Starting phenix.real_space_refine
on Fri Dec 27 20:23:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7evp_31339/12_2024/7evp_31339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7evp_31339/12_2024/7evp_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_31339/12_2024/7evp_31339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7evp_31339/12_2024/7evp_31339.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7evp_31339/12_2024/7evp_31339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7evp_31339/12_2024/7evp_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-5532/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: 5.29, per 1000 atoms: 0.80
  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: 1.56
  Conformation dependent library (CDL) restraints added in 938.1 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 18 sheets defined
      25.2% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  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: 2.46

  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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.580
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.370
-------------------------------------------------------------------------------
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  : 0.760 
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: 0.2088
  time to fit residues: 39.5747
Evaluate side-chains
  105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
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  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ILE cc_start: 0.7215 (pt) cc_final: 0.6958 (pt)
REVERT: A   86 ILE cc_start: 0.7832 (mm) cc_final: 0.7615 (mt)
REVERT: A  102 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7801 (mp10)
REVERT: A  106 LEU cc_start: 0.7167 (mp) cc_final: 0.6546 (pp)
REVERT: A  149 GLN cc_start: 0.7613 (mt0) cc_final: 0.7246 (mt0)
REVERT: A  158 GLU cc_start: 0.7762 (mp0) cc_final: 0.7305 (tm-30)
REVERT: A  171 GLN cc_start: 0.8442 (pt0) cc_final: 0.8001 (mt0)
REVERT: A  206 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7996 (mtmm)
REVERT: A  246 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7642 (mm-30)
REVERT: A  263 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7456 (ttmm)
REVERT: A  313 GLU cc_start: 0.8012 (mp0) cc_final: 0.7396 (mp0)
REVERT: A  349 GLU cc_start: 0.8071 (pt0) cc_final: 0.7788 (pt0)
REVERT: B   44 ILE cc_start: 0.7223 (pt) cc_final: 0.6959 (pt)
REVERT: B   86 ILE cc_start: 0.7824 (mm) cc_final: 0.7609 (mt)
REVERT: B  102 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7803 (mp10)
REVERT: B  106 LEU cc_start: 0.7178 (mp) cc_final: 0.6555 (pp)
REVERT: B  149 GLN cc_start: 0.7622 (mt0) cc_final: 0.7252 (mt0)
REVERT: B  158 GLU cc_start: 0.7751 (mp0) cc_final: 0.7301 (tm-30)
REVERT: B  171 GLN cc_start: 0.8442 (pt0) cc_final: 0.8004 (mt0)
REVERT: B  206 LYS cc_start: 0.8259 (ptpp) cc_final: 0.7995 (mtmm)
REVERT: B  246 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7639 (mm-30)
REVERT: B  263 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7520 (ttmm)
REVERT: B  270 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: B  313 GLU cc_start: 0.8011 (mp0) cc_final: 0.7400 (mp0)
REVERT: B  349 GLU cc_start: 0.8073 (pt0) cc_final: 0.7782 (pt0)
  outliers start: 17
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1660
  time to fit residues: 27.4077
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  : 0.743 
-------------------------------------------------------------------------------
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 41 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6718  Z= 0.236
  Angle     :  0.530   6.844   9100  Z= 0.271
  Chirality :  0.047   0.160   1068
  Planarity :  0.003   0.024   1186
  Dihedral  :  4.827  23.354    886
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  :  8.86 %
    Favored  : 87.70 %
  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: -3.57 (0.27), residues: 832
  helix: -1.63 (0.31), residues: 228
  sheet: -2.80 (0.27), residues: 308
  loop : -2.07 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 168 
 HIS   0.001   0.001   HIS D  19 
 PHE   0.011   0.001   PHE B 103 
 TYR   0.007   0.001   TYR C  15 
 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
  122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ILE cc_start: 0.7194 (pt) cc_final: 0.6933 (pt)
REVERT: A  102 GLN cc_start: 0.8133 (mp10) cc_final: 0.7909 (mp10)
REVERT: A  106 LEU cc_start: 0.7192 (mp) cc_final: 0.6893 (mm)
REVERT: A  149 GLN cc_start: 0.7622 (mt0) cc_final: 0.7235 (mt0)
REVERT: A  158 GLU cc_start: 0.7783 (mp0) cc_final: 0.7331 (tm-30)
REVERT: A  171 GLN cc_start: 0.8501 (pt0) cc_final: 0.8028 (mt0)
REVERT: A  206 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7949 (mtmm)
REVERT: A  246 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7856 (mm-30)
REVERT: A  263 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7500 (ttmm)
REVERT: A  313 GLU cc_start: 0.8109 (mp0) cc_final: 0.7461 (mp0)
REVERT: B   44 ILE cc_start: 0.7199 (pt) cc_final: 0.6932 (pt)
REVERT: B   86 ILE cc_start: 0.7813 (mm) cc_final: 0.7613 (mt)
REVERT: B  102 GLN cc_start: 0.8137 (mp10) cc_final: 0.7913 (mp10)
REVERT: B  106 LEU cc_start: 0.7201 (mp) cc_final: 0.6898 (mm)
REVERT: B  149 GLN cc_start: 0.7627 (mt0) cc_final: 0.7237 (mt0)
REVERT: B  158 GLU cc_start: 0.7773 (mp0) cc_final: 0.7328 (tm-30)
REVERT: B  171 GLN cc_start: 0.8500 (pt0) cc_final: 0.8031 (mt0)
REVERT: B  206 LYS cc_start: 0.8227 (ptpp) cc_final: 0.7949 (mtmm)
REVERT: B  246 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7855 (mm-30)
REVERT: B  263 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7514 (ttmm)
REVERT: B  313 GLU cc_start: 0.8098 (mp0) cc_final: 0.7458 (mp0)
  outliers start: 26
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1559
  time to fit residues: 26.0561
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
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 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 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 73 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0170
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 79 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6718  Z= 0.162
  Angle     :  0.491   6.082   9100  Z= 0.247
  Chirality :  0.046   0.140   1068
  Planarity :  0.003   0.020   1186
  Dihedral  :  4.422  20.501    886
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  :  8.73 %
    Favored  : 88.10 %
  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: -3.04 (0.28), residues: 832
  helix: -1.06 (0.32), residues: 232
  sheet: -2.52 (0.29), residues: 284
  loop : -1.99 (0.33), residues: 316

