Starting phenix.real_space_refine
on Tue Mar  3 15:28:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7evp_31339/03_2026/7evp_31339.map"
  }
  resolution = 3.2
  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=   0.008 sd=   0.097
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      18      5.16       5
     C    4184      2.51       5
     N    1064      2.21       5
     O    1350      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6616
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2944
          Classifications: {'peptide': 377}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 360}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 364
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 1.69, per 1000 atoms: 0.26
  Number of scatterers: 6616
  At special positions: 0
  Unit cell: (107.42, 97.58, 66.42, 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      18     16.00
     O    1350      8.00
     N    1064      7.00
     C    4184      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 432.1 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 18 sheets defined
      25.2% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 16
      removed outlier: 4.225A  pdb=" N   THR A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.745A  pdb=" N   VAL A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 124
      removed outlier: 3.557A  pdb=" N   GLN A 123 " --> pdb=" O   ASP A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 151
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.538A  pdb=" N   LEU A 255 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 256 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 256'
    Processing helix  chain 'A' and resid 268 through 279
      removed outlier: 3.773A  pdb=" N   ILE A 275 " --> pdb=" O   PHE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 284
      removed outlier: 3.746A  pdb=" N   ARG A 283 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 284 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 284'
    Processing helix  chain 'A' and resid 331 through 340
      removed outlier: 3.578A  pdb=" N   ALA A 337 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 25
    Processing helix  chain 'C' and resid 32 through 54
      removed outlier: 3.615A  pdb=" N   LEU C  36 " --> pdb=" O   TYR C  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 16
      removed outlier: 4.225A  pdb=" N   THR B  13 " --> pdb=" O   ASP B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.745A  pdb=" N   VAL B  84 " --> pdb=" O   GLY B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 124
      removed outlier: 3.557A  pdb=" N   GLN B 123 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 151
    Processing helix  chain 'B' and resid 206 through 208
      No H-bonds generated for 'chain 'B' and resid 206 through 208'
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.538A  pdb=" N   LEU B 255 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE B 256 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 252 through 256'
    Processing helix  chain 'B' and resid 268 through 279
      removed outlier: 3.773A  pdb=" N   ILE B 275 " --> pdb=" O   PHE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 284
      removed outlier: 3.746A  pdb=" N   ARG B 283 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 284 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 280 through 284'
    Processing helix  chain 'B' and resid 331 through 340
      removed outlier: 3.578A  pdb=" N   ALA B 337 " --> pdb=" O   TYR B 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 25
    Processing helix  chain 'D' and resid 32 through 54
      removed outlier: 3.614A  pdb=" N   LEU D  36 " --> pdb=" O   TYR D  32 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72
      removed outlier: 6.321A  pdb=" N   GLU A   3 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59
      removed outlier: 4.961A  pdb=" N   SER A  48 " --> pdb=" O   GLY A  33 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   GLY A  33 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59
    Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62
      removed outlier: 3.537A  pdb=" N   GLU A  65 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109
    Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 204
      removed outlier: 3.562A  pdb=" N   VAL A 187 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS A 360 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 262 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 199 through 204
      removed outlier: 3.562A  pdb=" N   VAL A 187 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS A 360 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 299
    Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 305
    Processing sheet with id=AB2, first strand: chain 'B' and resid 70 through 72
      removed outlier: 6.321A  pdb=" N   GLU B   3 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59
      removed outlier: 4.961A  pdb=" N   SER B  48 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   GLY B  33 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 59
    Processing sheet with id=AB5, first strand: chain 'B' and resid 61 through 62
      removed outlier: 3.537A  pdb=" N   GLU B  65 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 204
      removed outlier: 3.562A  pdb=" N   VAL B 187 " --> pdb=" O   THR B 368 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS B 360 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE B 262 " --> pdb=" O   PHE B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 204
