Starting phenix.real_space_refine
on Tue Feb 11 20:44:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_31339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_31339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_31339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_31339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7evp_31339/02_2025/7evp_31339.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.94, per 1000 atoms: 0.75
  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: 1.54
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.18
  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: 2.48

  Time building geometry restraints manager: 1.81 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: 0.03
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.000
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.800
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.250
-------------------------------------------------------------------------------
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= 0.511
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.033   0.007   TRP B 168 
 HIS   0.010   0.002   HIS C  19 
 PHE   0.029   0.004   PHE B  11 
 TYR   0.019   0.003   TYR C  32 
 ARG   0.007   0.001   ARG B 283 

*********************** 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  : 0.783 
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: 0.7718 (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: 0.7987 (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: 0.2151
  time to fit residues: 40.8165
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  : 1.082 
-------------------------------------------------------------------------------
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 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.149587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.118434 restraints weight = 7822.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 3.28
r_work: 0.3490 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6718  Z= 0.191
  Angle     :  0.547   5.890   9100  Z= 0.283
  Chirality :  0.047   0.155   1068
  Planarity :  0.004   0.034   1186
  Dihedral  :  5.123  22.515    886
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  6.61 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.26), residues: 832
  helix: -2.35 (0.29), residues: 224
  sheet: -2.84 (0.27), residues: 294
  loop : -2.50 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 168 
 HIS   0.004   0.001   HIS D  19 
 PHE   0.009   0.001   PHE B 357 
 TYR   0.008   0.001   TYR D  14 
 ARG   0.002   0.000   ARG A   8 

*********************** 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
  123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7548 (mp) cc_final: 0.7326 (tp)
REVERT: A   44 ILE cc_start: 0.7773 (pt) cc_final: 0.7486 (pt)
REVERT: A   86 ILE cc_start: 0.8396 (mm) cc_final: 0.8158 (mt)
REVERT: A  102 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7935 (mp10)
REVERT: A  106 LEU cc_start: 0.7599 (mp) cc_final: 0.7029 (pp)
REVERT: A  149 GLN cc_start: 0.7972 (mt0) cc_final: 0.7628 (mt0)
REVERT: A  158 GLU cc_start: 0.7797 (mp0) cc_final: 0.7396 (tm-30)
REVERT: A  171 GLN cc_start: 0.8468 (pt0) cc_final: 0.8078 (mt0)
REVERT: A  206 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8324 (mtmm)
REVERT: A  246 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7748 (mm-30)
REVERT: A  263 LYS cc_start: 0.8383 (ttmt) cc_final: 0.7806 (ttmm)
REVERT: A  313 GLU cc_start: 0.8202 (mp0) cc_final: 0.7733 (mp0)
REVERT: A  349 GLU cc_start: 0.8391 (pt0) cc_final: 0.8165 (pt0)
REVERT: B   28 LEU cc_start: 0.7544 (mp) cc_final: 0.7322 (tp)
REVERT: B   44 ILE cc_start: 0.7749 (pt) cc_final: 0.7463 (pt)
REVERT: B   86 ILE cc_start: 0.8400 (mm) cc_final: 0.8165 (mt)
REVERT: B  102 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7941 (mp10)
REVERT: B  106 LEU cc_start: 0.7602 (mp) cc_final: 0.7030 (pp)
REVERT: B  149 GLN cc_start: 0.7972 (mt0) cc_final: 0.7627 (mt0)
