain 'B' and resid 33 through 37
      removed outlier: 3.737A  pdb=" N   ASP B  37 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.517A  pdb=" N   LEU B  44 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 78
    Processing helix  chain 'B' and resid 113 through 132
    Processing helix  chain 'B' and resid 271 through 276
    Processing helix  chain 'B' and resid 301 through 309
    Processing helix  chain 'B' and resid 310 through 313
      removed outlier: 3.689A  pdb=" N   TYR B 313 " --> pdb=" O   GLY B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 313'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
      removed outlier: 8.627A  pdb=" N   SER A  65 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A  30 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE A  29 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE A  91 " --> pdb=" O   GLN A 257 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   VAL A 259 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   PHE A  93 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87
      removed outlier: 8.426A  pdb=" N   LYS A 243 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 184 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168
    Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176
      removed outlier: 3.733A  pdb=" N   VAL A 173 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197
      removed outlier: 4.276A  pdb=" N   VAL A 206 " --> pdb=" O   GLY B 208 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLY B 208 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY A 208 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL B 206 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65
      removed outlier: 8.627A  pdb=" N   SER B  65 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU B  30 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   PHE B  29 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B  91 " --> pdb=" O   GLN B 257 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   VAL B 259 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   PHE B  93 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87
      removed outlier: 8.426A  pdb=" N   LYS B 243 " --> pdb=" O   PRO B 186 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU B 184 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168
    Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 176
      removed outlier: 3.732A  pdb=" N   VAL B 173 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 318

    120 hydrogen bonds defined for protein.
    312 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: 0.86

  Time building geometry restraints manager: 0.88 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: 1682
        1.34 -     1.46: 1772
        1.46 -     1.58: 2546
        1.58 -     1.70: 0
        1.70 -     1.82: 28
  Bond restraints: 6028
  Sorted by residual:
  bond pdb=" C   PHE A 108 "
       pdb=" N   PRO A 109 "
    ideal  model  delta    sigma   weight residual
    1.334  1.503 -0.169 2.34e-02 1.83e+03 5.20e+01
  bond pdb=" C   PHE B 108 "
       pdb=" N   PRO B 109 "
    ideal  model  delta    sigma   weight residual
    1.334  1.503 -0.169 2.34e-02 1.83e+03 5.20e+01
  bond pdb=" C1  NAG B 405 "
       pdb=" O5  NAG B 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.50e+00
  bond pdb=" C1  NAG A 405 "
       pdb=" O5  NAG A 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.44e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.42e+00
  ... (remaining 6023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 7885
        2.41 -     4.81: 252
        4.81 -     7.22: 51
        7.22 -     9.63: 6
        9.63 -    12.04: 4
  Bond angle restraints: 8198
  Sorted by residual:
  angle pdb=" C   PHE A 108 "
        pdb=" N   PRO A 109 "
        pdb=" CA  PRO A 109 "
      ideal   model   delta    sigma   weight residual
     119.84  131.88  -12.04 1.25e+00 6.40e-01 9.27e+01
  angle pdb=" C   PHE B 108 "
        pdb=" N   PRO B 109 "
        pdb=" CA  PRO B 109 "
      ideal   model   delta    sigma   weight residual
     119.84  131.84  -12.00 1.25e+00 6.40e-01 9.22e+01
  angle pdb=" CA  PHE A 108 "
        pdb=" C   PHE A 108 "
        pdb=" N   PRO A 109 "
      ideal   model   delta    sigma   weight residual
     118.56  125.78   -7.22 1.31e+00 5.83e-01 3.03e+01
  angle pdb=" CA  PHE B 108 "
        pdb=" C   PHE B 108 "
        pdb=" N   PRO B 109 "
      ideal   model   delta    sigma   weight residual
     118.56  125.74   -7.18 1.31e+00 5.83e-01 3.00e+01