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 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
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ILE cc_start: 0.7199 (pt) cc_final: 0.6934 (pt)
REVERT: A  106 LEU cc_start: 0.7176 (mp) cc_final: 0.6861 (mm)
REVERT: A  149 GLN cc_start: 0.7495 (mt0) cc_final: 0.7098 (mt0)
REVERT: A  158 GLU cc_start: 0.7733 (mp0) cc_final: 0.7330 (tm-30)
REVERT: A  171 GLN cc_start: 0.8517 (pt0) cc_final: 0.7999 (mt0)
REVERT: A  206 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7951 (mtmm)
REVERT: A  230 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8434 (mm-40)
REVERT: A  246 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7826 (mm-30)
REVERT: A  263 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7597 (ttmm)
REVERT: A  313 GLU cc_start: 0.8060 (mp0) cc_final: 0.7520 (mp0)
REVERT: C   25 MET cc_start: 0.7407 (mtt) cc_final: 0.7105 (mtt)
REVERT: B   44 ILE cc_start: 0.7197 (pt) cc_final: 0.6929 (pt)
REVERT: B  106 LEU cc_start: 0.7175 (mp) cc_final: 0.6858 (mm)
REVERT: B  149 GLN cc_start: 0.7501 (mt0) cc_final: 0.7103 (mt0)
REVERT: B  158 GLU cc_start: 0.7727 (mp0) cc_final: 0.7329 (tm-30)
REVERT: B  171 GLN cc_start: 0.8516 (pt0) cc_final: 0.8001 (mt0)
REVERT: B  181 ASP cc_start: 0.6915 (p0) cc_final: 0.6623 (p0)
REVERT: B  206 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7949 (mtmm)
REVERT: B  230 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8435 (mm-40)
REVERT: B  246 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7824 (mm-30)
REVERT: B  263 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7637 (ttmm)
REVERT: B  313 GLU cc_start: 0.8052 (mp0) cc_final: 0.7507 (mp0)
REVERT: D   25 MET cc_start: 0.7389 (mtt) cc_final: 0.7081 (mtt)
  outliers start: 24
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1607
  time to fit residues: 24.3225
Evaluate side-chains
  101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
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 A residue  370 LEU
Chi-restraints excluded: chain C residue   32 TYR
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   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 B residue  370 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 66 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6718  Z= 0.246
  Angle     :  0.531   6.802   9100  Z= 0.263
  Chirality :  0.047   0.149   1068
  Planarity :  0.003   0.016   1186
  Dihedral  :  4.540  24.478    886
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 11.64 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.82 (0.28), residues: 832
  helix: -0.79 (0.34), residues: 232
  sheet: -2.87 (0.29), residues: 268
  loop : -1.50 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 168 
 HIS   0.001   0.000   HIS A 183 
 PHE   0.011   0.001   PHE A 357 
 TYR   0.007   0.001   TYR D  15 
 ARG   0.002   0.000   ARG A 283 