REVERT: B  158 GLU cc_start: 0.7803 (mp0) cc_final: 0.7401 (tm-30)
REVERT: B  171 GLN cc_start: 0.8468 (pt0) cc_final: 0.8081 (mt0)
REVERT: B  206 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8311 (mtmm)
REVERT: B  246 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7756 (mm-30)
REVERT: B  263 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7862 (ttmm)
REVERT: B  313 GLU cc_start: 0.8204 (mp0) cc_final: 0.7739 (mp0)
REVERT: B  349 GLU cc_start: 0.8396 (pt0) cc_final: 0.8163 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1655
  time to fit residues: 27.2105
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0020
   chunk 40 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.6188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.148483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.115860 restraints weight = 7705.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.41
r_work: 0.3421 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6718  Z= 0.168
  Angle     :  0.499   6.096   9100  Z= 0.256
  Chirality :  0.046   0.144   1068
  Planarity :  0.003   0.025   1186
  Dihedral  :  4.682  21.093    886
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  :  8.07 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.27), residues: 832
  helix: -1.62 (0.30), residues: 230
  sheet: -2.71 (0.28), residues: 304
  loop : -2.05 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 168 
 HIS   0.003   0.000   HIS D  19 
 PHE   0.009   0.001   PHE B 103 
 TYR   0.007   0.001   TYR C  14 
 ARG   0.003   0.000   ARG A   8 

*********************** 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
  120 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5412 (ttm) cc_final: 0.5041 (ttp)
REVERT: A   28 LEU cc_start: 0.7522 (mp) cc_final: 0.7310 (tp)
REVERT: A   37 ASP cc_start: 0.7503 (t0) cc_final: 0.6498 (m-30)
REVERT: A   44 ILE cc_start: 0.7637 (pt) cc_final: 0.7346 (pt)
REVERT: A  102 GLN cc_start: 0.8221 (mp10) cc_final: 0.7962 (mp10)
REVERT: A  106 LEU cc_start: 0.7474 (mp) cc_final: 0.7227 (mm)
REVERT: A  149 GLN cc_start: 0.7872 (mt0) cc_final: 0.7492 (mt0)
REVERT: A  158 GLU cc_start: 0.7748 (mp0) cc_final: 0.7365 (tm-30)
REVERT: A  171 GLN cc_start: 0.8533 (pt0) cc_final: 0.8071 (mt0)
REVERT: A  206 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8242 (mtmm)
REVERT: A  246 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7723 (mm-30)
REVERT: A  263 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7803 (ttmm)
REVERT: A  313 GLU cc_start: 0.8229 (mp0) cc_final: 0.7788 (mp0)
REVERT: B   28 LEU cc_start: 0.7509 (mp) cc_final: 0.7298 (tp)
REVERT: B   37 ASP cc_start: 0.7492 (t0) cc_final: 0.6482 (m-30)
REVERT: B   44 ILE cc_start: 0.7607 (pt) cc_final: 0.7321 (pt)
REVERT: B  106 LEU cc_start: 0.7458 (mp) cc_final: 0.7215 (mm)
REVERT: B  149 GLN cc_start: 0.7877 (mt0) cc_final: 0.7498 (mt0)
REVERT: B  158 GLU cc_start: 0.7737 (mp0) cc_final: 0.7367 (tm-30)
REVERT: B  171 GLN cc_start: 0.8548 (pt0) cc_final: 0.8086 (mt0)
REVERT: B  206 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8239 (mtmm)
REVERT: B  246 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7747 (mm-30)
REVERT: B  263 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7792 (ttmm)
REVERT: B  313 GLU cc_start: 0.8227 (mp0) cc_final: 0.7794 (mp0)
REVERT: B  349 GLU cc_start: 0.8315 (pt0) cc_final: 0.8085 (pt0)
  outliers start: 26
  outliers final: 15
  residues processed: 114
  average time/residue: 0.1706
  time to fit residues: 27.9108
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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  367 VAL
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 6 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.146057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.114133 restraints weight = 7986.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 3.33
r_work: 0.3435 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6718  Z= 0.268