      removed outlier: 3.562A  pdb=" N   VAL B 187 " --> pdb=" O   THR B 368 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS B 360 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 289 through 291
    Processing sheet with id=AB9, first strand: chain 'B' and resid 298 through 299

    310 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1687
        1.33 -     1.45: 1095
        1.45 -     1.57: 3902
        1.57 -     1.68: 0
        1.68 -     1.80: 34
  Bond restraints: 6718
  Sorted by residual:
  bond pdb=" CG  LEU B 370 "
       pdb=" CD1 LEU B 370 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.19e+00
  bond pdb=" CG  LEU A 370 "
       pdb=" CD1 LEU A 370 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.19e+00
  bond pdb=" CA  ILE B 107 "
       pdb=" CB  ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.540  1.521  0.019 1.36e-02 5.41e+03 2.03e+00
  bond pdb=" CA  ILE A 107 "
       pdb=" CB  ILE A 107 "
    ideal  model  delta    sigma   weight residual
    1.540  1.521  0.019 1.36e-02 5.41e+03 2.03e+00
  bond pdb=" CG  LEU A 359 "
       pdb=" CD2 LEU A 359 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.02e+00
  ... (remaining 6713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 8605
        1.73 -     3.46: 417
        3.46 -     5.20: 58
        5.20 -     6.93: 16
        6.93 -     8.66: 4
  Bond angle restraints: 9100
  Sorted by residual:
  angle pdb=" C   MET A 354 "
        pdb=" N   LYS A 355 "
        pdb=" CA  LYS A 355 "
      ideal   model   delta    sigma   weight residual
     122.56  127.94   -5.38 1.58e+00 4.01e-01 1.16e+01
  angle pdb=" C   MET B 354 "
        pdb=" N   LYS B 355 "
        pdb=" CA  LYS B 355 "
      ideal   model   delta    sigma   weight residual
     122.56  127.94   -5.38 1.58e+00 4.01e-01 1.16e+01
  angle pdb=" C   PRO B 306 "
        pdb=" N   GLU B 307 "
        pdb=" CA  GLU B 307 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  angle pdb=" C   PRO A 306 "
        pdb=" N   GLU A 307 "
        pdb=" CA  GLU A 307 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  angle pdb=" CG1 ILE A 374 "
        pdb=" CB  ILE A 374 "
        pdb=" CG2 ILE A 374 "
      ideal   model   delta    sigma   weight residual
     110.70  102.04    8.66 3.00e+00 1.11e-01 8.33e+00
  ... (remaining 9095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.84: 3632
       10.84 -    21.68: 388
       21.68 -    32.52: 64
       32.52 -    43.36: 26
       43.36 -    54.20: 8
  Dihedral angle restraints: 4118
    sinusoidal: 1672
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CA  ALA B 282 "
           pdb=" C   ALA B 282 "
           pdb=" N   ARG B 283 "
           pdb=" CA  ARG B 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.64   31.36     0      5.00e+00 4.00e-02 3.93e+01
  dihedral pdb=" CA  ALA A 282 "
           pdb=" C   ALA A 282 "
           pdb=" N   ARG A 283 "
           pdb=" CA  ARG A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.64   31.36     0      5.00e+00 4.00e-02 3.93e+01
  dihedral pdb=" CA  ASN A 151 "
           pdb=" C   ASN A 151 "
           pdb=" N   PHE A 152 "
           pdb=" CA  PHE A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 4115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 615
       0.045 -    0.091: 317
       0.091 -    0.136: 114
       0.136 -    0.181: 14
       0.181 -    0.226: 8
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CG  LEU C  36 "
            pdb=" CB  LEU C  36 "
            pdb=" CD1 LEU C  36 "
            pdb=" CD2 LEU C  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU D  36 "
            pdb=" CB  LEU D  36 "
            pdb=" CD1 LEU D  36 "
            pdb=" CD2 LEU D  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE B 374 "
            pdb=" CA  ILE B 374 "
            pdb=" CG1 ILE B 374 "
            pdb=" CG2 ILE B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1065 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 168 "    0.013 2.00e-02 2.50e+03   1.26e-02 3.96e+00
        pdb=" CG  TRP B 168 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 168 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 168 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 168 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 168 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 168 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 168 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 168 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 168 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 168 "    0.013 2.00e-02 2.50e+03   1.26e-02 3.96e+00
        pdb=" CG  TRP A 168 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 168 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 168 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 168 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 168 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 168 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 168 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 168 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 168 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 282 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.59e+00
        pdb=" C   ALA A 282 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ALA A 282 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A 283 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2099
        2.84 -     3.36: 6096