*********************** 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
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ILE cc_start: 0.7092 (pt) cc_final: 0.6834 (pt)
REVERT: A  106 LEU cc_start: 0.7320 (mp) cc_final: 0.6967 (mm)
REVERT: A  151 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8110 (t0)
REVERT: A  158 GLU cc_start: 0.7717 (mp0) cc_final: 0.7330 (tm-30)
REVERT: A  171 GLN cc_start: 0.8514 (pt0) cc_final: 0.7987 (mt0)
REVERT: A  206 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7881 (mtmm)
REVERT: A  230 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8375 (mm-40)
REVERT: A  246 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7818 (mm-30)
REVERT: A  263 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7593 (ttmm)
REVERT: A  313 GLU cc_start: 0.8114 (mp0) cc_final: 0.7471 (mp0)
REVERT: C   25 MET cc_start: 0.7542 (mtt) cc_final: 0.7258 (mtt)
REVERT: B   44 ILE cc_start: 0.7091 (pt) cc_final: 0.6831 (pt)
REVERT: B  106 LEU cc_start: 0.7308 (mp) cc_final: 0.6950 (mm)
REVERT: B  151 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8123 (t0)
REVERT: B  158 GLU cc_start: 0.7709 (mp0) cc_final: 0.7332 (tm-30)
REVERT: B  171 GLN cc_start: 0.8515 (pt0) cc_final: 0.7990 (mt0)
REVERT: B  181 ASP cc_start: 0.7131 (p0) cc_final: 0.6930 (p0)
REVERT: B  206 LYS cc_start: 0.8169 (ptpp) cc_final: 0.7884 (mtmm)
REVERT: B  230 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8375 (mm-40)
REVERT: B  246 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7816 (mm-30)
REVERT: B  263 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7591 (ttmm)
REVERT: B  313 GLU cc_start: 0.8121 (mp0) cc_final: 0.7475 (mp0)
REVERT: D   25 MET cc_start: 0.7433 (mtt) cc_final: 0.7124 (mtt)
  outliers start: 22
  outliers final: 18
  residues processed: 100
  average time/residue: 0.1767
  time to fit residues: 24.7564
Evaluate side-chains
  97 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
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 B residue    5 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  151 ASN
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  349 GLU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 71 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0170
   chunk 41 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.4818