  Angle     :  0.536   6.838   9100  Z= 0.271
  Chirality :  0.047   0.151   1068
  Planarity :  0.003   0.018   1186
  Dihedral  :  4.750  24.330    886
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  :  8.99 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.28), residues: 832
  helix: -1.16 (0.32), residues: 230
  sheet: -2.66 (0.28), residues: 304
  loop : -1.85 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B 168 
 HIS   0.001   0.001   HIS B 273 
 PHE   0.010   0.002   PHE B 357 
 TYR   0.007   0.001   TYR B  10 
 ARG   0.003   0.000   ARG B 283 

*********************** 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
  118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7567 (mp) cc_final: 0.7347 (tp)
REVERT: A   44 ILE cc_start: 0.7692 (pt) cc_final: 0.7408 (pt)
REVERT: A   86 ILE cc_start: 0.8376 (mm) cc_final: 0.8168 (mt)
REVERT: A  106 LEU cc_start: 0.7647 (mp) cc_final: 0.7401 (mm)
REVERT: A  158 GLU cc_start: 0.7760 (mp0) cc_final: 0.7401 (tm-30)
REVERT: A  171 GLN cc_start: 0.8540 (pt0) cc_final: 0.8092 (mt0)
REVERT: A  181 ASP cc_start: 0.7760 (p0) cc_final: 0.7508 (p0)
REVERT: A  206 LYS cc_start: 0.8461 (ptpp) cc_final: 0.8218 (mtmm)
REVERT: A  230 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8609 (mm-40)
REVERT: A  246 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7881 (mm-30)
REVERT: A  263 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7956 (ttmm)
REVERT: A  313 GLU cc_start: 0.8322 (mp0) cc_final: 0.7843 (mp0)
REVERT: C   25 MET cc_start: 0.8003 (mtt) cc_final: 0.7646 (mtt)
REVERT: B   28 LEU cc_start: 0.7571 (mp) cc_final: 0.7350 (tp)
REVERT: B   44 ILE cc_start: 0.7671 (pt) cc_final: 0.7389 (pt)
REVERT: B   86 ILE cc_start: 0.8382 (mm) cc_final: 0.8176 (mt)
REVERT: B  106 LEU cc_start: 0.7690 (mp) cc_final: 0.7425 (mm)
REVERT: B  158 GLU cc_start: 0.7744 (mp0) cc_final: 0.7418 (tm-30)
REVERT: B  171 GLN cc_start: 0.8530 (pt0) cc_final: 0.8096 (mt0)
REVERT: B  181 ASP cc_start: 0.7739 (p0) cc_final: 0.7491 (p0)
REVERT: B  206 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8205 (mtmm)
REVERT: B  230 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8595 (mm-40)
REVERT: B  246 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7926 (mm-30)
REVERT: B  263 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7894 (ttmm)
REVERT: B  313 GLU cc_start: 0.8330 (mp0) cc_final: 0.7845 (mp0)
REVERT: D   25 MET cc_start: 0.7974 (mtt) cc_final: 0.7622 (mtt)
  outliers start: 23
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1583
  time to fit residues: 25.4507
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
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  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  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 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 49 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 15 optimal weight:    0.4980
   chunk 34 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.148947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.117166 restraints weight = 7862.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 3.30
r_work: 0.3467 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6718  Z= 0.168
  Angle     :  0.485   6.363   9100  Z= 0.245
  Chirality :  0.046   0.142   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.367  21.433    886
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  :  9.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.28), residues: 832
  helix: -0.68 (0.34), residues: 232
  sheet: -2.57 (0.28), residues: 304
  loop : -1.67 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 168 
 HIS   0.002   0.000   HIS D  19 
 PHE   0.009   0.001   PHE B 357 
 TYR   0.007   0.001   TYR D  14 
 ARG   0.003   0.000   ARG A   8 

*********************** 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
  113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7537 (mp) cc_final: 0.7333 (tp)
REVERT: A   44 ILE cc_start: 0.7675 (pt) cc_final: 0.7379 (pt)