        3.36 -     3.87: 10574
        3.87 -     4.39: 12402
        4.39 -     4.90: 21631
  Nonbonded interactions: 52802
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OD1 ASN B 218 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OD1 ASN A 218 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OE2 GLU C  48 "
            pdb=" NZ  LYS D  20 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" NZ  LYS C  20 "
            pdb=" OE2 GLU D  48 "
     model   vdw
     2.406 3.120
  nonbonded pdb=" O   ASN A  16 "
            pdb=" NZ  LYS A  20 "
     model   vdw
     2.418 3.120
  ... (remaining 52797 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 'D'
}

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=0.00 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.590
  Find NCS groups from input model:        0.040
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
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   0.052   6718  Z= 0.319
  Angle     :  0.868   8.660   9100  Z= 0.464
  Chirality :  0.060   0.226   1068
  Planarity :  0.006   0.047   1186
  Dihedral  :  9.798  54.203   2530
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.44 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 are not related in a simple way.
  whole: -5.27 (0.22), residues: 832
  helix: -3.56 (0.22), residues: 226
  sheet: -3.63 (0.24), residues: 298
  loop : -2.87 (0.29), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 283 
 TYR   0.019   0.003   TYR C  32 
 PHE   0.029   0.004   PHE B  11 
 TRP   0.033   0.007   TRP B 168 
 HIS   0.010   0.002   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00783 ( 6718)
  covalent geometry    : angle       0.86776 ( 9100)
  hydrogen bonds       : bond        0.20079 (  258)
  hydrogen bonds       : angle       8.72871 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7231 (tttm)
REVERT: A   44 ILE cc_start: 0.7399 (pt) cc_final: 0.7186 (pt)
REVERT: A  106 LEU cc_start: 0.7356 (mp) cc_final: 0.6824 (pp)
REVERT: A  131 SER cc_start: 0.8802 (m) cc_final: 0.8592 (p)
REVERT: A  149 GLN cc_start: 0.7717 (mt0) cc_final: 0.7367 (mt0)
REVERT: A  158 GLU cc_start: 0.7791 (mp0) cc_final: 0.7275 (tm-30)
REVERT: A  171 GLN cc_start: 0.8408 (pt0) cc_final: 0.8094 (mt0)
REVERT: A  206 LYS cc_start: 0.8342 (ptpp) cc_final: 0.8079 (ptpp)
REVERT: A  243 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6568 (ttm110)
REVERT: A  246 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7647 (mm-30)
REVERT: A  263 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7378 (ttmm)
REVERT: A  270 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: A  349 GLU cc_start: 0.8176 (pt0) cc_final: 0.7951 (pt0)
REVERT: B    7 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7229 (tttm)
REVERT: B   44 ILE cc_start: 0.7404 (pt) cc_final: 0.7183 (pt)
REVERT: B  106 LEU cc_start: 0.7363 (mp) cc_final: 0.6827 (pp)
REVERT: B  131 SER cc_start: 0.8805 (m) cc_final: 0.8598 (p)
REVERT: B  149 GLN cc_start: 0.7724 (mt0) cc_final: 0.7369 (mt0)
REVERT: B  158 GLU cc_start: 0.7785 (mp0) cc_final: 0.7272 (tm-30)
REVERT: B  171 GLN cc_start: 0.8407 (pt0) cc_final: 0.8099 (mt0)
REVERT: B  206 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8083 (ptpp)
REVERT: B  243 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6572 (ttm110)
REVERT: B  246 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7645 (mm-30)
REVERT: B  262 ILE cc_start: 0.8187 (pt) cc_final: 0.7986 (pt)
REVERT: B  263 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7385 (ttmm)
REVERT: B  270 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7494 (mt-10)
REVERT: B  349 GLU cc_start: 0.8176 (pt0) cc_final: 0.7954 (pt0)
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.0904
  time to fit residues: 17.3687
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain B residue  238 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
A 102 GLN
A 212 ASN
B  16 ASN
B 102 GLN
B 212 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.148928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.117657 restraints weight = 7915.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 3.29
r_work: 0.3486 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6718  Z= 0.138
  Angle     :  0.550   6.095   9100  Z= 0.284
  Chirality :  0.047   0.147   1068
  Planarity :  0.004   0.033   1186
  Dihedral  :  5.140  22.645    886
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  6.75 %
    Favored  : 91.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.26), residues: 832
  helix: -2.32 (0.29), residues: 224
  sheet: -2.85 (0.27), residues: 294
  loop : -2.49 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 283 
 TYR   0.008   0.001   TYR D  14 
 PHE   0.010   0.001   PHE B 357 
 TRP   0.011   0.002   TRP A 168 
 HIS   0.004   0.001   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6718)
  covalent geometry    : angle       0.55003 ( 9100)
  hydrogen bonds       : bond        0.03590 (  258)
  hydrogen bonds       : angle       5.49313 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7562 (mp) cc_final: 0.7331 (tp)
REVERT: A   44 ILE cc_start: 0.7767 (pt) cc_final: 0.7474 (pt)
REVERT: A   86 ILE cc_start: 0.8365 (mm) cc_final: 0.8125 (mt)
REVERT: A  102 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7934 (mp10)
REVERT: A  106 LEU cc_start: 0.7559 (mp) cc_final: 0.7323 (mm)
REVERT: A  149 GLN cc_start: 0.7991 (mt0) cc_final: 0.7637 (mt0)
REVERT: A  158 GLU cc_start: 0.7698 (mp0) cc_final: 0.7348 (tm-30)
REVERT: A  171 GLN cc_start: 0.8453 (pt0) cc_final: 0.8082 (mt0)