  angle pdb=" CA  PHE B 108 "
        pdb=" C   PHE B 108 "
        pdb=" O   PHE B 108 "
      ideal   model   delta    sigma   weight residual
     119.22  114.87    4.35 1.02e+00 9.61e-01 1.82e+01
  ... (remaining 8193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.52: 3720
       21.52 -    43.04: 138
       43.04 -    64.56: 20
       64.56 -    86.07: 38
       86.07 -   107.59: 24
  Dihedral angle restraints: 3940
    sinusoidal: 1960
      harmonic: 1980
  Sorted by residual:
  dihedral pdb=" CA  ASN A 168 "
           pdb=" C   ASN A 168 "
           pdb=" N   TYR A 169 "
           pdb=" CA  TYR A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASN B 168 "
           pdb=" C   ASN B 168 "
           pdb=" N   TYR B 169 "
           pdb=" CA  TYR B 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.47  -21.53     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  SER A 147 "
           pdb=" C   SER A 147 "
           pdb=" N   LEU A 148 "
           pdb=" CA  LEU A 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 3937 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 780
       0.076 -    0.152: 155
       0.152 -    0.228: 17
       0.228 -    0.305: 8
       0.305 -    0.381: 4
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 328 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C1  NAG J   1 "
            pdb=" ND2 ASN B 328 "
            pdb=" C2  NAG J   1 "
            pdb=" O5  NAG J   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C1  NAG B 406 "
            pdb=" ND2 ASN B 145 "
            pdb=" C2  NAG B 406 "
            pdb=" O5  NAG B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.41e+00
  ... (remaining 961 not shown)

  Planarity restraints: 1006
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 107 "    0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   CYS A 107 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   CYS A 107 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PHE A 108 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 107 "   -0.017 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   CYS B 107 "    0.057 2.00e-02 2.50e+03
        pdb=" O   CYS B 107 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   PHE B 108 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 100 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO A 101 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1003 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1822
        2.82 -     3.34: 4959
        3.34 -     3.86: 10213
        3.86 -     4.38: 11600
        4.38 -     4.90: 20014
  Nonbonded interactions: 48608
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 253 "
            pdb=" OH  TYR B 336 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR A 336 "
            pdb=" O   PHE B 253 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR A 283 "
            pdb=" O   TYR A 336 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OH  TYR B 283 "
            pdb=" O   TYR B 336 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OG  SER B 319 "
            pdb=" O   GLY B 322 "
     model   vdw
     2.344 3.040
  ... (remaining 48603 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
}

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=0.44 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.860
  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:                     8.230
  Find NCS groups from input model:        0.050
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.169   6074  Z= 0.344
  Angle     :  1.078  12.036   8324  Z= 0.518
  Chirality :  0.067   0.381    964
  Planarity :  0.007   0.058    992
  Dihedral  : 17.088 107.593   2644
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.89 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -4.44 (0.27), residues: 660
  helix: -2.69 (0.36), residues: 102
  sheet: -2.19 (0.39), residues: 172
  loop : -3.54 (0.25), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 125 
 TYR   0.025   0.003   TYR B 128 
 PHE   0.026   0.003   PHE B  93 
 TRP   0.013   0.003   TRP B 116 
 HIS   0.004   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 ( 6028)
  covalent geometry    : angle       1.04165 ( 8198)
  SS BOND              : bond        0.00312 (   12)
  SS BOND              : angle       0.88053 (   24)
  hydrogen bonds       : bond        0.21892 (  120)
  hydrogen bonds       : angle       9.02188 (  312)
  link_ALPHA1-3        : bond        0.00280 (    4)
  link_ALPHA1-3        : angle       1.59151 (   12)