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6718  Z= 0.150
  Angle     :  0.480   6.090   9100  Z= 0.239
  Chirality :  0.046   0.143   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.254  20.932    886
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 11.51 %
    Favored  : 85.19 %
  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: -2.60 (0.29), residues: 832
  helix: -0.49 (0.35), residues: 232
  sheet: -2.55 (0.28), residues: 304
  loop : -1.44 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 168 
 HIS   0.002   0.000   HIS D  19 
 PHE   0.007   0.001   PHE B 357 
 TYR   0.007   0.001   TYR D  14 
 ARG   0.003   0.000   ARG B   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
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  106 LEU cc_start: 0.7247 (mp) cc_final: 0.6912 (mm)
REVERT: A  151 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7905 (t0)
REVERT: A  158 GLU cc_start: 0.7640 (mp0) cc_final: 0.7324 (tm-30)
REVERT: A  171 GLN cc_start: 0.8531 (pt0) cc_final: 0.7989 (mt0)
REVERT: A  206 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7901 (mtmm)
REVERT: A  230 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8386 (mm-40)
REVERT: A  243 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6531 (ttm110)
REVERT: A  246 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7821 (mm-30)
REVERT: A  263 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7601 (ttmm)
REVERT: A  313 GLU cc_start: 0.8018 (mp0) cc_final: 0.7473 (mp0)
REVERT: A  347 GLU cc_start: 0.7744 (tt0) cc_final: 0.6928 (tt0)
REVERT: C   25 MET cc_start: 0.7466 (mtt) cc_final: 0.7199 (mtt)
REVERT: B  106 LEU cc_start: 0.7222 (mp) cc_final: 0.6889 (mm)
REVERT: B  151 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7904 (t0)
REVERT: B  158 GLU cc_start: 0.7634 (mp0) cc_final: 0.7324 (tm-30)
REVERT: B  171 GLN cc_start: 0.8530 (pt0) cc_final: 0.7992 (mt0)
REVERT: B  181 ASP cc_start: 0.6857 (p0) cc_final: 0.6653 (p0)
REVERT: B  206 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7903 (mtmm)
REVERT: B  230 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8390 (mm-40)
REVERT: B  243 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6536 (ttm110)
REVERT: B  246 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7818 (mm-30)
REVERT: B  263 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7603 (ttmm)
REVERT: B  313 GLU cc_start: 0.8070 (mp0) cc_final: 0.7495 (mp0)
REVERT: B  347 GLU cc_start: 0.7729 (tt0) cc_final: 0.6913 (tt0)
REVERT: D   25 MET cc_start: 0.7260 (mtt) cc_final: 0.6953 (mtt)
  outliers start: 25
  outliers final: 19
  residues processed: 105
  average time/residue: 0.1834
  time to fit residues: 26.2189
Evaluate side-chains
  99 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  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    5 THR
Chi-restraints excluded: chain B residue   12 ILE
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 8 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2619

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= 0.264
  Angle     :  0.531   6.977   9100  Z= 0.265
  Chirality :  0.047   0.148   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.488  24.431    886
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 12.70 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.47 (0.35), residues: 232
  sheet: -2.62 (0.28), residues: 288
  loop : -1.40 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 168 
 HIS   0.001   0.000   HIS B 273 
 PHE   0.009   0.001   PHE A 357 
 TYR   0.006   0.001   TYR A  10 
 ARG   0.003   0.000   ARG A 283 

*********************** 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
  111 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.7365 (mp) cc_final: 0.7005 (mm)
REVERT: A  158 GLU cc_start: 0.7646 (mp0) cc_final: 0.7326 (tm-30)
REVERT: A  171 GLN cc_start: 0.8524 (pt0) cc_final: 0.7990 (mt0)
REVERT: A  206 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7869 (mtmm)
REVERT: A  230 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8360 (mm-40)
REVERT: A  243 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6506 (ttm110)
REVERT: A  246 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7816 (mm-30)
REVERT: A  263 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7630 (ttmm)
REVERT: A  301 LEU cc_start: 0.8044 (mt) cc_final: 0.7722 (mt)
REVERT: A  313 GLU cc_start: 0.8165 (mp0) cc_final: 0.7460 (mp0)
REVERT: C   25 MET cc_start: 0.7551 (mtt) cc_final: 0.7294 (mtt)
REVERT: B  106 LEU cc_start: 0.7324 (mp) cc_final: 0.6951 (mm)
REVERT: B  158 GLU cc_start: 0.7639 (mp0) cc_final: 0.7328 (tm-30)
REVERT: B  171 GLN cc_start: 0.8523 (pt0) cc_final: 0.7995 (mt0)
REVERT: B  206 LYS cc_start: 0.8157 (ptpp) cc_final: 0.7872 (mtmm)
REVERT: B  230 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8362 (mm-40)
REVERT: B  243 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6510 (ttm110)
REVERT: B  246 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7815 (mm-30)
REVERT: B  263 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7654 (ttmm)
REVERT: B  301 LEU cc_start: 0.8055 (mt) cc_final: 0.7728 (mt)
REVERT: B  313 GLU cc_start: 0.8183 (mp0) cc_final: 0.7471 (mp0)
REVERT: D   25 MET cc_start: 0.7395 (mtt) cc_final: 0.7106 (mtt)
  outliers start: 21
  outliers final: 18
  residues processed: 106
  average time/residue: 0.2276
  time to fit residues: 32.8679
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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  140 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  349 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  140 VAL
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 23 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0870
   overall best weight:    0.7758

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6718  Z= 0.195
  Angle     :  0.502   6.673   9100  Z= 0.251
  Chirality :  0.047   0.150   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.306  21.989    886
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 11.90 %
    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: -2.40 (0.29), residues: 832
  helix: -0.24 (0.35), residues: 228
  sheet: -2.55 (0.28), residues: 288
  loop : -1.36 (0.34), residues: 316