REVERT: A  181 ASP cc_start: 0.7648 (p0) cc_final: 0.7342 (p0)
REVERT: A  206 LYS cc_start: 0.8530 (ptpp) cc_final: 0.8293 (mtmm)
REVERT: A  246 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7672 (mm-30)
REVERT: A  263 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7799 (ttmm)
REVERT: A  313 GLU cc_start: 0.8231 (mp0) cc_final: 0.7723 (mp0)
REVERT: A  349 GLU cc_start: 0.8392 (pt0) cc_final: 0.8165 (pt0)
REVERT: B   28 LEU cc_start: 0.7552 (mp) cc_final: 0.7320 (tp)
REVERT: B   44 ILE cc_start: 0.7732 (pt) cc_final: 0.7440 (pt)
REVERT: B   86 ILE cc_start: 0.8366 (mm) cc_final: 0.8128 (mt)
REVERT: B  102 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7928 (mp10)
REVERT: B  106 LEU cc_start: 0.7562 (mp) cc_final: 0.7327 (mm)
REVERT: B  149 GLN cc_start: 0.7997 (mt0) cc_final: 0.7639 (mt0)
REVERT: B  158 GLU cc_start: 0.7703 (mp0) cc_final: 0.7356 (tm-30)
REVERT: B  171 GLN cc_start: 0.8461 (pt0) cc_final: 0.8097 (mt0)
REVERT: B  181 ASP cc_start: 0.7633 (p0) cc_final: 0.7326 (p0)
REVERT: B  206 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8269 (mtmm)
REVERT: B  246 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7697 (mm-30)
REVERT: B  263 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7859 (ttmm)
REVERT: B  313 GLU cc_start: 0.8237 (mp0) cc_final: 0.7735 (mp0)
REVERT: B  349 GLU cc_start: 0.8393 (pt0) cc_final: 0.8159 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 123
  average time/residue: 0.0671
  time to fit residues: 11.7434
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  102 GLN
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.148586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.117169 restraints weight = 7832.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 3.31
r_work: 0.3466 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6718  Z= 0.131
  Angle     :  0.514   6.452   9100  Z= 0.263
  Chirality :  0.047   0.147   1068
  Planarity :  0.003   0.023   1186
  Dihedral  :  4.769  22.116    886
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  8.33 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.27), residues: 832
  helix: -1.58 (0.31), residues: 230
  sheet: -2.74 (0.28), residues: 304
  loop : -2.01 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B   8 
 TYR   0.008   0.001   TYR C  15 
 PHE   0.010   0.001   PHE B 357 
 TRP   0.005   0.001   TRP B 168 
 HIS   0.002   0.001   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6718)
  covalent geometry    : angle       0.51387 ( 9100)
  hydrogen bonds       : bond        0.03159 (  258)
  hydrogen bonds       : angle       4.88671 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7571 (mp) cc_final: 0.7358 (tp)
REVERT: A   37 ASP cc_start: 0.7594 (t0) cc_final: 0.6598 (m-30)
REVERT: A   44 ILE cc_start: 0.7736 (pt) cc_final: 0.7480 (pt)
REVERT: A   86 ILE cc_start: 0.8409 (mm) cc_final: 0.8194 (mt)
REVERT: A  102 GLN cc_start: 0.8268 (mp10) cc_final: 0.8067 (mp10)
REVERT: A  106 LEU cc_start: 0.7643 (mp) cc_final: 0.7413 (mm)
REVERT: A  149 GLN cc_start: 0.7932 (mt0) cc_final: 0.7548 (mt0)
REVERT: A  158 GLU cc_start: 0.7817 (mp0) cc_final: 0.7417 (tm-30)
REVERT: A  171 GLN cc_start: 0.8546 (pt0) cc_final: 0.8107 (mt0)
REVERT: A  181 ASP cc_start: 0.7653 (p0) cc_final: 0.7301 (p0)
REVERT: A  206 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8300 (mtmm)
REVERT: A  246 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7969 (mm-30)
REVERT: A  263 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7861 (ttmm)
REVERT: A  313 GLU cc_start: 0.8252 (mp0) cc_final: 0.7774 (mp0)
REVERT: B   28 LEU cc_start: 0.7572 (mp) cc_final: 0.7359 (tp)
REVERT: B   37 ASP cc_start: 0.7565 (t0) cc_final: 0.6573 (m-30)
REVERT: B   44 ILE cc_start: 0.7705 (pt) cc_final: 0.7452 (pt)
REVERT: B   86 ILE cc_start: 0.8405 (mm) cc_final: 0.8193 (mt)
REVERT: B  102 GLN cc_start: 0.8264 (mp10) cc_final: 0.8059 (mp10)
REVERT: B  106 LEU cc_start: 0.7649 (mp) cc_final: 0.7418 (mm)
REVERT: B  149 GLN cc_start: 0.7940 (mt0) cc_final: 0.7560 (mt0)
REVERT: B  158 GLU cc_start: 0.7824 (mp0) cc_final: 0.7426 (tm-30)
REVERT: B  171 GLN cc_start: 0.8535 (pt0) cc_final: 0.8106 (mt0)
REVERT: B  181 ASP cc_start: 0.7626 (p0) cc_final: 0.7278 (p0)
REVERT: B  206 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8294 (mtmm)
REVERT: B  246 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7990 (mm-30)
REVERT: B  263 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7881 (ttmm)
REVERT: B  313 GLU cc_start: 0.8261 (mp0) cc_final: 0.7786 (mp0)
  outliers start: 31
  outliers final: 17
  residues processed: 122
  average time/residue: 0.0593
  time to fit residues: 10.3271
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 76 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.145556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.111756 restraints weight = 7931.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 3.56
r_work: 0.3359 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6718  Z= 0.145
  Angle     :  0.523   6.536   9100  Z= 0.262
  Chirality :  0.047   0.145   1068
  Planarity :  0.003   0.018   1186
  Dihedral  :  4.638  22.941    886
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  :  9.66 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.28), residues: 832
  helix: -1.11 (0.32), residues: 232
  sheet: -2.61 (0.28), residues: 302
  loop : -1.82 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   8 
 TYR   0.007   0.001   TYR D  15 
 PHE   0.010   0.001   PHE B 357 
 TRP   0.004   0.001   TRP A 168 