  link_ALPHA1-6        : bond        0.00112 (    2)
  link_ALPHA1-6        : angle       1.45179 (    6)
  link_BETA1-4         : bond        0.01095 (   14)
  link_BETA1-4         : angle       2.31312 (   42)
  link_NAG-ASN         : bond        0.00496 (   14)
  link_NAG-ASN         : angle       3.40886 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7501 (pp20)
REVERT: A  155 LYS cc_start: 0.7031 (pmtt) cc_final: 0.5975 (tptt)
REVERT: A  316 SER cc_start: 0.8801 (m) cc_final: 0.8557 (p)
REVERT: B   95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7478 (pp20)
REVERT: B  155 LYS cc_start: 0.7056 (pmtt) cc_final: 0.6018 (tptt)
REVERT: B  316 SER cc_start: 0.8775 (m) cc_final: 0.8526 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.0963
  time to fit residues: 17.7993
Evaluate side-chains
  83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain B residue  108 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
B  55 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.125948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.097836 restraints weight = 9213.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.10
r_work: 0.3176 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6074  Z= 0.176
  Angle     :  0.793  11.708   8324  Z= 0.369
  Chirality :  0.052   0.401    964
  Planarity :  0.005   0.040    992
  Dihedral  : 15.487  76.153   1434
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  8.14 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -3.48 (0.30), residues: 660
  helix: -1.22 (0.49), residues: 102
  sheet: -1.84 (0.39), residues: 172
  loop : -2.97 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 125 
 TYR   0.016   0.002   TYR A 102 
 PHE   0.015   0.002   PHE A  78 
 TRP   0.010   0.001   TRP A 116 
 HIS   0.003   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6028)
  covalent geometry    : angle       0.72748 ( 8198)
  SS BOND              : bond        0.00480 (   12)
  SS BOND              : angle       0.52355 (   24)
  hydrogen bonds       : bond        0.04089 (  120)
  hydrogen bonds       : angle       6.50676 (  312)
  link_ALPHA1-3        : bond        0.00910 (    4)
  link_ALPHA1-3        : angle       2.12857 (   12)
  link_ALPHA1-6        : bond        0.00436 (    2)
  link_ALPHA1-6        : angle       1.83553 (    6)
  link_BETA1-4         : bond        0.00460 (   14)
  link_BETA1-4         : angle       2.14304 (   42)
  link_NAG-ASN         : bond        0.00981 (   14)
  link_NAG-ASN         : angle       3.83444 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.224 
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   95 GLU cc_start: 0.8121 (pp20) cc_final: 0.7792 (pp20)
REVERT: A  197 TYR cc_start: 0.8788 (m-80) cc_final: 0.8360 (m-80)
REVERT: A  316 SER cc_start: 0.8928 (m) cc_final: 0.8627 (p)
REVERT: B   95 GLU cc_start: 0.8073 (pp20) cc_final: 0.7719 (pp20)
REVERT: B  316 SER cc_start: 0.8948 (m) cc_final: 0.8640 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0708
  time to fit residues: 9.9756
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.125571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098524 restraints weight = 9090.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.03
r_work: 0.3204 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6074  Z= 0.158
  Angle     :  0.723  10.670   8324  Z= 0.332
  Chirality :  0.052   0.424    964
  Planarity :  0.005   0.038    992
  Dihedral  : 11.643  59.976   1434
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.61 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.95 (0.32), residues: 660
  helix: -0.45 (0.56), residues: 102
  sheet: -1.62 (0.39), residues: 180
  loop : -2.67 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 340 
 TYR   0.021   0.002   TYR B 197 
 PHE   0.016   0.002   PHE A 329 
 TRP   0.009   0.001   TRP B 116 
 HIS   0.003   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6028)
  covalent geometry    : angle       0.66493 ( 8198)
  SS BOND              : bond        0.00282 (   12)
  SS BOND              : angle       0.44119 (   24)
  hydrogen bonds       : bond        0.03575 (  120)
  hydrogen bonds       : angle       5.81662 (  312)
  link_ALPHA1-3        : bond        0.01013 (    4)
  link_ALPHA1-3        : angle       1.43186 (   12)
  link_ALPHA1-6        : bond        0.00507 (    2)
  link_ALPHA1-6        : angle       1.70518 (    6)
  link_BETA1-4         : bond        0.00514 (   14)
  link_BETA1-4         : angle       1.81157 (   42)