REVERT: A  106 LEU cc_start: 0.7633 (mp) cc_final: 0.7378 (mm)
REVERT: A  149 GLN cc_start: 0.7925 (mt0) cc_final: 0.7525 (mt0)
REVERT: A  158 GLU cc_start: 0.7693 (mp0) cc_final: 0.7385 (tm-30)
REVERT: A  171 GLN cc_start: 0.8537 (pt0) cc_final: 0.8059 (mt0)
REVERT: A  206 LYS cc_start: 0.8476 (ptpp) cc_final: 0.8226 (mtmm)
REVERT: A  215 MET cc_start: 0.8072 (mtp) cc_final: 0.7818 (mtm)
REVERT: A  230 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8588 (mm-40)
REVERT: A  243 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6876 (ttm110)
REVERT: A  246 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7896 (mm-30)
REVERT: A  263 LYS cc_start: 0.8528 (ttmt) cc_final: 0.7917 (ttmm)
REVERT: A  313 GLU cc_start: 0.8245 (mp0) cc_final: 0.7816 (mp0)
REVERT: C   25 MET cc_start: 0.7880 (mtt) cc_final: 0.7557 (mtt)
REVERT: B   28 LEU cc_start: 0.7548 (mp) cc_final: 0.7340 (tp)
REVERT: B   44 ILE cc_start: 0.7647 (pt) cc_final: 0.7357 (pt)
REVERT: B  106 LEU cc_start: 0.7617 (mp) cc_final: 0.7358 (mm)
REVERT: B  149 GLN cc_start: 0.7934 (mt0) cc_final: 0.7541 (mt0)
REVERT: B  158 GLU cc_start: 0.7684 (mp0) cc_final: 0.7401 (tm-30)
REVERT: B  171 GLN cc_start: 0.8547 (pt0) cc_final: 0.8071 (mt0)
REVERT: B  206 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8226 (mtmm)
REVERT: B  215 MET cc_start: 0.8070 (mtp) cc_final: 0.7815 (mtm)
REVERT: B  230 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8579 (mm-40)
REVERT: B  243 ARG cc_start: 0.7533 (ttp80) cc_final: 0.6874 (ttm110)
REVERT: B  246 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7912 (mm-30)
REVERT: B  263 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7954 (ttmm)
REVERT: B  313 GLU cc_start: 0.8260 (mp0) cc_final: 0.7828 (mp0)
REVERT: D   25 MET cc_start: 0.7840 (mtt) cc_final: 0.7507 (mtt)
  outliers start: 26
  outliers final: 18
  residues processed: 109
  average time/residue: 0.1791
  time to fit residues: 26.6724
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
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  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   28 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   12 ILE
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  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.147386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.115788 restraints weight = 7872.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 3.29
r_work: 0.3452 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6718  Z= 0.215
  Angle     :  0.506   6.572   9100  Z= 0.252
  Chirality :  0.047   0.144   1068
  Planarity :  0.002   0.015   1186
  Dihedral  :  4.394  22.912    886
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 10.19 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.28), residues: 832
  helix: -0.53 (0.35), residues: 232
  sheet: -2.83 (0.29), residues: 268
  loop : -1.44 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 168 
 HIS   0.001   0.000   HIS A 183 
 PHE   0.008   0.001   PHE A 357 
 TYR   0.007   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A   8 

*********************** 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
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7561 (mp) cc_final: 0.7341 (tp)
REVERT: A  106 LEU cc_start: 0.7708 (mp) cc_final: 0.7432 (mm)
REVERT: A  151 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8319 (t0)
REVERT: A  158 GLU cc_start: 0.7652 (mp0) cc_final: 0.7412 (tm-30)
REVERT: A  171 GLN cc_start: 0.8552 (pt0) cc_final: 0.8072 (mt0)
REVERT: A  206 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8222 (mtmm)
REVERT: A  215 MET cc_start: 0.8107 (mtp) cc_final: 0.7806 (mtm)
REVERT: A  230 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8563 (mm-40)
REVERT: A  243 ARG cc_start: 0.7548 (ttp80) cc_final: 0.6872 (ttm110)
REVERT: A  246 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7885 (mm-30)
REVERT: A  263 LYS cc_start: 0.8543 (ttmt) cc_final: 0.7856 (ttmm)