 HIS   0.001   0.000   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6718)
  covalent geometry    : angle       0.52252 ( 9100)
  hydrogen bonds       : bond        0.03033 (  258)
  hydrogen bonds       : angle       4.61077 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7517 (mp) cc_final: 0.7302 (tp)
REVERT: A   44 ILE cc_start: 0.7749 (pt) cc_final: 0.7461 (pt)
REVERT: A  106 LEU cc_start: 0.7566 (mp) cc_final: 0.7316 (mm)
REVERT: A  151 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8251 (t0)
REVERT: A  158 GLU cc_start: 0.7777 (mp0) cc_final: 0.7371 (tm-30)
REVERT: A  171 GLN cc_start: 0.8593 (pt0) cc_final: 0.8095 (mt0)
REVERT: A  181 ASP cc_start: 0.7609 (p0) cc_final: 0.7342 (p0)
REVERT: A  206 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8199 (mtmm)
REVERT: A  230 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8568 (mm-40)
REVERT: A  246 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7877 (mm-30)
REVERT: A  263 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7864 (ttmm)
REVERT: A  313 GLU cc_start: 0.8317 (mp0) cc_final: 0.7790 (mp0)
REVERT: C   25 MET cc_start: 0.7944 (mtt) cc_final: 0.7617 (mtt)
REVERT: B   28 LEU cc_start: 0.7504 (mp) cc_final: 0.7288 (tp)
REVERT: B   44 ILE cc_start: 0.7727 (pt) cc_final: 0.7442 (pt)
REVERT: B  106 LEU cc_start: 0.7550 (mp) cc_final: 0.7301 (mm)
REVERT: B  151 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8233 (t0)
REVERT: B  158 GLU cc_start: 0.7769 (mp0) cc_final: 0.7378 (tm-30)
REVERT: B  171 GLN cc_start: 0.8583 (pt0) cc_final: 0.8097 (mt0)
REVERT: B  181 ASP cc_start: 0.7601 (p0) cc_final: 0.7335 (p0)
REVERT: B  206 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8203 (mtmm)
REVERT: B  230 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8549 (mm-40)
REVERT: B  246 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7904 (mm-30)
REVERT: B  263 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7878 (ttmm)
REVERT: B  313 GLU cc_start: 0.8316 (mp0) cc_final: 0.7792 (mp0)
REVERT: D   25 MET cc_start: 0.7875 (mtt) cc_final: 0.7518 (mtt)
  outliers start: 23
  outliers final: 18
  residues processed: 105
  average time/residue: 0.0644
  time to fit residues: 9.5772
Evaluate side-chains
  104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 8 optimal weight:    0.3980
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.146068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.113218 restraints weight = 7881.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.38
r_work: 0.3385 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6718  Z= 0.123
  Angle     :  0.500   6.430   9100  Z= 0.250
  Chirality :  0.046   0.143   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.460  22.426    886
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  :  9.92 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.28), residues: 832
  helix: -0.78 (0.34), residues: 232
  sheet: -2.60 (0.28), residues: 304
  loop : -1.64 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.007   0.001   TYR D  15 
 PHE   0.009   0.001   PHE A 357 
 TRP   0.002   0.001   TRP A 168 
 HIS   0.001   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6718)
  covalent geometry    : angle       0.49980 ( 9100)
  hydrogen bonds       : bond        0.02874 (  258)
  hydrogen bonds       : angle       4.45133 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7511 (mp) cc_final: 0.7301 (tp)
REVERT: A   44 ILE cc_start: 0.7730 (pt) cc_final: 0.7438 (pt)
REVERT: A  106 LEU cc_start: 0.7616 (mp) cc_final: 0.7343 (mm)
REVERT: A  158 GLU cc_start: 0.7723 (mp0) cc_final: 0.7373 (tm-30)
REVERT: A  171 GLN cc_start: 0.8582 (pt0) cc_final: 0.8069 (mt0)
REVERT: A  181 ASP cc_start: 0.7481 (p0) cc_final: 0.7143 (p0)
REVERT: A  206 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8191 (mtmm)
REVERT: A  215 MET cc_start: 0.8016 (mtp) cc_final: 0.7720 (mtm)
REVERT: A  230 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8517 (mm-40)
REVERT: A  246 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7884 (mm-30)
REVERT: A  263 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7850 (ttmm)
REVERT: A  313 GLU cc_start: 0.8278 (mp0) cc_final: 0.7760 (mp0)
REVERT: C   25 MET cc_start: 0.7879 (mtt) cc_final: 0.7589 (mtt)
REVERT: B   28 LEU cc_start: 0.7513 (mp) cc_final: 0.7299 (tp)
REVERT: B   44 ILE cc_start: 0.7695 (pt) cc_final: 0.7410 (pt)
REVERT: B  106 LEU cc_start: 0.7597 (mp) cc_final: 0.7326 (mm)
REVERT: B  158 GLU cc_start: 0.7716 (mp0) cc_final: 0.7381 (tm-30)
REVERT: B  171 GLN cc_start: 0.8576 (pt0) cc_final: 0.8073 (mt0)
REVERT: B  181 ASP cc_start: 0.7465 (p0) cc_final: 0.7128 (p0)
REVERT: B  206 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8184 (mtmm)
REVERT: B  215 MET cc_start: 0.8017 (mtp) cc_final: 0.7722 (mtm)
REVERT: B  230 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8500 (mm-40)
REVERT: B  246 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7899 (mm-30)
REVERT: B  263 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7886 (ttmm)
REVERT: B  313 GLU cc_start: 0.8279 (mp0) cc_final: 0.7763 (mp0)
REVERT: D   25 MET cc_start: 0.7805 (mtt) cc_final: 0.7481 (mtt)
  outliers start: 26
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0618
  time to fit residues: 9.1636
Evaluate side-chains
  97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   12 ILE
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.147481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.115609 restraints weight = 7936.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 3.32