  link_NAG-ASN         : bond        0.00798 (   14)
  link_NAG-ASN         : angle       3.58326 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.207 
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: A   95 GLU cc_start: 0.8110 (pp20) cc_final: 0.7855 (pp20)
REVERT: A  197 TYR cc_start: 0.8772 (m-80) cc_final: 0.8287 (m-80)
REVERT: A  316 SER cc_start: 0.8989 (m) cc_final: 0.8670 (p)
REVERT: B   95 GLU cc_start: 0.8135 (pp20) cc_final: 0.7850 (pp20)
REVERT: B  316 SER cc_start: 0.8971 (m) cc_final: 0.8648 (p)
  outliers start: 14
  outliers final: 13
  residues processed: 97
  average time/residue: 0.0689
  time to fit residues: 9.0916
Evaluate side-chains
  85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0050
   chunk 52 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.125248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098535 restraints weight = 9129.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 3.02
r_work: 0.3198 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3208
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3208 r_free = 0.3208    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3208
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6074  Z= 0.138
  Angle     :  0.669  10.460   8324  Z= 0.311
  Chirality :  0.050   0.411    964
  Planarity :  0.005   0.038    992
  Dihedral  :  9.121  54.761   1434
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.73 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.73 (0.32), residues: 660
  helix: -0.10 (0.57), residues: 102
  sheet: -1.49 (0.39), residues: 180
  loop : -2.56 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.012   0.001   TYR B 169 
 PHE   0.012   0.002   PHE A 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.002   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6028)
  covalent geometry    : angle       0.61247 ( 8198)
  SS BOND              : bond        0.00264 (   12)
  SS BOND              : angle       0.35739 (   24)
  hydrogen bonds       : bond        0.03270 (  120)
  hydrogen bonds       : angle       5.52292 (  312)
  link_ALPHA1-3        : bond        0.01145 (    4)
  link_ALPHA1-3        : angle       1.50749 (   12)
  link_ALPHA1-6        : bond        0.00738 (    2)
  link_ALPHA1-6        : angle       1.57313 (    6)
  link_BETA1-4         : bond        0.00498 (   14)
  link_BETA1-4         : angle       1.59766 (   42)
  link_NAG-ASN         : bond        0.00649 (   14)
  link_NAG-ASN         : angle       3.42854 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.231 
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   95 GLU cc_start: 0.8147 (pp20) cc_final: 0.7907 (pp20)
REVERT: A  197 TYR cc_start: 0.8776 (m-80) cc_final: 0.8282 (m-80)
REVERT: A  316 SER cc_start: 0.8971 (m) cc_final: 0.8655 (p)
REVERT: A  340 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7867 (mtt-85)
REVERT: B   95 GLU cc_start: 0.8157 (pp20) cc_final: 0.7921 (pp20)
REVERT: B  316 SER cc_start: 0.8971 (m) cc_final: 0.8635 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0656
  time to fit residues: 7.9686
Evaluate side-chains
  79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 17 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.123699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.096804 restraints weight = 9266.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.06
r_work: 0.3176 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   6074  Z= 0.153
  Angle     :  0.667  10.643   8324  Z= 0.310
  Chirality :  0.049   0.398    964
  Planarity :  0.004   0.037    992
  Dihedral  :  8.492  55.126   1434
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.89 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.63 (0.32), residues: 660
  helix:  0.02 (0.57), residues: 102
  sheet: -1.38 (0.40), residues: 180
  loop : -2.55 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.012   0.001   TYR A 169 
 PHE   0.016   0.002   PHE B 151 
 TRP   0.009   0.001   TRP A 116 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6028)
  covalent geometry    : angle       0.61746 ( 8198)
  SS BOND              : bond        0.00257 (   12)
  SS BOND              : angle       0.45631 (   24)
  hydrogen bonds       : bond        0.03210 (  120)
  hydrogen bonds       : angle       5.43208 (  312)
  link_ALPHA1-3        : bond        0.01170 (    4)
  link_ALPHA1-3        : angle       1.37837 (   12)
  link_ALPHA1-6        : bond        0.00760 (    2)
  link_ALPHA1-6        : angle       1.43601 (    6)
  link_BETA1-4         : bond        0.00481 (   14)