REVERT: A  313 GLU cc_start: 0.8283 (mp0) cc_final: 0.7827 (mp0)
REVERT: A  347 GLU cc_start: 0.8230 (tt0) cc_final: 0.7654 (tt0)
REVERT: C   25 MET cc_start: 0.7930 (mtt) cc_final: 0.7586 (mtt)
REVERT: B   28 LEU cc_start: 0.7562 (mp) cc_final: 0.7339 (tp)
REVERT: B  106 LEU cc_start: 0.7694 (mp) cc_final: 0.7413 (mm)
REVERT: B  151 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8324 (t0)
REVERT: B  158 GLU cc_start: 0.7666 (mp0) cc_final: 0.7425 (tm-30)
REVERT: B  171 GLN cc_start: 0.8551 (pt0) cc_final: 0.8073 (mt0)
REVERT: B  206 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8218 (mtmm)
REVERT: B  215 MET cc_start: 0.8108 (mtp) cc_final: 0.7807 (mtm)
REVERT: B  230 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8559 (mm-40)
REVERT: B  243 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6872 (ttm110)
REVERT: B  246 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7912 (mm-30)
REVERT: B  263 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7960 (ttmm)
REVERT: B  313 GLU cc_start: 0.8285 (mp0) cc_final: 0.7823 (mp0)
REVERT: D   25 MET cc_start: 0.7907 (mtt) cc_final: 0.7581 (mtt)
  outliers start: 26
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1836
  time to fit residues: 27.2351
Evaluate side-chains
  101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain D residue   32 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.147410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.115583 restraints weight = 7827.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 3.29
r_work: 0.3452 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2603

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= 0.196
  Angle     :  0.500   6.511   9100  Z= 0.247
  Chirality :  0.046   0.138   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.332  22.745    886
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 11.38 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.29), residues: 832
  helix: -0.42 (0.35), residues: 232
  sheet: -2.79 (0.29), residues: 268
  loop : -1.37 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 168 
 HIS   0.001   0.000   HIS D  19 
 PHE   0.008   0.001   PHE B 357 
 TYR   0.006   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A   8 

*********************** 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
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7558 (mp) cc_final: 0.7340 (tp)
REVERT: A   44 ILE cc_start: 0.7731 (pt) cc_final: 0.7487 (pt)
REVERT: A  106 LEU cc_start: 0.7708 (mp) cc_final: 0.7431 (mm)
REVERT: A  158 GLU cc_start: 0.7620 (mp0) cc_final: 0.7397 (tm-30)
REVERT: A  171 GLN cc_start: 0.8552 (pt0) cc_final: 0.8071 (mt0)
REVERT: A  181 ASP cc_start: 0.7513 (p0) cc_final: 0.7272 (p0)
REVERT: A  206 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8227 (mtmm)
REVERT: A  215 MET cc_start: 0.8064 (mtp) cc_final: 0.7734 (mtm)
REVERT: A  230 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8547 (mm-40)
REVERT: A  243 ARG cc_start: 0.7558 (ttp80) cc_final: 0.6849 (ttm110)
REVERT: A  246 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7877 (mm-30)
REVERT: A  263 LYS cc_start: 0.8565 (ttmt) cc_final: 0.7921 (ttmm)
REVERT: A  301 LEU cc_start: 0.8272 (mt) cc_final: 0.8062 (mt)
REVERT: A  313 GLU cc_start: 0.8295 (mp0) cc_final: 0.7797 (mp0)
REVERT: A  347 GLU cc_start: 0.8212 (tt0) cc_final: 0.7637 (tt0)
REVERT: C   25 MET cc_start: 0.7930 (mtt) cc_final: 0.7635 (mtt)
REVERT: B    1 MET cc_start: 0.6387 (ttp) cc_final: 0.6059 (tpp)
REVERT: B   28 LEU cc_start: 0.7564 (mp) cc_final: 0.7342 (tp)
REVERT: B   44 ILE cc_start: 0.7707 (pt) cc_final: 0.7469 (pt)
REVERT: B  106 LEU cc_start: 0.7697 (mp) cc_final: 0.7408 (mm)
REVERT: B  158 GLU cc_start: 0.7633 (mp0) cc_final: 0.7410 (tm-30)
REVERT: B  171 GLN cc_start: 0.8555 (pt0) cc_final: 0.8074 (mt0)
REVERT: B  181 ASP cc_start: 0.7501 (p0) cc_final: 0.7257 (p0)
REVERT: B  206 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8218 (mtmm)
REVERT: B  215 MET cc_start: 0.8060 (mtp) cc_final: 0.7727 (mtm)