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 B   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
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.7271 (mp) cc_final: 0.6921 (mm)
REVERT: A  149 GLN cc_start: 0.7542 (mt0) cc_final: 0.7161 (mt0)
REVERT: A  151 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (t0)
REVERT: A  158 GLU cc_start: 0.7630 (mp0) cc_final: 0.7319 (tm-30)
REVERT: A  171 GLN cc_start: 0.8497 (pt0) cc_final: 0.7955 (mt0)
REVERT: A  206 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7897 (mtmm)
REVERT: A  230 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8378 (mm-40)
REVERT: A  243 ARG cc_start: 0.7106 (ttp80) cc_final: 0.6489 (ttm110)
REVERT: A  246 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7815 (mm-30)
REVERT: A  263 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7654 (ttmm)
REVERT: A  301 LEU cc_start: 0.8097 (mt) cc_final: 0.7823 (mt)
REVERT: A  313 GLU cc_start: 0.8170 (mp0) cc_final: 0.7519 (mp0)
REVERT: C   25 MET cc_start: 0.7508 (mtt) cc_final: 0.7251 (mtt)
REVERT: B  106 LEU cc_start: 0.7258 (mp) cc_final: 0.6899 (mm)
REVERT: B  149 GLN cc_start: 0.7564 (mt0) cc_final: 0.7166 (mt0)
REVERT: B  151 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8000 (t0)
REVERT: B  158 GLU cc_start: 0.7627 (mp0) cc_final: 0.7321 (tm-30)
REVERT: B  171 GLN cc_start: 0.8496 (pt0) cc_final: 0.7960 (mt0)
REVERT: B  206 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7897 (mtmm)
REVERT: B  230 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8382 (mm-40)
REVERT: B  243 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6493 (ttm110)
REVERT: B  246 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7813 (mm-30)
REVERT: B  263 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7655 (ttmm)
REVERT: B  301 LEU cc_start: 0.8121 (mt) cc_final: 0.7838 (mt)
REVERT: B  313 GLU cc_start: 0.8179 (mp0) cc_final: 0.7519 (mp0)
REVERT: D   25 MET cc_start: 0.7301 (mtt) cc_final: 0.7026 (mtt)
  outliers start: 24
  outliers final: 20
  residues processed: 108
  average time/residue: 0.1845
  time to fit residues: 27.1379
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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 75 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0070
   chunk 48 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7202

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6718  Z= 0.185
  Angle     :  0.503   6.561   9100  Z= 0.250
  Chirality :  0.046   0.136   1068
  Planarity :  0.002   0.016   1186
  Dihedral  :  4.275  21.870    886
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.30 %
    Favored  : 84.66 %
  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: -2.28 (0.29), residues: 832
  helix: -0.21 (0.35), residues: 232
  sheet: -2.75 (0.29), residues: 268
  loop : -1.09 (0.34), 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   0.007   0.001   PHE A 233 
 TYR   0.006   0.001   TYR A  10 
 ARG   0.002   0.000   ARG B   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
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.7305 (mp) cc_final: 0.6951 (mm)
REVERT: A  151 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7775 (t0)
REVERT: A  158 GLU cc_start: 0.7663 (mp0) cc_final: 0.7335 (tm-30)
REVERT: A  171 GLN cc_start: 0.8501 (pt0) cc_final: 0.7938 (mt0)
REVERT: A  230 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8381 (mm-40)
REVERT: A  243 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6471 (ttm110)
REVERT: A  246 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7819 (mm-30)
REVERT: A  263 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7665 (ttmm)
REVERT: A  301 LEU cc_start: 0.8119 (mt) cc_final: 0.7844 (mt)
REVERT: A  313 GLU cc_start: 0.8155 (mp0) cc_final: 0.7505 (mp0)
REVERT: C   25 MET cc_start: 0.7521 (mtt) cc_final: 0.7279 (mtt)
REVERT: B  106 LEU cc_start: 0.7271 (mp) cc_final: 0.6908 (mm)
REVERT: B  151 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7776 (t0)
REVERT: B  158 GLU cc_start: 0.7658 (mp0) cc_final: 0.7336 (tm-30)
REVERT: B  171 GLN cc_start: 0.8501 (pt0) cc_final: 0.7944 (mt0)
REVERT: B  206 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7900 (mtmm)
REVERT: B  230 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8386 (mm-40)
REVERT: B  243 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6479 (ttm110)
REVERT: B  246 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7816 (mm-30)
REVERT: B  263 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7662 (ttmm)
REVERT: B  301 LEU cc_start: 0.8140 (mt) cc_final: 0.7860 (mt)
REVERT: B  313 GLU cc_start: 0.8186 (mp0) cc_final: 0.7532 (mp0)
REVERT: D   25 MET cc_start: 0.7314 (mtt) cc_final: 0.7042 (mtt)
  outliers start: 23
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1870
  time to fit residues: 27.1420
Evaluate side-chains
  107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0470
   chunk 81 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.6880