  link_BETA1-4         : angle       1.43689 (   42)
  link_NAG-ASN         : bond        0.00645 (   14)
  link_NAG-ASN         : angle       3.27264 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.147 
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   95 GLU cc_start: 0.8182 (pp20) cc_final: 0.7940 (pp20)
REVERT: A  197 TYR cc_start: 0.8795 (m-80) cc_final: 0.8319 (m-80)
REVERT: A  316 SER cc_start: 0.9003 (m) cc_final: 0.8668 (p)
REVERT: B   95 GLU cc_start: 0.8166 (pp20) cc_final: 0.7906 (pp20)
REVERT: B  316 SER cc_start: 0.9006 (m) cc_final: 0.8666 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0608
  time to fit residues: 7.2786
Evaluate side-chains
  83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    0.2980
   chunk 4 optimal weight:    0.0570
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.124531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.097780 restraints weight = 9204.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.03
r_work: 0.3192 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6074  Z= 0.125
  Angle     :  0.647  10.123   8324  Z= 0.300
  Chirality :  0.049   0.395    964
  Planarity :  0.004   0.038    992
  Dihedral  :  7.930  54.475   1434
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.38 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.48 (0.32), residues: 660
  helix:  0.13 (0.57), residues: 102
  sheet: -1.22 (0.40), residues: 180
  loop : -2.47 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 340 
 TYR   0.012   0.001   TYR B 197 
 PHE   0.014   0.002   PHE A 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.002   0.001   HIS B 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6028)
  covalent geometry    : angle       0.59732 ( 8198)
  SS BOND              : bond        0.00231 (   12)
  SS BOND              : angle       0.36580 (   24)
  hydrogen bonds       : bond        0.02929 (  120)
  hydrogen bonds       : angle       5.22696 (  312)
  link_ALPHA1-3        : bond        0.01122 (    4)
  link_ALPHA1-3        : angle       1.32739 (   12)
  link_ALPHA1-6        : bond        0.00807 (    2)
  link_ALPHA1-6        : angle       1.32521 (    6)
  link_BETA1-4         : bond        0.00519 (   14)
  link_BETA1-4         : angle       1.44243 (   42)
  link_NAG-ASN         : bond        0.00650 (   14)
  link_NAG-ASN         : angle       3.21441 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.147 
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: A   95 GLU cc_start: 0.8140 (pp20) cc_final: 0.7934 (pp20)
REVERT: A  197 TYR cc_start: 0.8751 (m-80) cc_final: 0.8299 (m-80)
REVERT: A  316 SER cc_start: 0.9013 (m) cc_final: 0.8670 (p)
REVERT: B   95 GLU cc_start: 0.8168 (pp20) cc_final: 0.7963 (pp20)
REVERT: B  316 SER cc_start: 0.9004 (m) cc_final: 0.8653 (p)
  outliers start: 15
  outliers final: 13
  residues processed: 90
  average time/residue: 0.0677
  time to fit residues: 8.3585
Evaluate side-chains
  85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 52 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.096889 restraints weight = 9283.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.01
r_work: 0.3172 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6074  Z= 0.144
  Angle     :  0.652   9.965   8324  Z= 0.302
  Chirality :  0.049   0.387    964
  Planarity :  0.004   0.037    992
  Dihedral  :  7.792  55.090   1434
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.03 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.41 (0.33), residues: 660
  helix:  0.18 (0.57), residues: 102
  sheet: -1.14 (0.40), residues: 180
  loop : -2.44 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 340 
 TYR   0.017   0.001   TYR A 295 
 PHE   0.016   0.002   PHE A 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.002   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6028)
  covalent geometry    : angle       0.60655 ( 8198)
  SS BOND              : bond        0.00253 (   12)
  SS BOND              : angle       0.41313 (   24)
  hydrogen bonds       : bond        0.03018 (  120)
  hydrogen bonds       : angle       5.23154 (  312)
  link_ALPHA1-3        : bond        0.01057 (    4)
  link_ALPHA1-3        : angle       1.24228 (   12)
  link_ALPHA1-6        : bond        0.00789 (    2)
  link_ALPHA1-6        : angle       1.32759 (    6)
  link_BETA1-4         : bond        0.00479 (   14)
  link_BETA1-4         : angle       1.40301 (   42)
  link_NAG-ASN         : bond        0.00620 (   14)
  link_NAG-ASN         : angle       3.12541 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.220 