REVERT: B  230 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8552 (mm-40)
REVERT: B  243 ARG cc_start: 0.7563 (ttp80) cc_final: 0.6846 (ttm110)
REVERT: B  246 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7805 (mm-30)
REVERT: B  263 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8032 (ttmm)
REVERT: B  301 LEU cc_start: 0.8280 (mt) cc_final: 0.8070 (mt)
REVERT: B  313 GLU cc_start: 0.8316 (mp0) cc_final: 0.7807 (mp0)
REVERT: D   25 MET cc_start: 0.7878 (mtt) cc_final: 0.7551 (mtt)
  outliers start: 22
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1749
  time to fit residues: 26.3199
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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   28 LEU
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   28 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 51 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.147117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.115277 restraints weight = 7870.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.28
r_work: 0.3439 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2678

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= 0.220
  Angle     :  0.516   6.793   9100  Z= 0.256
  Chirality :  0.047   0.142   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.374  23.459    886
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.29), residues: 832
  helix: -0.35 (0.35), residues: 232
  sheet: -2.80 (0.29), residues: 268
  loop : -1.32 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 168 
 HIS   0.001   0.000   HIS B 273 
 PHE   0.009   0.001   PHE B 357 
 TYR   0.007   0.001   TYR A  10 
 ARG   0.002   0.000   ARG A   8 

*********************** 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
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7550 (mp) cc_final: 0.7338 (tp)
REVERT: A   44 ILE cc_start: 0.7764 (pt) cc_final: 0.7527 (pt)
REVERT: A  106 LEU cc_start: 0.7781 (mp) cc_final: 0.7503 (mm)
REVERT: A  151 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8335 (t0)
REVERT: A  158 GLU cc_start: 0.7649 (mp0) cc_final: 0.7382 (tm-30)
REVERT: A  171 GLN cc_start: 0.8566 (pt0) cc_final: 0.8076 (mt0)
REVERT: A  181 ASP cc_start: 0.7604 (p0) cc_final: 0.7371 (p0)
REVERT: A  230 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8540 (mm-40)
REVERT: A  243 ARG cc_start: 0.7525 (ttp80) cc_final: 0.6831 (ttm110)
REVERT: A  246 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7812 (mm-30)
REVERT: A  263 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7998 (ttmm)
REVERT: A  313 GLU cc_start: 0.8330 (mp0) cc_final: 0.7843 (mp0)
REVERT: C   25 MET cc_start: 0.7975 (mtt) cc_final: 0.7660 (mtt)
REVERT: B    1 MET cc_start: 0.6507 (ttp) cc_final: 0.6122 (tpp)
REVERT: B   28 LEU cc_start: 0.7550 (mp) cc_final: 0.7335 (tp)
REVERT: B   44 ILE cc_start: 0.7757 (pt) cc_final: 0.7520 (pt)
REVERT: B  106 LEU cc_start: 0.7776 (mp) cc_final: 0.7486 (mm)
REVERT: B  151 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8339 (t0)
REVERT: B  158 GLU cc_start: 0.7669 (mp0) cc_final: 0.7393 (tm-30)
REVERT: B  171 GLN cc_start: 0.8565 (pt0) cc_final: 0.8076 (mt0)
REVERT: B  181 ASP cc_start: 0.7592 (p0) cc_final: 0.7356 (p0)
REVERT: B  230 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8537 (mm-40)
REVERT: B  243 ARG cc_start: 0.7524 (ttp80) cc_final: 0.6831 (ttm110)
REVERT: B  246 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7844 (mm-30)
REVERT: B  263 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8006 (ttmm)
REVERT: B  301 LEU cc_start: 0.8419 (mt) cc_final: 0.8187 (mt)
REVERT: B  313 GLU cc_start: 0.8336 (mp0) cc_final: 0.7812 (mp0)
REVERT: D   25 MET cc_start: 0.7913 (mtt) cc_final: 0.7591 (mtt)
  outliers start: 24
  outliers final: 20
  residues processed: 111
  average time/residue: 0.1784
  time to fit residues: 27.1581
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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  140 VAL