r_work: 0.3447 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6718  Z= 0.127
  Angle     :  0.505   6.518   9100  Z= 0.249
  Chirality :  0.047   0.144   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.375  22.482    886
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 11.24 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.28), residues: 832
  helix: -0.59 (0.34), residues: 232
  sheet: -2.82 (0.29), residues: 268
  loop : -1.42 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.007   0.001   TYR B  10 
 PHE   0.009   0.001   PHE A 357 
 TRP   0.002   0.001   TRP A 168 
 HIS   0.001   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6718)
  covalent geometry    : angle       0.50503 ( 9100)
  hydrogen bonds       : bond        0.02827 (  258)
  hydrogen bonds       : angle       4.32220 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7558 (mp) cc_final: 0.7342 (tp)
REVERT: A   44 ILE cc_start: 0.7731 (pt) cc_final: 0.7447 (pt)
REVERT: A  106 LEU cc_start: 0.7714 (mp) cc_final: 0.7438 (mm)
REVERT: A  151 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8321 (t0)
REVERT: A  158 GLU cc_start: 0.7668 (mp0) cc_final: 0.7419 (tm-30)
REVERT: A  171 GLN cc_start: 0.8553 (pt0) cc_final: 0.8072 (mt0)
REVERT: A  181 ASP cc_start: 0.7517 (p0) cc_final: 0.7284 (p0)
REVERT: A  206 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8228 (mtmm)
REVERT: A  215 MET cc_start: 0.8105 (mtp) cc_final: 0.7822 (mtm)
REVERT: A  230 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8553 (mm-40)
REVERT: A  243 ARG cc_start: 0.7533 (ttp80) cc_final: 0.6853 (ttm110)
REVERT: A  246 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7872 (mm-30)
REVERT: A  263 LYS cc_start: 0.8549 (ttmt) cc_final: 0.7938 (ttmm)
REVERT: A  313 GLU cc_start: 0.8306 (mp0) cc_final: 0.7779 (mp0)
REVERT: C   25 MET cc_start: 0.7907 (mtt) cc_final: 0.7598 (mtt)
REVERT: B   28 LEU cc_start: 0.7569 (mp) cc_final: 0.7351 (tp)
REVERT: B   44 ILE cc_start: 0.7704 (pt) cc_final: 0.7427 (pt)
REVERT: B  106 LEU cc_start: 0.7711 (mp) cc_final: 0.7432 (mm)
REVERT: B  151 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (t0)
REVERT: B  158 GLU cc_start: 0.7655 (mp0) cc_final: 0.7428 (tm-30)
REVERT: B  171 GLN cc_start: 0.8554 (pt0) cc_final: 0.8079 (mt0)
REVERT: B  181 ASP cc_start: 0.7493 (p0) cc_final: 0.7259 (p0)
REVERT: B  206 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8225 (mtmm)
REVERT: B  215 MET cc_start: 0.8099 (mtp) cc_final: 0.7814 (mtm)
REVERT: B  230 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8550 (mm-40)
REVERT: B  243 ARG cc_start: 0.7541 (ttp80) cc_final: 0.6856 (ttm110)
REVERT: B  246 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7895 (mm-30)
REVERT: B  263 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7946 (ttmm)
REVERT: B  313 GLU cc_start: 0.8309 (mp0) cc_final: 0.7783 (mp0)
REVERT: D   25 MET cc_start: 0.7887 (mtt) cc_final: 0.7563 (mtt)
  outliers start: 24
  outliers final: 19
  residues processed: 107
  average time/residue: 0.0767
  time to fit residues: 11.2298
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  151 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 68 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0050
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:    0.2980
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.2152

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.151556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.120266 restraints weight = 7714.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 3.25
r_work: 0.3504 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6718  Z= 0.084
  Angle     :  0.472   5.663   9100  Z= 0.236
  Chirality :  0.046   0.136   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.066  19.621    886
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.43 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.29), residues: 832
  helix: -0.29 (0.35), residues: 232
  sheet: -2.42 (0.28), residues: 304
  loop : -1.42 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.007   0.001   TYR D  14 
 PHE   0.006   0.001   PHE C  26 
 TRP   0.001   0.000   TRP A 168 
 HIS   0.004   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 6718)
  covalent geometry    : angle       0.47248 ( 9100)
  hydrogen bonds       : bond        0.02578 (  258)
  hydrogen bonds       : angle       4.11458 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   44 ILE cc_start: 0.7709 (pt) cc_final: 0.7419 (pt)
REVERT: A  106 LEU cc_start: 0.7643 (mp) cc_final: 0.7402 (mm)
REVERT: A  158 GLU cc_start: 0.7684 (mp0) cc_final: 0.7431 (tm-30)
REVERT: A  171 GLN cc_start: 0.8581 (pt0) cc_final: 0.8067 (mt0)
REVERT: A  181 ASP cc_start: 0.7318 (p0) cc_final: 0.6953 (p0)
REVERT: A  215 MET cc_start: 0.7947 (mtp) cc_final: 0.7563 (mtm)
REVERT: A  230 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8578 (mm-40)
REVERT: A  243 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6828 (ttm110)
REVERT: A  246 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7938 (mm-30)
REVERT: A  263 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7941 (ttmm)
REVERT: A  313 GLU cc_start: 0.8180 (mp0) cc_final: 0.7784 (mp0)
REVERT: A  347 GLU cc_start: 0.8176 (tt0) cc_final: 0.7641 (tt0)
REVERT: C   25 MET cc_start: 0.7697 (mtt) cc_final: 0.7387 (mtt)
REVERT: B   44 ILE cc_start: 0.7687 (pt) cc_final: 0.7400 (pt)
REVERT: B  106 LEU cc_start: 0.7635 (mp) cc_final: 0.7394 (mm)
REVERT: B  158 GLU cc_start: 0.7704 (mp0) cc_final: 0.7444 (tm-30)
REVERT: B  171 GLN cc_start: 0.8586 (pt0) cc_final: 0.8070 (mt0)