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: A   95 GLU cc_start: 0.8119 (pp20) cc_final: 0.7909 (pp20)
REVERT: A  197 TYR cc_start: 0.8751 (m-80) cc_final: 0.8323 (m-80)
REVERT: A  316 SER cc_start: 0.8965 (m) cc_final: 0.8638 (p)
REVERT: B   95 GLU cc_start: 0.8155 (pp20) cc_final: 0.7941 (pp20)
REVERT: B  224 LEU cc_start: 0.9314 (mp) cc_final: 0.9111 (mt)
REVERT: B  316 SER cc_start: 0.8957 (m) cc_final: 0.8620 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 87
  average time/residue: 0.0621
  time to fit residues: 7.5431
Evaluate side-chains
  86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.123680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.096992 restraints weight = 9201.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.02
r_work: 0.3178 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6074  Z= 0.139
  Angle     :  0.648   9.860   8324  Z= 0.299
  Chirality :  0.048   0.383    964
  Planarity :  0.004   0.038    992
  Dihedral  :  7.612  55.369   1434
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 12.87 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.32 (0.32), residues: 660
  helix:  0.22 (0.57), residues: 102
  sheet: -1.07 (0.40), residues: 180
  loop : -2.38 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 285 
 TYR   0.016   0.001   TYR A 295 
 PHE   0.016   0.002   PHE A 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.002   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6028)
  covalent geometry    : angle       0.60337 ( 8198)
  SS BOND              : bond        0.00244 (   12)
  SS BOND              : angle       0.40618 (   24)
  hydrogen bonds       : bond        0.02953 (  120)
  hydrogen bonds       : angle       5.15202 (  312)
  link_ALPHA1-3        : bond        0.01012 (    4)
  link_ALPHA1-3        : angle       1.21259 (   12)
  link_ALPHA1-6        : bond        0.00786 (    2)
  link_ALPHA1-6        : angle       1.30447 (    6)
  link_BETA1-4         : bond        0.00486 (   14)
  link_BETA1-4         : angle       1.38918 (   42)
  link_NAG-ASN         : bond        0.00623 (   14)
  link_NAG-ASN         : angle       3.06832 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.163 
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  197 TYR cc_start: 0.8742 (m-80) cc_final: 0.8297 (m-80)
REVERT: A  262 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6478 (pmt100)
REVERT: A  316 SER cc_start: 0.8961 (m) cc_final: 0.8637 (p)
REVERT: B  316 SER cc_start: 0.8959 (m) cc_final: 0.8629 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 90
  average time/residue: 0.0750
  time to fit residues: 9.1393
Evaluate side-chains
  84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.122741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.096246 restraints weight = 9282.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 3.01
r_work: 0.3165 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6074  Z= 0.166
  Angle     :  0.681   9.697   8324  Z= 0.319
  Chirality :  0.048   0.377    964
  Planarity :  0.004   0.038    992
  Dihedral  :  7.590  55.899   1434
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.36 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.35 (0.32), residues: 660
  helix:  0.28 (0.57), residues: 102
  sheet: -1.10 (0.39), residues: 180
  loop : -2.42 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 285 
 TYR   0.013   0.001   TYR A 295 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6028)
  covalent geometry    : angle       0.64010 ( 8198)
  SS BOND              : bond        0.00278 (   12)
  SS BOND              : angle       0.44806 (   24)
  hydrogen bonds       : bond        0.03071 (  120)
  hydrogen bonds       : angle       5.16827 (  312)
  link_ALPHA1-3        : bond        0.00989 (    4)
  link_ALPHA1-3        : angle       1.19718 (   12)
  link_ALPHA1-6        : bond        0.00765 (    2)
  link_ALPHA1-6        : angle       1.31482 (    6)
  link_BETA1-4         : bond        0.00466 (   14)
  link_BETA1-4         : angle       1.37259 (   42)
  link_NAG-ASN         : bond        0.00614 (   14)
  link_NAG-ASN         : angle       3.03176 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.164 
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  197 TYR cc_start: 0.8749 (m-80) cc_final: 0.8314 (m-80)
REVERT: A  262 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6614 (pmt100)
REVERT: A  316 SER cc_start: 0.8956 (m) cc_final: 0.8638 (p)