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 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  140 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0870
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.147603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.115489 restraints weight = 7866.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 3.30
r_work: 0.3450 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2777

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= 0.187
  Angle     :  0.507   6.558   9100  Z= 0.251
  Chirality :  0.047   0.140   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.278  22.688    886
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 11.77 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.29), residues: 832
  helix: -0.03 (0.36), residues: 218
  sheet: -2.77 (0.29), residues: 268
  loop : -1.20 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 168 
 HIS   0.001   0.000   HIS D  19 
 PHE   0.008   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  10 
 ARG   0.003   0.000   ARG A   8 

*********************** 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
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7547 (mp) cc_final: 0.7345 (tp)
REVERT: A   44 ILE cc_start: 0.7740 (pt) cc_final: 0.7496 (pt)
REVERT: A  106 LEU cc_start: 0.7730 (mp) cc_final: 0.7446 (mm)
REVERT: A  151 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8151 (t0)
REVERT: A  158 GLU cc_start: 0.7636 (mp0) cc_final: 0.7395 (tm-30)
REVERT: A  171 GLN cc_start: 0.8550 (pt0) cc_final: 0.8052 (mt0)
REVERT: A  181 ASP cc_start: 0.7495 (p0) cc_final: 0.7176 (p0)
REVERT: A  230 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8547 (mm-40)
REVERT: A  243 ARG cc_start: 0.7530 (ttp80) cc_final: 0.6847 (ttm110)
REVERT: A  246 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7808 (mm-30)
REVERT: A  263 LYS cc_start: 0.8549 (ttmt) cc_final: 0.7984 (ttmm)
REVERT: A  301 LEU cc_start: 0.8263 (mt) cc_final: 0.8063 (mp)
REVERT: A  313 GLU cc_start: 0.8320 (mp0) cc_final: 0.7833 (mp0)
REVERT: C   25 MET cc_start: 0.7897 (mtt) cc_final: 0.7594 (mtt)
REVERT: B    1 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.5480 (ttp)
REVERT: B   28 LEU cc_start: 0.7542 (mp) cc_final: 0.7339 (tp)
REVERT: B   44 ILE cc_start: 0.7708 (pt) cc_final: 0.7473 (pt)
REVERT: B  106 LEU cc_start: 0.7716 (mp) cc_final: 0.7434 (mm)
REVERT: B  151 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8130 (t0)
REVERT: B  158 GLU cc_start: 0.7658 (mp0) cc_final: 0.7407 (tm-30)
REVERT: B  171 GLN cc_start: 0.8574 (pt0) cc_final: 0.8080 (mt0)
REVERT: B  181 ASP cc_start: 0.7472 (p0) cc_final: 0.7157 (p0)
REVERT: B  230 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8536 (mm-40)
REVERT: B  243 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6837 (ttm110)
REVERT: B  246 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7818 (mm-30)
REVERT: B  263 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8024 (ttmm)
REVERT: B  313 GLU cc_start: 0.8333 (mp0) cc_final: 0.7851 (mp0)
REVERT: D   25 MET cc_start: 0.7874 (mtt) cc_final: 0.7554 (mtt)
  outliers start: 25
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1788
  time to fit residues: 26.1738
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  140 VAL
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   32 TYR
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  102 GLN
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  140 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   chunk 80 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 77 optimal weight:    0.3980
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.148494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.116499 restraints weight = 7918.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.28
r_work: 0.3461 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6718  Z= 0.184
  Angle     :  0.507   6.497   9100  Z= 0.251
  Chirality :  0.047   0.140   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.298  22.444    886