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6718  Z= 0.181
  Angle     :  0.507   6.517   9100  Z= 0.250
  Chirality :  0.047   0.137   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.254  21.764    886
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.10 %
    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: -2.08 (0.29), residues: 832
  helix:  0.12 (0.37), residues: 218
  sheet: -2.71 (0.29), residues: 268
  loop : -1.00 (0.34), residues: 346

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   0.006   0.001   PHE A 233 
 TYR   0.007   0.001   TYR A  10 
 ARG   0.002   0.000   ARG B   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
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LEU cc_start: 0.7310 (mp) cc_final: 0.6955 (mm)
REVERT: A  149 GLN cc_start: 0.7546 (mt0) cc_final: 0.7159 (mt0)
REVERT: A  151 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8017 (t0)
REVERT: A  158 GLU cc_start: 0.7650 (mp0) cc_final: 0.7326 (tm-30)
REVERT: A  171 GLN cc_start: 0.8504 (pt0) cc_final: 0.7935 (mt0)
REVERT: A  230 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8376 (mm-40)
REVERT: A  243 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6468 (ttm110)
REVERT: A  246 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7722 (mm-30)
REVERT: A  263 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7671 (ttmm)
REVERT: A  301 LEU cc_start: 0.8153 (mt) cc_final: 0.7910 (mt)
REVERT: A  313 GLU cc_start: 0.8142 (mp0) cc_final: 0.7512 (mp0)
REVERT: C   25 MET cc_start: 0.7525 (mtt) cc_final: 0.7273 (mtt)
REVERT: B  106 LEU cc_start: 0.7305 (mp) cc_final: 0.6945 (mm)
REVERT: B  149 GLN cc_start: 0.7552 (mt0) cc_final: 0.7161 (mt0)
REVERT: B  151 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8017 (t0)
REVERT: B  158 GLU cc_start: 0.7644 (mp0) cc_final: 0.7327 (tm-30)
REVERT: B  171 GLN cc_start: 0.8504 (pt0) cc_final: 0.7940 (mt0)
REVERT: B  230 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8380 (mm-40)
REVERT: B  243 ARG cc_start: 0.7057 (ttp80) cc_final: 0.6474 (ttm110)
REVERT: B  246 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7721 (mm-30)
REVERT: B  263 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7693 (ttmm)
REVERT: B  301 LEU cc_start: 0.8163 (mt) cc_final: 0.7886 (mt)
REVERT: B  313 GLU cc_start: 0.8146 (mp0) cc_final: 0.7524 (mp0)
REVERT: D   25 MET cc_start: 0.7313 (mtt) cc_final: 0.7039 (mtt)
  outliers start: 23
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1981
  time to fit residues: 29.3688
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  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 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  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 59 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   overall best weight:    0.5758

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.148616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116994 restraints weight = 7755.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 3.24
r_work: 0.3465 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2925

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= 0.164
  Angle     :  0.495   6.563   9100  Z= 0.244
  Chirality :  0.046   0.147   1068
  Planarity :  0.002   0.017   1186
  Dihedral  :  4.183  21.177    886
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 13.89 %
    Favored  : 83.20 %
  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: -1.99 (0.29), residues: 832
  helix:  0.24 (0.36), residues: 218
  sheet: -2.67 (0.29), residues: 268
  loop : -0.96 (0.34), residues: 346

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   0.006   0.001   PHE C  26 
 TYR   0.007   0.001   TYR A  10 
 ARG   0.002   0.000   ARG B   8 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1685.38 seconds
wall clock time: 31 minutes 46.44 seconds (1906.44 seconds total)