REVERT: B  316 SER cc_start: 0.8966 (m) cc_final: 0.8634 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0829
  time to fit residues: 9.9284
Evaluate side-chains
  86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  262 ARG
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 16 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.123987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.097151 restraints weight = 9276.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 3.06
r_work: 0.3188 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6074  Z= 0.131
  Angle     :  0.665   9.652   8324  Z= 0.312
  Chirality :  0.048   0.372    964
  Planarity :  0.004   0.040    992
  Dihedral  :  7.495  56.152   1434
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.01 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.35 (0.32), residues: 660
  helix:  0.28 (0.56), residues: 102
  sheet: -1.09 (0.38), residues: 180
  loop : -2.43 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 340 
 TYR   0.019   0.001   TYR A 295 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.008   0.001   TRP A 116 
 HIS   0.002   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6028)
  covalent geometry    : angle       0.62363 ( 8198)
  SS BOND              : bond        0.00240 (   12)
  SS BOND              : angle       0.57696 (   24)
  hydrogen bonds       : bond        0.02915 (  120)
  hydrogen bonds       : angle       5.11221 (  312)
  link_ALPHA1-3        : bond        0.00952 (    4)
  link_ALPHA1-3        : angle       1.21673 (   12)
  link_ALPHA1-6        : bond        0.00779 (    2)
  link_ALPHA1-6        : angle       1.29393 (    6)
  link_BETA1-4         : bond        0.00490 (   14)
  link_BETA1-4         : angle       1.37180 (   42)
  link_NAG-ASN         : bond        0.00601 (   14)
  link_NAG-ASN         : angle       2.99359 (   42)

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.160 
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: A  197 TYR cc_start: 0.8750 (m-80) cc_final: 0.8297 (m-80)
REVERT: A  237 PHE cc_start: 0.8215 (m-80) cc_final: 0.8011 (m-80)
REVERT: A  316 SER cc_start: 0.8988 (m) cc_final: 0.8637 (p)
REVERT: B  316 SER cc_start: 0.8976 (m) cc_final: 0.8623 (p)
  outliers start: 16
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0741
  time to fit residues: 8.4987
Evaluate side-chains
  86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  341 CYS
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  108 PHE
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  246 CYS
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  341 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0970
   chunk 63 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0470
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.2274

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.126434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100072 restraints weight = 9125.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 3.02
r_work: 0.3226 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.108
  Angle     :  0.650   9.633   8324  Z= 0.304
  Chirality :  0.047   0.366    964
  Planarity :  0.004   0.040    992
  Dihedral  :  7.317  56.284   1434
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.50 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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: -2.27 (0.32), residues: 660
  helix:  0.46 (0.56), residues: 100
  sheet: -0.96 (0.38), residues: 180
  loop : -2.44 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 340 
 TYR   0.020   0.001   TYR A 295 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.010   0.001   TRP A 263 
 HIS   0.002   0.000   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6028)
  covalent geometry    : angle       0.60826 ( 8198)
  SS BOND              : bond        0.00231 (   12)
  SS BOND              : angle       0.55638 (   24)
  hydrogen bonds       : bond        0.02712 (  120)
  hydrogen bonds       : angle       4.92765 (  312)
  link_ALPHA1-3        : bond        0.00920 (    4)
  link_ALPHA1-3        : angle       1.23913 (   12)
  link_ALPHA1-6        : bond        0.00742 (    2)
  link_ALPHA1-6        : angle       1.28189 (    6)
  link_BETA1-4         : bond        0.00546 (   14)
  link_BETA1-4         : angle       1.38134 (   42)
  link_NAG-ASN         : bond        0.00599 (   14)
  link_NAG-ASN         : angle       2.95926 (   42)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1456.01 seconds
wall clock time: 25 minutes 44.79 seconds (1544.79 seconds total)