REVERT: B  181 ASP cc_start: 0.7302 (p0) cc_final: 0.6946 (p0)
REVERT: B  215 MET cc_start: 0.7950 (mtp) cc_final: 0.7564 (mtm)
REVERT: B  230 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8577 (mm-40)
REVERT: B  243 ARG cc_start: 0.7507 (ttp80) cc_final: 0.6829 (ttm110)
REVERT: B  246 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7938 (mm-30)
REVERT: B  263 LYS cc_start: 0.8540 (ttmt) cc_final: 0.7940 (ttmm)
REVERT: B  313 GLU cc_start: 0.8188 (mp0) cc_final: 0.7799 (mp0)
REVERT: B  347 GLU cc_start: 0.8170 (tt0) cc_final: 0.7635 (tt0)
REVERT: D   25 MET cc_start: 0.7686 (mtt) cc_final: 0.7379 (mtt)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0769
  time to fit residues: 10.6593
Evaluate side-chains
  96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 65 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0870
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.150683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.119216 restraints weight = 7814.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 3.26
r_work: 0.3493 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6718  Z= 0.097
  Angle     :  0.483   6.420   9100  Z= 0.240
  Chirality :  0.046   0.142   1068
  Planarity :  0.002   0.020   1186
  Dihedral  :  4.074  21.377    886
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.96 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.29), residues: 832
  helix: -0.09 (0.36), residues: 232
  sheet: -2.62 (0.29), residues: 268
  loop : -1.25 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   8 
 TYR   0.007   0.001   TYR B  10 
 PHE   0.007   0.001   PHE A 357 
 TRP   0.001   0.000   TRP A 168 
 HIS   0.001   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6718)
  covalent geometry    : angle       0.48290 ( 9100)
  hydrogen bonds       : bond        0.02612 (  258)
  hydrogen bonds       : angle       3.99349 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   44 ILE cc_start: 0.7678 (pt) cc_final: 0.7392 (pt)
REVERT: A  106 LEU cc_start: 0.7644 (mp) cc_final: 0.7401 (mm)
REVERT: A  149 GLN cc_start: 0.7867 (mt0) cc_final: 0.7470 (mt0)
REVERT: A  158 GLU cc_start: 0.7653 (mp0) cc_final: 0.7406 (tm-30)
REVERT: A  171 GLN cc_start: 0.8593 (pt0) cc_final: 0.8057 (mt0)
REVERT: A  181 ASP cc_start: 0.7376 (p0) cc_final: 0.7103 (p0)
REVERT: A  230 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8552 (mm-40)
REVERT: A  243 ARG cc_start: 0.7496 (ttp80) cc_final: 0.6807 (ttm110)
REVERT: A  246 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7831 (mm-30)
REVERT: A  263 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7933 (ttmm)
REVERT: A  313 GLU cc_start: 0.8196 (mp0) cc_final: 0.7788 (mp0)
REVERT: A  347 GLU cc_start: 0.8184 (tt0) cc_final: 0.7641 (tt0)
REVERT: C   25 MET cc_start: 0.7794 (mtt) cc_final: 0.7498 (mtt)
REVERT: B   44 ILE cc_start: 0.7659 (pt) cc_final: 0.7376 (pt)
REVERT: B  106 LEU cc_start: 0.7629 (mp) cc_final: 0.7383 (mm)
REVERT: B  149 GLN cc_start: 0.7874 (mt0) cc_final: 0.7473 (mt0)
REVERT: B  158 GLU cc_start: 0.7675 (mp0) cc_final: 0.7422 (tm-30)
REVERT: B  171 GLN cc_start: 0.8597 (pt0) cc_final: 0.8060 (mt0)
REVERT: B  181 ASP cc_start: 0.7390 (p0) cc_final: 0.7181 (p0)
REVERT: B  230 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8543 (mm-40)
REVERT: B  243 ARG cc_start: 0.7491 (ttp80) cc_final: 0.6810 (ttm110)
REVERT: B  246 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7852 (mm-30)
REVERT: B  263 LYS cc_start: 0.8557 (ttmt) cc_final: 0.7960 (ttmm)
REVERT: B  313 GLU cc_start: 0.8200 (mp0) cc_final: 0.7788 (mp0)
REVERT: B  347 GLU cc_start: 0.8156 (tt0) cc_final: 0.7599 (tt0)
REVERT: D   25 MET cc_start: 0.7779 (mtt) cc_final: 0.7470 (mtt)
  outliers start: 19
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0777
  time to fit residues: 10.8117
Evaluate side-chains
  100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0570
   chunk 50 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
B 102 GLN
B 151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.150635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118864 restraints weight = 7885.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 3.28
r_work: 0.3483 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6718  Z= 0.105
  Angle     :  0.500   6.461   9100  Z= 0.244
  Chirality :  0.046   0.143   1068
  Planarity :  0.002   0.023   1186
  Dihedral  :  4.056  21.751    886
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.36 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.29), residues: 832
  helix:  0.35 (0.37), residues: 218
  sheet: -2.30 (0.29), residues: 304
  loop : -1.26 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   8 
 TYR   0.007   0.001   TYR B  10 
 PHE   0.007   0.001   PHE A 357 
 TRP   0.001   0.000   TRP B 168 
 HIS   0.001   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6718)
  covalent geometry    : angle       0.49978 ( 9100)
  hydrogen bonds       : bond        0.02622 (  258)
  hydrogen bonds       : angle       3.94461 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLN cc_start: 0.7723 (mp10) cc_final: 0.7469 (pm20)
REVERT: A  106 LEU cc_start: 0.7647 (mp) cc_final: 0.7400 (mm)
REVERT: A  149 GLN cc_start: 0.7903 (mt0) cc_final: 0.7515 (mt0)
REVERT: A  158 GLU cc_start: 0.7626 (mp0) cc_final: 0.7419 (tm-30)
REVERT: A  171 GLN cc_start: 0.8601 (pt0) cc_final: 0.8165 (mt0)
REVERT: A  181 ASP cc_start: 0.7402 (p0) cc_final: 0.7147 (p0)
REVERT: A  230 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8542 (mm-40)