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 12.43 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.29), residues: 832
  helix:  0.17 (0.37), residues: 218
  sheet: -2.76 (0.29), residues: 268
  loop : -1.16 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 168 
 HIS   0.001   0.000   HIS D  19 
 PHE   0.008   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  10 
 ARG   0.003   0.000   ARG A   8 

********************** 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
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.7735 (mp) cc_final: 0.7455 (mm)
REVERT: A  149 GLN cc_start: 0.7970 (mt0) cc_final: 0.7566 (mt0)
REVERT: A  151 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (t0)
REVERT: A  158 GLU cc_start: 0.7624 (mp0) cc_final: 0.7391 (tm-30)
REVERT: A  171 GLN cc_start: 0.8548 (pt0) cc_final: 0.8043 (mt0)
REVERT: A  181 ASP cc_start: 0.7473 (p0) cc_final: 0.7244 (p0)
REVERT: A  230 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8512 (mm-40)
REVERT: A  243 ARG cc_start: 0.7506 (ttp80) cc_final: 0.6833 (ttm110)
REVERT: A  246 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7799 (mm-30)
REVERT: A  263 LYS cc_start: 0.8543 (ttmt) cc_final: 0.7980 (ttmm)
REVERT: A  313 GLU cc_start: 0.8314 (mp0) cc_final: 0.7840 (mp0)
REVERT: C   25 MET cc_start: 0.7859 (mtt) cc_final: 0.7534 (mtt)
REVERT: B    1 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.5589 (ttp)
REVERT: B  102 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7602 (pm20)
REVERT: B  106 LEU cc_start: 0.7695 (mp) cc_final: 0.7413 (mm)
REVERT: B  149 GLN cc_start: 0.7973 (mt0) cc_final: 0.7576 (mt0)
REVERT: B  151 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8256 (t0)
REVERT: B  158 GLU cc_start: 0.7659 (mp0) cc_final: 0.7404 (tm-30)
REVERT: B  171 GLN cc_start: 0.8571 (pt0) cc_final: 0.8074 (mt0)
REVERT: B  181 ASP cc_start: 0.7451 (p0) cc_final: 0.7224 (p0)
REVERT: B  230 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8511 (mm-40)
REVERT: B  243 ARG cc_start: 0.7496 (ttp80) cc_final: 0.6833 (ttm110)
REVERT: B  246 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7813 (mm-30)
REVERT: B  263 LYS cc_start: 0.8534 (ttmt) cc_final: 0.7994 (ttmm)
REVERT: B  313 GLU cc_start: 0.8329 (mp0) cc_final: 0.7855 (mp0)
REVERT: D   25 MET cc_start: 0.7887 (mtt) cc_final: 0.7568 (mtt)
  outliers start: 26
  outliers final: 21
  residues processed: 109
  average time/residue: 0.1760
  time to fit residues: 26.0112
Evaluate side-chains
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
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  140 VAL
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 B residue    1 MET
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  102 GLN
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  140 VAL
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
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 22 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 53 optimal weight:    0.4980
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4008 r_free = 0.4008 target = 0.148290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.116238 restraints weight = 7921.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.30
r_work: 0.3454 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6718  Z= 0.201
  Angle     :  0.514   6.683   9100  Z= 0.253
  Chirality :  0.047   0.139   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.281  22.762    886
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.29), residues: 832
  helix:  0.31 (0.37), residues: 218
  sheet: -2.49 (0.28), residues: 288
  loop : -1.29 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 168 
 HIS   0.001   0.000   HIS D  19 
 PHE   0.008   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  10 
 ARG   0.002   0.000   ARG A   8 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2754.63 seconds
wall clock time: 50 minutes 27.20 seconds (3027.20 seconds total)