REVERT: A  243 ARG cc_start: 0.7466 (ttp80) cc_final: 0.6776 (ttm110)
REVERT: A  246 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7838 (mm-30)
REVERT: A  263 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8027 (ttmm)
REVERT: A  313 GLU cc_start: 0.8216 (mp0) cc_final: 0.7796 (mp0)
REVERT: C   25 MET cc_start: 0.7871 (mtt) cc_final: 0.7548 (mtt)
REVERT: B  106 LEU cc_start: 0.7638 (mp) cc_final: 0.7392 (mm)
REVERT: B  149 GLN cc_start: 0.7901 (mt0) cc_final: 0.7519 (mt0)
REVERT: B  158 GLU cc_start: 0.7657 (mp0) cc_final: 0.7438 (tm-30)
REVERT: B  171 GLN cc_start: 0.8591 (pt0) cc_final: 0.8160 (mt0)
REVERT: B  181 ASP cc_start: 0.7403 (p0) cc_final: 0.7146 (p0)
REVERT: B  230 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8537 (mm-40)
REVERT: B  243 ARG cc_start: 0.7473 (ttp80) cc_final: 0.6786 (ttm110)
REVERT: B  246 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7861 (mm-30)
REVERT: B  263 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7954 (ttmm)
REVERT: B  313 GLU cc_start: 0.8202 (mp0) cc_final: 0.7787 (mp0)
REVERT: B  347 GLU cc_start: 0.8156 (tt0) cc_final: 0.7597 (tt0)
REVERT: D   25 MET cc_start: 0.7809 (mtt) cc_final: 0.7495 (mtt)
  outliers start: 21
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0846
  time to fit residues: 12.2860
Evaluate side-chains
  104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 102 GLN
A 151 ASN
B 151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.151149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.119232 restraints weight = 7858.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 3.29
r_work: 0.3490 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6718  Z= 0.101
  Angle     :  0.499   7.469   9100  Z= 0.245
  Chirality :  0.047   0.183   1068
  Planarity :  0.002   0.020   1186
  Dihedral  :  4.006  21.373    886
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.42 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.29), residues: 832
  helix:  0.60 (0.38), residues: 218
  sheet: -2.55 (0.29), residues: 268
  loop : -1.12 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   8 
 TYR   0.007   0.001   TYR B  10 
 PHE   0.007   0.001   PHE A 357 
 TRP   0.001   0.000   TRP A 168 
 HIS   0.002   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6718)
  covalent geometry    : angle       0.49947 ( 9100)
  hydrogen bonds       : bond        0.02582 (  258)
  hydrogen bonds       : angle       3.89322 (  840)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5648 (ttm) cc_final: 0.5392 (ttm)
REVERT: A  106 LEU cc_start: 0.7611 (mp) cc_final: 0.7358 (mm)
REVERT: A  149 GLN cc_start: 0.7877 (mt0) cc_final: 0.7491 (mt0)
REVERT: A  171 GLN cc_start: 0.8566 (pt0) cc_final: 0.8147 (mt0)
REVERT: A  181 ASP cc_start: 0.7337 (p0) cc_final: 0.7095 (p0)
REVERT: A  230 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8536 (mm-40)
REVERT: A  243 ARG cc_start: 0.7430 (ttp80) cc_final: 0.6754 (ttm110)
REVERT: A  246 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7777 (mm-30)
REVERT: A  263 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7911 (ttmm)
REVERT: A  313 GLU cc_start: 0.8237 (mp0) cc_final: 0.7810 (mp0)
REVERT: A  347 GLU cc_start: 0.8170 (tt0) cc_final: 0.7609 (tt0)
REVERT: C   25 MET cc_start: 0.7823 (mtt) cc_final: 0.7525 (mtt)
REVERT: B  106 LEU cc_start: 0.7606 (mp) cc_final: 0.7359 (mm)
REVERT: B  149 GLN cc_start: 0.7889 (mt0) cc_final: 0.7504 (mt0)
REVERT: B  171 GLN cc_start: 0.8559 (pt0) cc_final: 0.8144 (mt0)
REVERT: B  181 ASP cc_start: 0.7326 (p0) cc_final: 0.7083 (p0)
REVERT: B  230 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8528 (mm-40)
REVERT: B  243 ARG cc_start: 0.7429 (ttp80) cc_final: 0.6757 (ttm110)
REVERT: B  246 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7807 (mm-30)
REVERT: B  263 LYS cc_start: 0.8550 (ttmt) cc_final: 0.7938 (ttmm)
REVERT: B  313 GLU cc_start: 0.8236 (mp0) cc_final: 0.7808 (mp0)
REVERT: B  347 GLU cc_start: 0.8148 (tt0) cc_final: 0.7578 (tt0)
REVERT: D   25 MET cc_start: 0.7802 (mtt) cc_final: 0.7503 (mtt)
  outliers start: 19
  outliers final: 16
  residues processed: 104
  average time/residue: 0.0760
  time to fit residues: 10.7657
Evaluate side-chains
  98 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0070
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0670
   chunk 58 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.1634

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.153434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.121823 restraints weight = 7775.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 3.27
r_work: 0.3528 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6718  Z= 0.090
  Angle     :  0.507   6.830   9100  Z= 0.252
  Chirality :  0.046   0.163   1068
  Planarity :  0.003   0.025   1186
  Dihedral  :  3.905  19.824    886
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.21 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.30), residues: 832
  helix:  0.88 (0.38), residues: 218
  sheet: -2.44 (0.29), residues: 268
  loop : -1.00 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   8 
 TYR   0.006   0.001   TYR B  10 
 PHE   0.009   0.001   PHE A 103 
 TRP   0.001   0.000   TRP A 168 
 HIS   0.003   0.000   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 6718)
  covalent geometry    : angle       0.50678 ( 9100)
  hydrogen bonds       : bond        0.02523 (  258)
  hydrogen bonds       : angle       3.82348 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1450.94 seconds
wall clock time: 25 minutes 37.78 seconds (1537.78 seconds total)